Optical rogue waves for the inhomogeneous generalized nonlinear Schrödinger equation.

PubMed

Loomba, Shally; Kaur, Harleen

2013-12-01

We present optical rogue wave solutions for a generalized nonlinear Schrodinger equation by using similarity transformation. We have predicted the propagation of rogue waves through a nonlinear optical fiber for three cases: (i) dispersion increasing (decreasing) fiber, (ii) periodic dispersion parameter, and (iii) hyperbolic dispersion parameter. We found that the rogue waves and their interactions can be tuned by properly choosing the parameters. We expect that our results can be used to realize improved signal transmission through optical rogue waves.

Non-Standard Interactions in propagation at the Deep Underground Neutrino Experiment

DOE PAGES

Coloma, Pilar

2016-03-03

Here, we study the sensitivity of current and future long-baseline neutrino oscillation experiments to the effects of dimension six operators affecting neutrino propagation through Earth, commonly referred to as Non-Standard Interactions (NSI). All relevant parameters entering the oscillation probabilities (standard and non-standard) are considered at once, in order to take into account possible cancellations and degeneracies between them. We find that the Deep Underground Neutrino Experiment will significantly improve over current constraints for most NSI parameters. Most notably, it will be able to rule out the so-called LMA-dark solution, still compatible with current oscillation data, and will be sensitive to off-diagonal NSI parameters at the level of ε ~more » $$ \\mathcal{O} $$ (0.05 – 0.5). We also identify two degeneracies among standard and non-standard parameters, which could be partially resolved by combining T2HK and DUNE data.« less

Semi-empirical correlation for binary interaction parameters of the Peng-Robinson equation of state with the van der Waals mixing rules for the prediction of high-pressure vapor-liquid equilibrium.

PubMed

Fateen, Seif-Eddeen K; Khalil, Menna M; Elnabawy, Ahmed O

2013-03-01

Peng-Robinson equation of state is widely used with the classical van der Waals mixing rules to predict vapor liquid equilibria for systems containing hydrocarbons and related compounds. This model requires good values of the binary interaction parameter kij . In this work, we developed a semi-empirical correlation for kij partly based on the Huron-Vidal mixing rules. We obtained values for the adjustable parameters of the developed formula for over 60 binary systems and over 10 categories of components. The predictions of the new equation system were slightly better than the constant-kij model in most cases, except for 10 systems whose predictions were considerably improved with the new correlation.

Improved Design of Beam Tunnel for 42 GHz Gyrotron

NASA Astrophysics Data System (ADS)

Singh, Udaybir; Kumar, Nitin; Purohit, L. P.; Sinha, A. K.

2011-04-01

In gyrotron, there is the chance of generation and excitation of unwanted RF modes (parasite oscillations). These modes may interact with electron beam and consequently degrade the beam quality. This paper presents the improved design of the beam tunnel to reduce the parasite oscillations and the effect of beam tunnel geometry on the electron beam parameters. The design optimization of the beam tunnel has been done with the help of 3-D simulation software CST-Microwave Studio and the effect of beam tunnel geometry on the electron beam parameters has been analyzed by EGUN code.

Evolutionary model selection and parameter estimation for protein-protein interaction network based on differential evolution algorithm

PubMed Central

Huang, Lei; Liao, Li; Wu, Cathy H.

2016-01-01

Revealing the underlying evolutionary mechanism plays an important role in understanding protein interaction networks in the cell. While many evolutionary models have been proposed, the problem about applying these models to real network data, especially for differentiating which model can better describe evolutionary process for the observed network urgently remains as a challenge. The traditional way is to use a model with presumed parameters to generate a network, and then evaluate the fitness by summary statistics, which however cannot capture the complete network structures information and estimate parameter distribution. In this work we developed a novel method based on Approximate Bayesian Computation and modified Differential Evolution (ABC-DEP) that is capable of conducting model selection and parameter estimation simultaneously and detecting the underlying evolutionary mechanisms more accurately. We tested our method for its power in differentiating models and estimating parameters on the simulated data and found significant improvement in performance benchmark, as compared with a previous method. We further applied our method to real data of protein interaction networks in human and yeast. Our results show Duplication Attachment model as the predominant evolutionary mechanism for human PPI networks and Scale-Free model as the predominant mechanism for yeast PPI networks. PMID:26357273

Mixed Micelle System Produced by Interaction Between Transglycosylated Stevia and an Ionic Surfactant Improves Dissolution Profile of Mefenamic Acid.

PubMed

Fujimori, Miki; Kadota, Kazunori; Tozuka, Yuichi

2017-04-01

Transglycosylated stevia (stevia-G) can effectively improve the dissolution and bioavailability of poorly water-soluble drugs. Furthermore, addition of an ionic surfactant to stevia-G solution has been shown to enhance the dissolution effect of stevia-G on flurbiprofen. Herein, 4 surfactants, namely sodium dodecyl sulfate, sodium N-dodecanoylsarcosinate, sodium monododecyl phosphate, and lauryltrimethylammonium chloride (LTAC) were screened to investigate their synergistic effect with stevia-G in enhancing the solubility of mefenamic acid (MFA). The ternary formulation containing LTAC produced the highest increase in solubility, whereas the binary MFA/LTAC formulation did not increase the solubility of MFA. Surface tension was evaluated to analyze the interaction between stevia-G and each ionic surfactant, wherein the Rubingh model was applied to predict mixed micelle formation between stevia-G and LTAC. Interaction parameters calculated by the Rubingh model reflected mixed micelle formation between stevia-G and LTAC relative to the self-interactions of the 2 individual surfactants. All interaction parameters in this system showed negative values, indicating a favorable interaction (e.g., hydrogen bond or electrostatic and dipole) between binary components in the mixed micelles. Spray-dried particles of ternary formulations (MFA/stevia-G/LTAC) were prepared to evaluate the dissolution profile and physicochemical properties. Dissolution profiling showed that the concentration of MFA released from spray-dried particles was significantly higher than untreated MFA. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Solvation effects on chemical shifts by embedded cluster integral equation theory.

PubMed

Frach, Roland; Kast, Stefan M

2014-12-11

The accurate computational prediction of nuclear magnetic resonance (NMR) parameters like chemical shifts represents a challenge if the species studied is immersed in strongly polarizing environments such as water. Common approaches to treating a solvent in the form of, e.g., the polarizable continuum model (PCM) ignore strong directional interactions such as H-bonds to the solvent which can have substantial impact on magnetic shieldings. We here present a computational methodology that accounts for atomic-level solvent effects on NMR parameters by extending the embedded cluster reference interaction site model (EC-RISM) integral equation theory to the prediction of chemical shifts of N-methylacetamide (NMA) in aqueous solution. We examine the influence of various so-called closure approximations of the underlying three-dimensional RISM theory as well as the impact of basis set size and different treatment of electrostatic solute-solvent interactions. We find considerable and systematic improvement over reference PCM and gas phase calculations. A smaller basis set in combination with a simple point charge model already yields good performance which can be further improved by employing exact electrostatic quantum-mechanical solute-solvent interaction energies. A larger basis set benefits more significantly from exact over point charge electrostatics, which can be related to differences of the solvent's charge distribution.

O (a) improvement of 2D N = (2 , 2) lattice SYM theory

NASA Astrophysics Data System (ADS)

Hanada, Masanori; Kadoh, Daisuke; Matsuura, So; Sugino, Fumihiko

2018-04-01

We perform a tree-level O (a) improvement of two-dimensional N = (2 , 2) supersymmetric Yang-Mills theory on the lattice, motivated by the fast convergence in numerical simulations. The improvement respects an exact supersymmetry Q which is needed for obtaining the correct continuum limit without a parameter fine tuning. The improved lattice action is given within a milder locality condition in which the interactions are decaying as the exponential of the distance on the lattice. We also prove that the path-integral measure is invariant under the improved Q-transformation.

Data-driven approach of CUSUM algorithm in temporal aberrant event detection using interactive web applications.

PubMed

Li, Ye; Whelan, Michael; Hobbs, Leigh; Fan, Wen Qi; Fung, Cecilia; Wong, Kenny; Marchand-Austin, Alex; Badiani, Tina; Johnson, Ian

2016-06-27

In 2014/2015, Public Health Ontario developed disease-specific, cumulative sum (CUSUM)-based statistical algorithms for detecting aberrant increases in reportable infectious disease incidence in Ontario. The objective of this study was to determine whether the prospective application of these CUSUM algorithms, based on historical patterns, have improved specificity and sensitivity compared to the currently used Early Aberration Reporting System (EARS) algorithm, developed by the US Centers for Disease Control and Prevention. A total of seven algorithms were developed for the following diseases: cyclosporiasis, giardiasis, influenza (one each for type A and type B), mumps, pertussis, invasive pneumococcal disease. Historical data were used as baseline to assess known outbreaks. Regression models were used to model seasonality and CUSUM was applied to the difference between observed and expected counts. An interactive web application was developed allowing program staff to directly interact with data and tune the parameters of CUSUM algorithms using their expertise on the epidemiology of each disease. Using these parameters, a CUSUM detection system was applied prospectively and the results were compared to the outputs generated by EARS. The outcome was the detection of outbreaks, or the start of a known seasonal increase and predicting the peak in activity. The CUSUM algorithms detected provincial outbreaks earlier than the EARS algorithm, identified the start of the influenza season in advance of traditional methods, and had fewer false positive alerts. Additionally, having staff involved in the creation of the algorithms improved their understanding of the algorithms and improved use in practice. Using interactive web-based technology to tune CUSUM improved the sensitivity and specificity of detection algorithms.

Effects of a Program for Improving Biomechanical Characteristics During Walking and Running in Children Who Are Obese.

PubMed

Steinberg, Nili; Rubinstein, Meron; Nemet, Dan; Ayalon, Moshe; Zeev, Aviva; Pantanowitz, Michal; Brosh, Tamar; Eliakim, Alon

2017-10-01

To investigate the influence of a weight-reduction program with locomotion-emphasis on improving biomechanical characteristics of children who are obese (OW). Ten children who are OW participated in a 6-month multidisciplinary childhood obesity management program (GRP1); another 10 children who are OW participated in the same multidisciplinary childhood obesity management program with additional locomotion-emphasis exercises for improving biomechanical characteristics (GRP2); and 10 control children who are OW with no intervention program. Outcomes were anthropometric measurements and temporal and foot pressure parameters. GRP2 had significantly improved foot pressure in the different walking/running speeds compared with GRP1. In the temporal parameters, pretests by speed by group interactions were significantly improved for GRP2 compared with GRP1. We found evidence to support beneficial effects of combined dietary and physical activity/locomotion-emphasis exercises on the movement characteristics of children who are OW.

Behavioral and physiological reactions in dogs to a veterinary examination: Owner-dog interactions improve canine well-being.

PubMed

Csoltova, Erika; Martineau, Michaël; Boissy, Alain; Gilbert, Caroline

2017-08-01

In order to improve well-being of dogs during veterinary visits, we aimed to investigate the effect of human social interactions on behavior and physiology during routine examination. Firstly, we assessed the impact of a standardized veterinary examination on behavioral and physiological indicators of stress in dogs. Secondly, we examined whether the owner's tactile and verbal interactions with the dog influenced behavioral and physiological stress-associated parameters. A randomized within-subjects crossover design was used to examine behavior (n=33), rectal temperature (n=33), heart rate (HR) (n=18), maximal ocular surface temperature (max OST) (n=13) and salivary cortisol concentrations (n=10) in healthy privately owned pet dogs. The study consisted of two experimental conditions: a) "contact" - owner petting and talking to the dog during the examination; b) "non-contact" - owner present during the examination but not allowed to interact with the dog. Our findings showed that the veterinary examinations produced acute stress responses in dogs during both "contact" and "non-contact" conditions, with significant increases in lip licking, HR, and max OST. A significant decrease in attempts to jump off the examination table (p=0.002) was observed during the examination in the "contact" compared to the "non-contact" condition. In addition, interactions of owners showed an attenuating effect on HR (p=0.018) and max OST (p=0.011) in their dogs. The testing order (first vs. second visit) had no impact on behavioral and physiological parameters, suggesting that dogs did not habituate or sensitize to the examination procedure. Moreover, the duration of the owner-dog interactions had no significant impact on the behavioral and physiological responses of their dogs. This study demonstrates that owner-dog interactions improve the well-being of dogs during a veterinary examination. Future research may assist in further understanding the mechanisms associated with reducing stress in dogs in similar settings. Copyright © 2017 Elsevier Inc. All rights reserved.

Enhanced Particle Swarm Optimization Algorithm: Efficient Training of ReaxFF Reactive Force Fields.

PubMed

Furman, David; Carmeli, Benny; Zeiri, Yehuda; Kosloff, Ronnie

2018-06-12

Particle swarm optimization (PSO) is a powerful metaheuristic population-based global optimization algorithm. However, when it is applied to nonseparable objective functions, its performance on multimodal landscapes is significantly degraded. Here we show that a significant improvement in the search quality and efficiency on multimodal functions can be achieved by enhancing the basic rotation-invariant PSO algorithm with isotropic Gaussian mutation operators. The new algorithm demonstrates superior performance across several nonlinear, multimodal benchmark functions compared with the rotation-invariant PSO algorithm and the well-established simulated annealing and sequential one-parameter parabolic interpolation methods. A search for the optimal set of parameters for the dispersion interaction model in the ReaxFF- lg reactive force field was carried out with respect to accurate DFT-TS calculations. The resulting optimized force field accurately describes the equations of state of several high-energy molecular crystals where such interactions are of crucial importance. The improved algorithm also presents better performance compared to a genetic algorithm optimization method in the optimization of the parameters of a ReaxFF- lg correction model. The computational framework is implemented in a stand-alone C++ code that allows the straightforward development of ReaxFF reactive force fields.

Reparameterization of Solute—Solute Interactions for Amino Acid-Sugar Systems Using Isopiestic Osmotic Pressure Molecular Dynamics Simulations

PubMed Central

Lay, Wesley K.; Miller, Mark S.

2018-01-01

AMBER/GLYCAM and CHARMM are popular force fields for simulations of amino acids and sugars. Here we report excessively attractive amino acid-sugar interactions in both force fields, and corrections to nonbonded interactions that match experimental osmotic pressures of mixed aqueous solutions of diglycine and sucrose. The modified parameters also improve the ΔGtrans of diglycine from water to aqueous sucrose and, with AMBERff99SB/GLYCAM06, eliminate a caging effect seen in previous simulations of the protein ubiquitin with glucose. PMID:28437100

Can nonstandard interactions jeopardize the hierarchy sensitivity of DUNE?

NASA Astrophysics Data System (ADS)

Deepthi, K. N.; Goswami, Srubabati; Nath, Newton

2017-10-01

We study the effect of nonstandard interactions (NSIs) on the propagation of neutrinos through the Earth's matter and how it affects the hierarchy sensitivity of the DUNE experiment. We emphasize the special case when the diagonal NSI parameter ɛe e=-1 , nullifying the standard matter effect. We show that if, in addition, C P violation is maximal then this gives rise to an exact intrinsic hierarchy degeneracy in the appearance channel, irrespective of the baseline and energy. Introduction of the off diagonal NSI parameter, ɛe τ, shifts the position of this degeneracy to a different ɛe e. Moreover the unknown magnitude and phases of the off diagonal NSI parameters can give rise to additional degeneracies. Overall, given the current model independent limits on NSI parameters, the hierarchy sensitivity of DUNE can get seriously impacted. However, a more precise knowledge of the NSI parameters, especially ɛe e, can give rise to an improved sensitivity. Alternatively, if a NSI exists in nature, and still DUNE shows hierarchy sensitivity, certain ranges of the NSI parameters can be excluded. Additionally, we briefly discuss the implications of ɛe e=-1 (in the Earth) on the Mikheyev-Smirnov-Wolfenstein effect in the Sun.

More accurate depiction of adsorption energy on transition metals using work function as one additional descriptor.

PubMed

Shen, Xiaochen; Pan, Yanbo; Liu, Bin; Yang, Jinlong; Zeng, Jie; Peng, Zhenmeng

2017-05-24

The reaction mechanism and properties of a catalytic process are primarily determined by the interactions between reacting species and catalysts. However, the interactions are often challenging to be experimentally measured, especially for unstable intermediates. Therefore, it is of significant importance to establish an exact relationship between chemical-catalyst interactions and catalyst parameters, which will allow calculation of these interactions and thus advance their mechanistic understanding. Herein we report the description of adsorption energy on transition metals by considering both ionic bonding and covalent bonding contributions and introduce the work function as one additional responsible parameter. We find that the adsorption energy can be more accurately described using a two-dimensional (2D) polynomial model, which shows a significant improvement compared with the current adsorption energy-d-band center linear correlation. We also demonstrate the utilization of this new 2D polynomial model to calculate oxygen binding energy of different transition metals to help understand their catalytic properties in oxygen reduction reactions.

An experimental and numerical investigation of shock-wave induced turbulent boundary-layer separation at hypersonic speeds

NASA Technical Reports Server (NTRS)

Marvin, J. G.; Horstman, C. C.; Rubesin, M. W.; Coakley, T. J.; Kussoy, M. I.

1975-01-01

An experiment designed to test and guide computations of the interaction of an impinging shock wave with a turbulent boundary layer is described. Detailed mean flow-field and surface data are presented for two shock strengths which resulted in attached and separated flows, respectively. Numerical computations, employing the complete time-averaged Navier-Stokes equations along with algebraic eddy-viscosity and turbulent Prandtl number models to describe shear stress and heat flux, are used to illustrate the dependence of the computations on the particulars of the turbulence models. Models appropriate for zero-pressure-gradient flows predicted the overall features of the flow fields, but were deficient in predicting many of the details of the interaction regions. Improvements to the turbulence model parameters were sought through a combination of detailed data analysis and computer simulations which tested the sensitivity of the solutions to model parameter changes. Computer simulations using these improvements are presented and discussed.

Laser magnetic resonance in supersonic plasmas - The rotational spectrum of SH(+)

NASA Technical Reports Server (NTRS)

Hovde, David C.; Saykally, Richard J.

1987-01-01

The rotational spectrum of v = 0 and v = 1X3Sigma(-)SH(+) was measured by laser magnetic resonance. Rotationally cold (Tr = 30 K), vibrationally excited (Tv = 3000 K) ions were generated in a corona excited supersonic expansion. The use of this source to identify ion signals is described. Improved molecular parameters were obtained; term values are presented from which astrophysically important transitions may be calculated. Accurate hyperfine parameters for both vibrational levels were determined and the vibrational dependence of the Fermi contact interaction was resolved. The hyperfine parameters agree well with recent many-body perturbation theory calculations.

Optimization of the Design of Pre-Signal System Using Improved Cellular Automaton

PubMed Central

Li, Yan; Li, Ke; Tao, Siran; Chen, Kuanmin

2014-01-01

The pre-signal system can improve the efficiency of intersection approach under rational design. One of the main obstacles in optimizing the design of pre-signal system is that driving behaviors in the sorting area cannot be well evaluated. The NaSch model was modified by considering slow probability, turning-deceleration rules, and lane changing rules. It was calibrated with field observed data to explore the interactions among design parameters. The simulation results of the proposed model indicate that the length of sorting area, traffic demand, signal timing, and lane allocation are the most important influence factors. The recommendations of these design parameters are demonstrated. The findings of this paper can be foundations for the design of pre-signal system and show promising improvement in traffic mobility. PMID:25435871

Satellite Fault Diagnosis Using Support Vector Machines Based on a Hybrid Voting Mechanism

PubMed Central

Yang, Shuqiang; Zhu, Xiaoqian; Jin, Songchang; Wang, Xiang

2014-01-01

The satellite fault diagnosis has an important role in enhancing the safety, reliability, and availability of the satellite system. However, the problem of enormous parameters and multiple faults makes a challenge to the satellite fault diagnosis. The interactions between parameters and misclassifications from multiple faults will increase the false alarm rate and the false negative rate. On the other hand, for each satellite fault, there is not enough fault data for training. To most of the classification algorithms, it will degrade the performance of model. In this paper, we proposed an improving SVM based on a hybrid voting mechanism (HVM-SVM) to deal with the problem of enormous parameters, multiple faults, and small samples. Many experimental results show that the accuracy of fault diagnosis using HVM-SVM is improved. PMID:25215324

Assessing uncertainty and sensitivity of model parameterizations and parameters in WRF affecting simulated surface fluxes and land-atmosphere coupling over the Amazon region

NASA Astrophysics Data System (ADS)

Qian, Y.; Wang, C.; Huang, M.; Berg, L. K.; Duan, Q.; Feng, Z.; Shrivastava, M. B.; Shin, H. H.; Hong, S. Y.

2016-12-01

This study aims to quantify the relative importance and uncertainties of different physical processes and parameters in affecting simulated surface fluxes and land-atmosphere coupling strength over the Amazon region. We used two-legged coupling metrics, which include both terrestrial (soil moisture to surface fluxes) and atmospheric (surface fluxes to atmospheric state or precipitation) legs, to diagnose the land-atmosphere interaction and coupling strength. Observations made using the Department of Energy's Atmospheric Radiation Measurement (ARM) Mobile Facility during the GoAmazon field campaign together with satellite and reanalysis data are used to evaluate model performance. To quantify the uncertainty in physical parameterizations, we performed a 120 member ensemble of simulations with the WRF model using a stratified experimental design including 6 cloud microphysics, 3 convection, 6 PBL and surface layer, and 3 land surface schemes. A multiple-way analysis of variance approach is used to quantitatively analyze the inter- and intra-group (scheme) means and variances. To quantify parameter sensitivity, we conducted an additional 256 WRF simulations in which an efficient sampling algorithm is used to explore the multiple-dimensional parameter space. Three uncertainty quantification approaches are applied for sensitivity analysis (SA) of multiple variables of interest to 20 selected parameters in YSU PBL and MM5 surface layer schemes. Results show consistent parameter sensitivity across different SA methods. We found that 5 out of 20 parameters contribute more than 90% total variance, and first-order effects dominate comparing to the interaction effects. Results of this uncertainty quantification study serve as guidance for better understanding the roles of different physical processes in land-atmosphere interactions, quantifying model uncertainties from various sources such as physical processes, parameters and structural errors, and providing insights for improving the model physics parameterizations.

Towards accurate modeling of noncovalent interactions for protein rigidity analysis.

PubMed

Fox, Naomi; Streinu, Ileana

2013-01-01

Protein rigidity analysis is an efficient computational method for extracting flexibility information from static, X-ray crystallography protein data. Atoms and bonds are modeled as a mechanical structure and analyzed with a fast graph-based algorithm, producing a decomposition of the flexible molecule into interconnected rigid clusters. The result depends critically on noncovalent atomic interactions, primarily on how hydrogen bonds and hydrophobic interactions are computed and modeled. Ongoing research points to the stringent need for benchmarking rigidity analysis software systems, towards the goal of increasing their accuracy and validating their results, either against each other and against biologically relevant (functional) parameters. We propose two new methods for modeling hydrogen bonds and hydrophobic interactions that more accurately reflect a mechanical model, without being computationally more intensive. We evaluate them using a novel scoring method, based on the B-cubed score from the information retrieval literature, which measures how well two cluster decompositions match. To evaluate the modeling accuracy of KINARI, our pebble-game rigidity analysis system, we use a benchmark data set of 20 proteins, each with multiple distinct conformations deposited in the Protein Data Bank. Cluster decompositions for them were previously determined with the RigidFinder method from Gerstein's lab and validated against experimental data. When KINARI's default tuning parameters are used, an improvement of the B-cubed score over a crude baseline is observed in 30% of this data. With our new modeling options, improvements were observed in over 70% of the proteins in this data set. We investigate the sensitivity of the cluster decomposition score with case studies on pyruvate phosphate dikinase and calmodulin. To substantially improve the accuracy of protein rigidity analysis systems, thorough benchmarking must be performed on all current systems and future extensions. We have measured the gain in performance by comparing different modeling methods for noncovalent interactions. We showed that new criteria for modeling hydrogen bonds and hydrophobic interactions can significantly improve the results. The two new methods proposed here have been implemented and made publicly available in the current version of KINARI (v1.3), together with the benchmarking tools, which can be downloaded from our software's website, http://kinari.cs.umass.edu.

Towards accurate modeling of noncovalent interactions for protein rigidity analysis

PubMed Central

2013-01-01

Background Protein rigidity analysis is an efficient computational method for extracting flexibility information from static, X-ray crystallography protein data. Atoms and bonds are modeled as a mechanical structure and analyzed with a fast graph-based algorithm, producing a decomposition of the flexible molecule into interconnected rigid clusters. The result depends critically on noncovalent atomic interactions, primarily on how hydrogen bonds and hydrophobic interactions are computed and modeled. Ongoing research points to the stringent need for benchmarking rigidity analysis software systems, towards the goal of increasing their accuracy and validating their results, either against each other and against biologically relevant (functional) parameters. We propose two new methods for modeling hydrogen bonds and hydrophobic interactions that more accurately reflect a mechanical model, without being computationally more intensive. We evaluate them using a novel scoring method, based on the B-cubed score from the information retrieval literature, which measures how well two cluster decompositions match. Results To evaluate the modeling accuracy of KINARI, our pebble-game rigidity analysis system, we use a benchmark data set of 20 proteins, each with multiple distinct conformations deposited in the Protein Data Bank. Cluster decompositions for them were previously determined with the RigidFinder method from Gerstein's lab and validated against experimental data. When KINARI's default tuning parameters are used, an improvement of the B-cubed score over a crude baseline is observed in 30% of this data. With our new modeling options, improvements were observed in over 70% of the proteins in this data set. We investigate the sensitivity of the cluster decomposition score with case studies on pyruvate phosphate dikinase and calmodulin. Conclusion To substantially improve the accuracy of protein rigidity analysis systems, thorough benchmarking must be performed on all current systems and future extensions. We have measured the gain in performance by comparing different modeling methods for noncovalent interactions. We showed that new criteria for modeling hydrogen bonds and hydrophobic interactions can significantly improve the results. The two new methods proposed here have been implemented and made publicly available in the current version of KINARI (v1.3), together with the benchmarking tools, which can be downloaded from our software's website, http://kinari.cs.umass.edu. PMID:24564209

Using global sensitivity analysis to understand higher order interactions in complex models: an application of GSA on the Revised Universal Soil Loss Equation (RUSLE) to quantify model sensitivity and implications for ecosystem services management in Costa Rica

NASA Astrophysics Data System (ADS)

Fremier, A. K.; Estrada Carmona, N.; Harper, E.; DeClerck, F.

2011-12-01

Appropriate application of complex models to estimate system behavior requires understanding the influence of model structure and parameter estimates on model output. To date, most researchers perform local sensitivity analyses, rather than global, because of computational time and quantity of data produced. Local sensitivity analyses are limited in quantifying the higher order interactions among parameters, which could lead to incomplete analysis of model behavior. To address this concern, we performed a GSA on a commonly applied equation for soil loss - the Revised Universal Soil Loss Equation. USLE is an empirical model built on plot-scale data from the USA and the Revised version (RUSLE) includes improved equations for wider conditions, with 25 parameters grouped into six factors to estimate long-term plot and watershed scale soil loss. Despite RUSLE's widespread application, a complete sensitivity analysis has yet to be performed. In this research, we applied a GSA to plot and watershed scale data from the US and Costa Rica to parameterize the RUSLE in an effort to understand the relative importance of model factors and parameters across wide environmental space. We analyzed the GSA results using Random Forest, a statistical approach to evaluate parameter importance accounting for the higher order interactions, and used Classification and Regression Trees to show the dominant trends in complex interactions. In all GSA calculations the management of cover crops (C factor) ranks the highest among factors (compared to rain-runoff erosivity, topography, support practices, and soil erodibility). This is counter to previous sensitivity analyses where the topographic factor was determined to be the most important. The GSA finding is consistent across multiple model runs, including data from the US, Costa Rica, and a synthetic dataset of the widest theoretical space. The three most important parameters were: Mass density of live and dead roots found in the upper inch of soil (C factor), slope angle (L and S factor), and percentage of land area covered by surface cover (C factor). Our findings give further support to the importance of vegetation as a vital ecosystem service provider - soil loss reduction. Concurrent, progress is already been made in Costa Rica, where dam managers are moving forward on a Payment for Ecosystem Services scheme to help keep private lands forested and to improve crop management through targeted investments. Use of complex watershed models, such as RUSLE can help managers quantify the effect of specific land use changes. Moreover, effective land management of vegetation has other important benefits, such as bundled ecosystem services (e.g. pollination, habitat connectivity, etc) and improvements of communities' livelihoods.

Research on key factors and their interaction effects of electromagnetic force of high-speed solenoid valve.

PubMed

Liu, Peng; Fan, Liyun; Hayat, Qaisar; Xu, De; Ma, Xiuzhen; Song, Enzhe

2014-01-01

Analysis consisting of numerical simulations along with lab experiments of interaction effects between key parameters on the electromagnetic force based on response surface methodology (RSM) has been also proposed to optimize the design of high-speed solenoid valve (HSV) and improve its performance. Numerical simulation model of HSV has been developed in Ansoft Maxwell environment and its accuracy has been validated through lab experiments. Effect of change of core structure, coil structure, armature structure, working air gap, and drive current on the electromagnetic force of HSV has been analyzed through simulation model and influence rules of various parameters on the electromagnetic force have been established. The response surface model of the electromagnetic force has been utilized to analyze the interaction effect between major parameters. It has been concluded that six interaction factors including working air gap with armature radius, drive current with armature thickness, coil turns with side pole radius, armature thickness with its radius, armature thickness with side pole radius, and armature radius with side pole radius have significant influence on the electromagnetic force. Optimal match values between coil turns and side pole radius; armature thickness and side pole radius; and armature radius and side pole radius have also been determined.

Research on Key Factors and Their Interaction Effects of Electromagnetic Force of High-Speed Solenoid Valve

PubMed Central

Fan, Liyun; Xu, De; Ma, Xiuzhen; Song, Enzhe

2014-01-01

Analysis consisting of numerical simulations along with lab experiments of interaction effects between key parameters on the electromagnetic force based on response surface methodology (RSM) has been also proposed to optimize the design of high-speed solenoid valve (HSV) and improve its performance. Numerical simulation model of HSV has been developed in Ansoft Maxwell environment and its accuracy has been validated through lab experiments. Effect of change of core structure, coil structure, armature structure, working air gap, and drive current on the electromagnetic force of HSV has been analyzed through simulation model and influence rules of various parameters on the electromagnetic force have been established. The response surface model of the electromagnetic force has been utilized to analyze the interaction effect between major parameters. It has been concluded that six interaction factors including working air gap with armature radius, drive current with armature thickness, coil turns with side pole radius, armature thickness with its radius, armature thickness with side pole radius, and armature radius with side pole radius have significant influence on the electromagnetic force. Optimal match values between coil turns and side pole radius; armature thickness and side pole radius; and armature radius and side pole radius have also been determined. PMID:25243217

Subsurface damage distribution in the lapping process.

PubMed

Wang, Zhuo; Wu, Yulie; Dai, Yifan; Li, Shengyi

2008-04-01

To systematically investigate the influence of lapping parameters on subsurface damage (SSD) depth and characterize the damage feature comprehensively, maximum depth and distribution of SSD generated in the optical lapping process were measured with the magnetorheological finishing wedge technique. Then, an interaction of adjacent indentations was applied to interpret the generation of maximum depth of SSD. Eventually, the lapping procedure based on the influence of lapping parameters on the material removal rate and SSD depth was proposed to improve the lapping efficiency.

[Parameter sensitivity of simulating net primary productivity of Larix olgensis forest based on BIOME-BGC model].

PubMed

He, Li-hong; Wang, Hai-yan; Lei, Xiang-dong

2016-02-01

Model based on vegetation ecophysiological process contains many parameters, and reasonable parameter values will greatly improve simulation ability. Sensitivity analysis, as an important method to screen out the sensitive parameters, can comprehensively analyze how model parameters affect the simulation results. In this paper, we conducted parameter sensitivity analysis of BIOME-BGC model with a case study of simulating net primary productivity (NPP) of Larix olgensis forest in Wangqing, Jilin Province. First, with the contrastive analysis between field measurement data and the simulation results, we tested the BIOME-BGC model' s capability of simulating the NPP of L. olgensis forest. Then, Morris and EFAST sensitivity methods were used to screen the sensitive parameters that had strong influence on NPP. On this basis, we also quantitatively estimated the sensitivity of the screened parameters, and calculated the global, the first-order and the second-order sensitivity indices. The results showed that the BIOME-BGC model could well simulate the NPP of L. olgensis forest in the sample plot. The Morris sensitivity method provided a reliable parameter sensitivity analysis result under the condition of a relatively small sample size. The EFAST sensitivity method could quantitatively measure the impact of simulation result of a single parameter as well as the interaction between the parameters in BIOME-BGC model. The influential sensitive parameters for L. olgensis forest NPP were new stem carbon to new leaf carbon allocation and leaf carbon to nitrogen ratio, the effect of their interaction was significantly greater than the other parameter' teraction effect.

Parametric behaviors of CLUBB in simulations of low clouds in the Community Atmosphere Model (CAM)

DOE PAGES

Guo, Zhun; Wang, Minghuai; Qian, Yun; ...

2015-07-03

In this study, we investigate the sensitivity of simulated low clouds to 14 selected tunable parameters of Cloud Layers Unified By Binormals (CLUBB), a higher order closure (HOC) scheme, and 4 parameters of the Zhang-McFarlane (ZM) deep convection scheme in the Community Atmosphere Model version 5 (CAM5). A quasi-Monte Carlo (QMC) sampling approach is adopted to effectively explore the high-dimensional parameter space and a generalized linear model is applied to study the responses of simulated cloud fields to tunable parameters. Our results show that the variance in simulated low-cloud properties (cloud fraction and liquid water path) can be explained bymore » the selected tunable parameters in two different ways: macrophysics itself and its interaction with microphysics. First, the parameters related to dynamic and thermodynamic turbulent structure and double Gaussians closure are found to be the most influential parameters for simulating low clouds. The spatial distributions of the parameter contributions show clear cloud-regime dependence. Second, because of the coupling between cloud macrophysics and cloud microphysics, the coefficient of the dissipation term in the total water variance equation is influential. This parameter affects the variance of in-cloud cloud water, which further influences microphysical process rates, such as autoconversion, and eventually low-cloud fraction. Furthermore, this study improves understanding of HOC behavior associated with parameter uncertainties and provides valuable insights for the interaction of macrophysics and microphysics.« less

Development of a gluten-free rice noodle by utilizing protein-polyphenol interaction between soy protein isolate and extract of Acanthopanax sessiliflorus.

PubMed

Lee, Da-Som; Kim, Yang; Song, Youngwoon; Lee, Ji-Hye; Lee, Suyong; Yoo, Sang-Ho

2016-02-01

The potential of the protein-polyphenol interaction was applied to crosslinking reinforced protein networks in gluten-free rice noodles. Specifically, inter-component interaction between soy protein isolate and extract of Acanthopanax sessiliflorus fruit (ogaja) was examined with a view to improving its quality. In a components-interacting model system, a mixture of soy protein isolate (SPI) and ogaja extract (OE) induced a drastic increase in absorbance at 660 nm by haze formation, while the major anthocyanin of ogaja, cyanidin-3-O-sambubioside, sparsely interacted with SPI or gelatin. Individual or combined treatment of SPI and OE on rice dough decreased all the viscosity parameters in rapid visco analysis. However, SPI-OE treatment significantly increased all the texture parameters of rice dough derived from Mixolab(®) analysis (P < 0.05). Incorporation of SPI in rice dough significantly reduced endothermic ΔH, and SPI-OE treatment further decreased this value. SPI-OE interaction significantly increased the tensile properties of cooked noodle and decreased 53.7% of cooking loss compared to the untreated rice noodle. SPI-OE treatment caused a considerable reinforcement of the network as shown by reducing cooking loss and suggested the potential for utilizing protein-polyphenol interaction for gluten-free rice noodle production. © 2015 Society of Chemical Industry.

Classification of hydrological parameter sensitivity and evaluation of parameter transferability across 431 US MOPEX basins

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

Ren, Huiying; Hou, Zhangshuan; Huang, Maoyi

The Community Land Model (CLM) represents physical, chemical, and biological processes of the terrestrial ecosystems that interact with climate across a range of spatial and temporal scales. As CLM includes numerous sub-models and associated parameters, the high-dimensional parameter space presents a formidable challenge for quantifying uncertainty and improving Earth system predictions needed to assess environmental changes and risks. This study aims to evaluate the potential of transferring hydrologic model parameters in CLM through sensitivity analyses and classification across watersheds from the Model Parameter Estimation Experiment (MOPEX) in the United States. The sensitivity of CLM-simulated water and energy fluxes to hydrologicalmore » parameters across 431 MOPEX basins are first examined using an efficient stochastic sampling-based sensitivity analysis approach. Linear, interaction, and high-order nonlinear impacts are all identified via statistical tests and stepwise backward removal parameter screening. The basins are then classified accordingly to their parameter sensitivity patterns (internal attributes), as well as their hydrologic indices/attributes (external hydrologic factors) separately, using a Principal component analyses (PCA) and expectation-maximization (EM) –based clustering approach. Similarities and differences among the parameter sensitivity-based classification system (S-Class), the hydrologic indices-based classification (H-Class), and the Koppen climate classification systems (K-Class) are discussed. Within each S-class with similar parameter sensitivity characteristics, similar inversion modeling setups can be used for parameter calibration, and the parameters and their contribution or significance to water and energy cycling may also be more transferrable. This classification study provides guidance on identifiable parameters, and on parameterization and inverse model design for CLM but the methodology is applicable to other models. Inverting parameters at representative sites belonging to the same class can significantly reduce parameter calibration efforts.« less

Are quantitative sensitivity analysis methods always reliable?

NASA Astrophysics Data System (ADS)

Huang, X.

2016-12-01

Physical parameterizations developed to represent subgrid-scale physical processes include various uncertain parameters, leading to large uncertainties in today's Earth System Models (ESMs). Sensitivity Analysis (SA) is an efficient approach to quantitatively determine how the uncertainty of the evaluation metric can be apportioned to each parameter. Also, SA can identify the most influential parameters, as a result to reduce the high dimensional parametric space. In previous studies, some SA-based approaches, such as Sobol' and Fourier amplitude sensitivity testing (FAST), divide the parameters into sensitive and insensitive groups respectively. The first one is reserved but the other is eliminated for certain scientific study. However, these approaches ignore the disappearance of the interactive effects between the reserved parameters and the eliminated ones, which are also part of the total sensitive indices. Therefore, the wrong sensitive parameters might be identified by these traditional SA approaches and tools. In this study, we propose a dynamic global sensitivity analysis method (DGSAM), which iteratively removes the least important parameter until there are only two parameters left. We use the CLM-CASA, a global terrestrial model, as an example to verify our findings with different sample sizes ranging from 7000 to 280000. The result shows DGSAM has abilities to identify more influential parameters, which is confirmed by parameter calibration experiments using four popular optimization methods. For example, optimization using Top3 parameters filtered by DGSAM could achieve substantial improvement against Sobol' by 10%. Furthermore, the current computational cost for calibration has been reduced to 1/6 of the original one. In future, it is necessary to explore alternative SA methods emphasizing parameter interactions.

RAY-UI: A powerful and extensible user interface for RAY

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

Baumgärtel, P., E-mail: peter.baumgaertel@helmholtz-berlin.de; Erko, A.; Schäfers, F.

2016-07-27

The RAY-UI project started as a proof-of-concept for an interactive and graphical user interface (UI) for the well-known ray tracing software RAY [1]. In the meantime, it has evolved into a powerful enhanced version of RAY that will serve as the platform for future development and improvement of associated tools. The software as of today supports nearly all sophisticated simulation features of RAY. Furthermore, it delivers very significant usability and work efficiency improvements. Beamline elements can be quickly added or removed in the interactive sequence view. Parameters of any selected element can be accessed directly and in arbitrary order. Withmore » a single click, parameter changes can be tested and new simulation results can be obtained. All analysis results can be explored interactively right after ray tracing by means of powerful integrated image viewing and graphing tools. Unlimited image planes can be positioned anywhere in the beamline, and bundles of image planes can be created for moving the plane along the beam to identify the focus position with live updates of the simulated results. In addition to showing the features and workflow of RAY-UI, we will give an overview of the underlying software architecture as well as examples for use and an outlook for future developments.« less

An Improved Method for Measuring Chromatin-binding Dynamics Using Time-dependent Formaldehyde Crosslinking

PubMed Central

Hoffman, Elizabeth A.; Zaidi, Hussain; Shetty, Savera J.; Bekiranov, Stefan; Auble, David T.

2018-01-01

Formaldehyde crosslinking is widely used in combination with chromatin immunoprecipitation (ChIP) to measure the locations along DNA and relative levels of transcription factor (TF)-DNA interactions in vivo. However, the measurements that are typically made do not provide unambiguous information about the dynamic properties of these interactions. We have developed a method to estimate binding kinetic parameters from time-dependent formaldehyde crosslinking data, called crosslinking kinetics (CLK) analysis. Cultures of yeast cells are crosslinked with formaldehyde for various periods of time, yielding the relative ChIP signal at particular loci. We fit the data using the mass-action CLK model to extract kinetic parameters of the TF-chromatin interaction, including the on- and off-rates and crosslinking rate. From the on- and off-rate we obtain the occupancy and residence time. The following protocol is the second iteration of this method, CLKv2, updated with improved crosslinking and quenching conditions, more information about crosslinking rates, and systematic procedures for modeling the observed kinetic regimes. CLKv2 analysis has been applied to investigate the binding behavior of the TATA-binding protein (TBP), and a selected subset of other TFs. The protocol was developed using yeast cells, but may be applicable to cells from other organisms as well. PMID:29682595

Molecular Dynamics Simulations, Challenges and Opportunities: A Biologist's Prospective.

PubMed

Kumari, Indu; Sandhu, Padmani; Ahmed, Mushtaq; Akhter, Yusuf

2017-08-30

Molecular dynamics (MD) is a computational technique which is used to study biomolecules in virtual environment. Each of the constituent atoms represents a particle and hence the biomolecule embodies a multi-particle mechanical system analyzed within a simulation box during MD analysis. The potential energies of the atoms are explained by a mathematical expression consisting of different forces and space parameters. There are various software and force fields that have been developed for MD studies of the biomolecules. MD analysis has unravelled the various biological mechanisms (protein folding/unfolding, protein-small molecule interactions, protein-protein interactions, DNA/RNA-protein interactions, proteins embedded in membrane, lipid-lipid interactions, drug transport etc.) operating at the atomic and molecular levels. However, there are still some parameters including torsions in amino acids, carbohydrates (whose structure is extended and not well defined like that of proteins) and single stranded nucleic acids for which the force fields need further improvement, although there are several workers putting in constant efforts in these directions. The existing force fields are not efficient for studying the crowded environment inside the cells, since these interactions involve multiple factors in real time. Therefore, the improved force fields may provide the opportunities for their wider applications on the complex biosystems in diverse cellular conditions. In conclusion, the intervention of MD in the basic sciences involving interdisciplinary approaches will be helpful for understanding many fundamental biological and physiological processes at the molecular levels that may be further applied in various fields including biotechnology, fisheries, sustainable agriculture and biomedical research. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

The Taguchi Method Application to Improve the Quality of a Sustainable Process

NASA Astrophysics Data System (ADS)

Titu, A. M.; Sandu, A. V.; Pop, A. B.; Titu, S.; Ciungu, T. C.

2018-06-01

Taguchi’s method has always been a method used to improve the quality of the analyzed processes and products. This research shows an unusual situation, namely the modeling of some parameters, considered technical parameters, in a process that is wanted to be durable by improving the quality process and by ensuring quality using an experimental research method. Modern experimental techniques can be applied in any field and this study reflects the benefits of interacting between the agriculture sustainability principles and the Taguchi’s Method application. The experimental method used in this practical study consists of combining engineering techniques with experimental statistical modeling to achieve rapid improvement of quality costs, in fact seeking optimization at the level of existing processes and the main technical parameters. The paper is actually a purely technical research that promotes a technical experiment using the Taguchi method, considered to be an effective method since it allows for rapid achievement of 70 to 90% of the desired optimization of the technical parameters. The missing 10 to 30 percent can be obtained with one or two complementary experiments, limited to 2 to 4 technical parameters that are considered to be the most influential. Applying the Taguchi’s Method in the technique and not only, allowed the simultaneous study in the same experiment of the influence factors considered to be the most important in different combinations and, at the same time, determining each factor contribution.

Postprandial glycaemic response: how is it influenced by characteristics of cereal products?

PubMed

Meynier, Alexandra; Goux, Aurélie; Atkinson, Fiona; Brack, Olivier; Vinoy, Sophie

2015-06-28

Cereal products exhibit a wide range of glycaemic indexes (GI), but the interaction of their different nutrients and starch digestibility on blood glucose response is not well known. The objective of this analysis was to evaluate how cereal product characteristics can contribute to GI and insulinaemic index and to the parameters describing glycaemic or insulinaemic responses (incremental AUC, maximum concentration and Δpeak). Moreover, interactions between the different cereal products characteristics and glycaemic response parameters were assessed for the first time. Relationships between the cereal products characteristics and the glycaemic response were analysed by partial least square regressions, followed by modelling. A database including 190 cereal products tested by the usual GI methodology was used. The model on glycaemic responses showed that slowly digestible starch (SDS), rapidly digestible starch (RDS) and fat and fibres, and several interactions involving them, significantly explain GI by 53 % and Δpeak of glycaemia by 60 %. Fat and fibres had important contributions to glycaemic response at low and medium SDS contents in cereal products, but this effect disappears at high SDS levels. We showed also for the first time that glycaemic response parameters are dependent on interactions between starch digestibility (interaction between SDS and RDS) and nutritional composition (interaction between fat and fibres) of the cereal products. We also demonstrated the non-linear effect of fat and fibres (significant effect of their quadratic terms). Hence, optimising both the formula and the manufacturing process of cereal products can improve glucose metabolism, which is recognised as strongly influential on human health.

Use of the Flory-Huggins theory to predict the solubility of nifedipine and sulfamethoxazole in the triblock, graft copolymer Soluplus.

PubMed

Altamimi, Mohammad A; Neau, Steven H

2016-01-01

Drug dispersed in a polymer can improve bioavailability; dispersed amorphous drug undergoes recrystallization. Solid solutions eliminate amorphous regions, but require a measure of the solubility. Use the Flory-Huggins Theory to predict crystalline drugs solubility in the triblock, graft copolymer Soluplus® to provide a solid solution. Physical mixtures of the two drugs with similar melting points but different glass forming ability, sulfamethoxazole and nifedipine, were prepared with Soluplus® using a quick technique. Drug melting point depression (MPD) was measured using differential scanning calorimetry. The Flory-Huggins Theory allowed: (1) interaction parameter, χ, calculation using MPD data to provide a measure of drug-polymer interaction strength and (2) estimation of the free energy of mixing. A phase diagram was constructed with the MPD data and glass transition temperature (Tg) curves. The interaction parameters with Soluplus® and the free energy of mixing were estimated. Drug solubility was calculated by the intersection of solubility equations and that of MPD and Tg curves in the phase diagram. Negative interaction parameters indicated strong drug-polymer interactions. The phase diagram and solubility equations provided comparable solubility estimates for each drug in Soluplus®. Results using the onset of melting rather than the end of melting support the use of the onset of melting. The Flory-Huggins Theory indicates that Soluplus® interacts effectively with each drug, making solid solution formation feasible. The predicted solubility of the drugs in Soluplus® compared favorably across the methods and supports the use of the onset of melting.

Use of the Flory-Huggins theory to predict the solubility of nifedipine and sulfamethoxazole in the triblock, graft copolymer Soluplus.

PubMed

Altamimi, Mohammad A; Neau, Steven H

2016-03-01

Drug dispersed in a polymer can improve bioavailability; dispersed amorphous drug undergoes recrystallization. Solid solutions eliminate amorphous regions, but require a measure of the solubility. Use the Flory-Huggins Theory to predict crystalline drugs solubility in the triblock, graft copolymer Soluplus® to provide a solid solution. Physical mixtures of the two drugs with similar melting points but different glass forming ability, sulfamethoxazole and nifedipine, were prepared with Soluplus® using a quick technique. Drug melting point depression (MPD) was measured using differential scanning calorimetry. The Flory-Huggins Theory allowed: (1) interaction parameter, χ, calculation using MPD data to provide a measure of drug-polymer interaction strength and (2) estimation of the free energy of mixing. A phase diagram was constructed with the MPD data and glass transition temperature (T g ) curves. The interaction parameters with Soluplus® and the free energy of mixing were estimated. Drug solubility was calculated by the intersection of solubility equations and that of MPD and T g curves in the phase diagram. Negative interaction parameters indicated strong drug-polymer interactions. The phase diagram and solubility equations provided comparable solubility estimates for each drug in Soluplus®. Results using the onset of melting rather than the end of melting support the use of the onset of melting. The Flory-Huggins Theory indicates that Soluplus® interacts effectively with each drug, making solid solution formation feasible. The predicted solubility of the drugs in Soluplus® compared favorably across the methods and supports the use of the onset of melting.

Modeling strategic behavior in human-automation interaction - Why an 'aid' can (and should) go unused

NASA Technical Reports Server (NTRS)

Kirlik, Alex

1993-01-01

Task-offload aids (e.g., an autopilot, an 'intelligent' assistant) can be selectively engaged by the human operator to dynamically delegate tasks to automation. Introducing such aids eliminates some task demands but creates new ones associated with programming, engaging, and disengaging the aiding device via an interface. The burdens associated with managing automation can sometimes outweigh the potential benefits of automation to improved system performance. Aid design parameters and features of the overall multitask context combine to determine whether or not a task-offload aid will effectively support the operator. A modeling and sensitivity analysis approach is presented that identifies effective strategies for human-automation interaction as a function of three task-context parameters and three aid design parameters. The analysis and modeling approaches provide resources for predicting how a well-adapted operator will use a given task-offload aid, and for specifying aid design features that ensure that automation will provide effective operator support in a multitask environment.

[Arterial pressure curve and fluid status].

PubMed

Pestel, G; Fukui, K

2009-04-01

Fluid optimization is a major contributor to improved outcome in patients. Unfortunately, anesthesiologists are often in doubt whether an additional fluid bolus will improve the hemodynamics of the patient or not as excess fluid may even jeopardize the condition. This article discusses physiological concepts of liberal versus restrictive fluid management followed by a discussion on the respective capabilities of various monitors to predict fluid responsiveness. The parameter difference in pulse pressure (dPP), derived from heart-lung interaction in mechanically ventilated patients is discussed in detail. The dPP cutoff value of 13% to predict fluid responsiveness is presented together with several assessment techniques of dPP. Finally, confounding variables on dPP measurements, such as ventilation parameters, pneumoperitoneum and use of norepinephrine are also mentioned.

Physiologically based pharmacokinetic modelling of methotrexate and 6-mercaptopurine in adults and children. Part 2: 6-mercaptopurine and its interaction with methotrexate.

PubMed

Ogungbenro, Kayode; Aarons, Leon

2014-04-01

6-mercaptopurine (6-MP) is a purine antimetabolite and prodrug that undergoes extensive intracellular metabolism to produce thionucleotides, active metabolites which have cytotoxic and immunosuppressive properties. Combination therapies involving 6-MP and methotrexate have shown remarkable results in the cure of childhood acute lymphoblastic leukaemia (ALL) in the last 30 years. 6-MP undergoes very extensive intestinal and hepatic metabolism following oral dosing due to the activity of xanthine oxidase leading to very low and highly variable bioavailability and methotrexate has been demonstrated as an inhibitor of xanthine oxidase. Despite the success recorded in the use of 6-MP in ALL, there is still lack of effect and life threatening toxicity in some patients due to variability in the pharmacokinetics of 6-MP. Also, dose adjustment during treatment is still based on toxicity. The aim of the current work was to develop a mechanistic model that can be used to simulate trial outcomes and help to improve dose individualisation and dosage regimen optimisation. A physiological based pharmacokinetic model was proposed for 6-MP, this model has compartments for stomach, gut lumen, enterocyte, gut tissue, spleen, liver vascular, liver tissue, kidney vascular, kidney tissue, skin, bone marrow, thymus, muscle, rest of body and red blood cells. The model was based on the assumption of the same elimination pathways in adults and children. Parameters of the model include physiological parameters and drug-specific parameter which were obtained from the literature or estimated using plasma and red blood cell concentration data. Age-dependent changes in parameters were implemented for scaling and variability was also introduced on the parameters for prediction. Inhibition of 6-MP first-pass effect by methotrexate was implemented to predict observed clinical interaction between the two drugs. The model was developed successfully and plasma and red blood cell concentrations were adequately predicted both in terms of mean prediction and variability. The predicted interaction between 6-MP and methotrexate was slightly lower than the reported clinical interaction between the two drugs. The model can be used to predict plasma and tissue concentration in adults and children following oral and intravenous dosing and may ultimately help to improve treatment outcome in childhood ALL patients.

Levels and interactions of plasma xanthine oxidase, catalase and liver function parameters in Nigerian children with Plasmodium falciparum infection.

PubMed

Iwalokun, B A; Bamiro, S B; Ogunledun, A

2006-12-01

Elevated plasma levels of xanthine oxidase and liver function parameters have been associated with inflammatory events in several human diseases. While xanthine oxidase provides in vitro protection against malaria, its pathophysiological functions in vivo and interactions with liver function parameters remain unclear. This study examined the interactions and plasma levels of xanthine oxidase (XO) and uric acid (UA), catalase (CAT) and liver function parameters GOT, GPT and bilirubin in asymptomatic (n=20), uncomplicated (n=32), and severe (n=18) falciparum malaria children aged 3-13 years. Compared to age-matched control (n=16), significant (p<0.05) elevation in xanthine oxidase by 100-550%, uric acid by 15.4-153.8%, GOT and GPT by 22.1-102.2%, and total bilirubin by 2.3-86% according to parasitaemia (geometric mean parasite density (GMPD)=850-87100 parasites/microL) was observed in the malarial children. Further comparison with control revealed higher CAT level (16.2+/-0.5 vs 14.6+/-0.4 U/L; p<0.05) lacking significant (p>0.05) correlation with XO, but lower CAT level (13.4-5.4 U/L) with improved correlations (r=-0.53 to -0.91; p<0.05) with XO among the asymptomatic and symptomatic malaria children studied. 75% of control, 45% of asymptomatic, 21.9% of uncomplicated, and none of severe malaria children had Hb level>11.0 g/dL. Multivariate analyses further revealed significant (p<0.05) correlations between liver function parameters and xanthine oxidase (r=0.57-0.64) only in the severe malaria group. We conclude that elevated levels of XO and liver enzymes are biochemical features of Plasmodium falciparum parasitaemia in Nigerian children, with both parameters interacting differently to modulate the catalase response in asymptomatic and symptomatic falciparum malaria.

[Benefits of an educational intervention on diet and anthropometric profile of women with one cardiovascular risk factor].

PubMed

Soto Rodríguez, Anxela; García Soidán, José Luís; de Toro Santos, Manuel; Lagoa Labrador, Fiz; Failde Garrido, José M; Pérez Fernández, María Reyes

2016-05-20

To assess whether an educational intervention in perimenopausal women with hypertension, diabetes mellitus and/or dyslipidaemia would improve adherence to a Mediterranean diet pattern and achieve changes in anthropometric parameters. Randomized clinical trial of parallel groups: 320 women (45-60 years) in 2 urban primary care services. hip and waist circumference, body mass index (BMI), total, visceral and trunk fat (bioimpedance measures) and adherence to Mediterranean diet (MEDAS-14 questionnaire). Intervention group: 3 interactive workshops on prevention of cardiovascular disease, and control group: information by post. Two hundred and thirty women completed the study (113 control group and 117 intervention group). The differences between groups were significant in all parameters one year later. In the intragroup comparison, the intervention group maintained their BMI and improved adherence to the Mediterranean diet. The control group increased their BMI, abdominal and hip circumference and fat parameters (total, visceral and trunk fat). A simple educational intervention in perimenopausal women with cardiovascular risk can improve their healthy habits. Copyright © 2016 Elsevier España, S.L.U. All rights reserved.

An Interactive Image Segmentation Method in Hand Gesture Recognition

PubMed Central

Chen, Disi; Li, Gongfa; Sun, Ying; Kong, Jianyi; Jiang, Guozhang; Tang, Heng; Ju, Zhaojie; Yu, Hui; Liu, Honghai

2017-01-01

In order to improve the recognition rate of hand gestures a new interactive image segmentation method for hand gesture recognition is presented, and popular methods, e.g., Graph cut, Random walker, Interactive image segmentation using geodesic star convexity, are studied in this article. The Gaussian Mixture Model was employed for image modelling and the iteration of Expectation Maximum algorithm learns the parameters of Gaussian Mixture Model. We apply a Gibbs random field to the image segmentation and minimize the Gibbs Energy using Min-cut theorem to find the optimal segmentation. The segmentation result of our method is tested on an image dataset and compared with other methods by estimating the region accuracy and boundary accuracy. Finally five kinds of hand gestures in different backgrounds are tested on our experimental platform, and the sparse representation algorithm is used, proving that the segmentation of hand gesture images helps to improve the recognition accuracy. PMID:28134818

Estimation of the solubility parameters of model plant surfaces and agrochemicals: a valuable tool for understanding plant surface interactions

PubMed Central

2012-01-01

Background Most aerial plant parts are covered with a hydrophobic lipid-rich cuticle, which is the interface between the plant organs and the surrounding environment. Plant surfaces may have a high degree of hydrophobicity because of the combined effects of surface chemistry and roughness. The physical and chemical complexity of the plant cuticle limits the development of models that explain its internal structure and interactions with surface-applied agrochemicals. In this article we introduce a thermodynamic method for estimating the solubilities of model plant surface constituents and relating them to the effects of agrochemicals. Results Following the van Krevelen and Hoftyzer method, we calculated the solubility parameters of three model plant species and eight compounds that differ in hydrophobicity and polarity. In addition, intact tissues were examined by scanning electron microscopy and the surface free energy, polarity, solubility parameter and work of adhesion of each were calculated from contact angle measurements of three liquids with different polarities. By comparing the affinities between plant surface constituents and agrochemicals derived from (a) theoretical calculations and (b) contact angle measurements we were able to distinguish the physical effect of surface roughness from the effect of the chemical nature of the epicuticular waxes. A solubility parameter model for plant surfaces is proposed on the basis of an increasing gradient from the cuticular surface towards the underlying cell wall. Conclusions The procedure enabled us to predict the interactions among agrochemicals, plant surfaces, and cuticular and cell wall components, and promises to be a useful tool for improving our understanding of biological surface interactions. PMID:23151272

Estimation of the solubility parameters of model plant surfaces and agrochemicals: a valuable tool for understanding plant surface interactions.

PubMed

Khayet, Mohamed; Fernández, Victoria

2012-11-14

Most aerial plant parts are covered with a hydrophobic lipid-rich cuticle, which is the interface between the plant organs and the surrounding environment. Plant surfaces may have a high degree of hydrophobicity because of the combined effects of surface chemistry and roughness. The physical and chemical complexity of the plant cuticle limits the development of models that explain its internal structure and interactions with surface-applied agrochemicals. In this article we introduce a thermodynamic method for estimating the solubilities of model plant surface constituents and relating them to the effects of agrochemicals. Following the van Krevelen and Hoftyzer method, we calculated the solubility parameters of three model plant species and eight compounds that differ in hydrophobicity and polarity. In addition, intact tissues were examined by scanning electron microscopy and the surface free energy, polarity, solubility parameter and work of adhesion of each were calculated from contact angle measurements of three liquids with different polarities. By comparing the affinities between plant surface constituents and agrochemicals derived from (a) theoretical calculations and (b) contact angle measurements we were able to distinguish the physical effect of surface roughness from the effect of the chemical nature of the epicuticular waxes. A solubility parameter model for plant surfaces is proposed on the basis of an increasing gradient from the cuticular surface towards the underlying cell wall. The procedure enabled us to predict the interactions among agrochemicals, plant surfaces, and cuticular and cell wall components, and promises to be a useful tool for improving our understanding of biological surface interactions.

Stability of the two-dimensional Fermi polaron

NASA Astrophysics Data System (ADS)

Griesemer, Marcel; Linden, Ulrich

2018-02-01

A system composed of an ideal gas of N fermions interacting with an impurity particle in two space dimensions is considered. The interaction between impurity and fermions is given in terms of two-body point interactions whose strength is determined by the two-body binding energy, which is a free parameter of the model. If the mass of the impurity is 1.225 times larger than the mass of a fermion, it is shown that the energy is bounded below uniformly in the number N of fermions. This result improves previous, N-dependent lower bounds, and it complements a recent, similar bound for the Fermi polaron in three space dimensions.

Exclusion Bounds for Extended Anyons

NASA Astrophysics Data System (ADS)

Larson, Simon; Lundholm, Douglas

2018-01-01

We introduce a rigorous approach to the many-body spectral theory of extended anyons, that is quantum particles confined to two dimensions that interact via attached magnetic fluxes of finite extent. Our main results are many-body magnetic Hardy inequalities and local exclusion principles for these particles, leading to estimates for the ground-state energy of the anyon gas over the full range of the parameters. This brings out further non-trivial aspects in the dependence on the anyonic statistics parameter, and also gives improvements in the ideal (non-extended) case.

Revisiting Hansen Solubility Parameters by Including Thermodynamics.

PubMed

Louwerse, Manuel J; Maldonado, Ana; Rousseau, Simon; Moreau-Masselon, Chloe; Roux, Bernard; Rothenberg, Gadi

2017-11-03

The Hansen solubility parameter approach is revisited by implementing the thermodynamics of dissolution and mixing. Hansen's pragmatic approach has earned its spurs in predicting solvents for polymer solutions, but for molecular solutes improvements are needed. By going into the details of entropy and enthalpy, several corrections are suggested that make the methodology thermodynamically sound without losing its ease of use. The most important corrections include accounting for the solvent molecules' size, the destruction of the solid's crystal structure, and the specificity of hydrogen-bonding interactions, as well as opportunities to predict the solubility at extrapolated temperatures. Testing the original and the improved methods on a large industrial dataset including solvent blends, fit qualities improved from 0.89 to 0.97 and the percentage of correct predictions rose from 54 % to 78 %. Full Matlab scripts are included in the Supporting Information, allowing readers to implement these improvements on their own datasets. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Assessment of the Potential Impacts of Wheat Plant Traits across Environments by Combining Crop Modeling and Global Sensitivity Analysis

PubMed Central

Casadebaig, Pierre; Zheng, Bangyou; Chapman, Scott; Huth, Neil; Faivre, Robert; Chenu, Karine

2016-01-01

A crop can be viewed as a complex system with outputs (e.g. yield) that are affected by inputs of genetic, physiology, pedo-climatic and management information. Application of numerical methods for model exploration assist in evaluating the major most influential inputs, providing the simulation model is a credible description of the biological system. A sensitivity analysis was used to assess the simulated impact on yield of a suite of traits involved in major processes of crop growth and development, and to evaluate how the simulated value of such traits varies across environments and in relation to other traits (which can be interpreted as a virtual change in genetic background). The study focused on wheat in Australia, with an emphasis on adaptation to low rainfall conditions. A large set of traits (90) was evaluated in a wide target population of environments (4 sites × 125 years), management practices (3 sowing dates × 3 nitrogen fertilization levels) and CO2 (2 levels). The Morris sensitivity analysis method was used to sample the parameter space and reduce computational requirements, while maintaining a realistic representation of the targeted trait × environment × management landscape (∼ 82 million individual simulations in total). The patterns of parameter × environment × management interactions were investigated for the most influential parameters, considering a potential genetic range of +/- 20% compared to a reference cultivar. Main (i.e. linear) and interaction (i.e. non-linear and interaction) sensitivity indices calculated for most of APSIM-Wheat parameters allowed the identification of 42 parameters substantially impacting yield in most target environments. Among these, a subset of parameters related to phenology, resource acquisition, resource use efficiency and biomass allocation were identified as potential candidates for crop (and model) improvement. PMID:26799483

Assessment of the Potential Impacts of Wheat Plant Traits across Environments by Combining Crop Modeling and Global Sensitivity Analysis.

PubMed

Casadebaig, Pierre; Zheng, Bangyou; Chapman, Scott; Huth, Neil; Faivre, Robert; Chenu, Karine

2016-01-01

A crop can be viewed as a complex system with outputs (e.g. yield) that are affected by inputs of genetic, physiology, pedo-climatic and management information. Application of numerical methods for model exploration assist in evaluating the major most influential inputs, providing the simulation model is a credible description of the biological system. A sensitivity analysis was used to assess the simulated impact on yield of a suite of traits involved in major processes of crop growth and development, and to evaluate how the simulated value of such traits varies across environments and in relation to other traits (which can be interpreted as a virtual change in genetic background). The study focused on wheat in Australia, with an emphasis on adaptation to low rainfall conditions. A large set of traits (90) was evaluated in a wide target population of environments (4 sites × 125 years), management practices (3 sowing dates × 3 nitrogen fertilization levels) and CO2 (2 levels). The Morris sensitivity analysis method was used to sample the parameter space and reduce computational requirements, while maintaining a realistic representation of the targeted trait × environment × management landscape (∼ 82 million individual simulations in total). The patterns of parameter × environment × management interactions were investigated for the most influential parameters, considering a potential genetic range of +/- 20% compared to a reference cultivar. Main (i.e. linear) and interaction (i.e. non-linear and interaction) sensitivity indices calculated for most of APSIM-Wheat parameters allowed the identification of 42 parameters substantially impacting yield in most target environments. Among these, a subset of parameters related to phenology, resource acquisition, resource use efficiency and biomass allocation were identified as potential candidates for crop (and model) improvement.

A factorial assessment of the sensitivity of the BATS land-surface parameterization scheme. [BATS (Biosphere-Atmosphere Transfer Scheme)

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

Henderson-Sellers, A.

Land-surface schemes developed for incorporation into global climate models include parameterizations that are not yet fully validated and depend upon the specification of a large (20-50) number of ecological and soil parameters, the values of which are not yet well known. There are two methods of investigating the sensitivity of a land-surface scheme to prescribed values: simple one-at-a-time changes or factorial experiments. Factorial experiments offer information about interactions between parameters and are thus a more powerful tool. Here the results of a suite of factorial experiments are reported. These are designed (i) to illustrate the usefulness of this methodology andmore » (ii) to identify factors important to the performance of complex land-surface schemes. The Biosphere-Atmosphere Transfer Scheme (BATS) is used and its sensitivity is considered (a) to prescribed ecological and soil parameters and (b) to atmospheric forcing used in the off-line tests undertaken. Results indicate that the most important atmospheric forcings are mean monthly temperature and the interaction between mean monthly temperature and total monthly precipitation, although fractional cloudiness and other parameters are also important. The most important ecological parameters are vegetation roughness length, soil porosity, and a factor describing the sensitivity of the stomatal resistance of vegetation to the amount of photosynthetically active solar radiation and, to a lesser extent, soil and vegetation albedos. Two-factor interactions including vegetation roughness length are more important than many of the 23 specified single factors. The results of factorial sensitivity experiments such as these could form the basis for intercomparison of land-surface parameterization schemes and for field experiments and satellite-based observation programs aimed at improving evaluation of important parameters.« less

Investigation of Sb-Containing Precursors for Cu(In, Ga)Se2 Thin Films Through Design of Experiments

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

Mansfield, Lorelle M.; To, Bobby; Reedy, Robert C.

2016-11-21

The Design of Experiments (DoE) module in JMP statistical software was used to determine the best parameters for Sb-containing CIGS precursors with a fixed selenization step. Solar cells were fabricated and measured for all completed films. The most important factor influencing the current-voltage device parameters was identified as the temperature and antimony flux interaction. The DoE prediction profiler and predictive contour plots provided guidance to further improve the device parameters. In one follow-up run, we increased device efficiency from 14.9% to 15.5% Additional gains in efficiency to 16.9% were realized by introducing an intentional Ga gradient and an antireflective coating.

Effects of Pulse Parameters on Weld Microstructure and Mechanical Properties of Extra Pulse Current Aided Laser Welded 2219 Aluminum Alloy Joints.

PubMed

Zhang, Xinge; Li, Liqun; Chen, Yanbin; Yang, Zhaojun; Chen, Yanli; Guo, Xinjian

2017-09-15

In order to expand the application range of laser welding and improve weld quality, an extra pulse current was used to aid laser-welded 2219 aluminum alloy, and the effects of pulse current parameters on the weld microstructure and mechanical properties were investigated. The effect mechanisms of the pulse current interactions with the weld pool were evaluated. The results indicated that the coarse dendritic structure in the weld zone changed to a fine equiaxed structure using an extra pulse current, and the pulse parameters, including medium peak current, relatively high pulse frequency, and low pulse duty ratio benefited to improving the weld structure. The effect mechanisms of the pulse current were mainly ascribed to the magnetic pinch effect, thermal effect, and electromigration effect caused by the pulse current. The effect of the pulse parameters on the mechanical properties of welded joints were consistent with that of the weld microstructure. The tensile strength and elongation of the optimal pulse current-aided laser-welded joint increased by 16.4% and 105%, respectively, compared with autogenous laser welding.

Effects of Pulse Parameters on Weld Microstructure and Mechanical Properties of Extra Pulse Current Aided Laser Welded 2219 Aluminum Alloy Joints

PubMed Central

Zhang, Xinge; Li, Liqun; Chen, Yanbin; Yang, Zhaojun; Chen, Yanli; Guo, Xinjian

2017-01-01

In order to expand the application range of laser welding and improve weld quality, an extra pulse current was used to aid laser-welded 2219 aluminum alloy, and the effects of pulse current parameters on the weld microstructure and mechanical properties were investigated. The effect mechanisms of the pulse current interactions with the weld pool were evaluated. The results indicated that the coarse dendritic structure in the weld zone changed to a fine equiaxed structure using an extra pulse current, and the pulse parameters, including medium peak current, relatively high pulse frequency, and low pulse duty ratio benefited to improving the weld structure. The effect mechanisms of the pulse current were mainly ascribed to the magnetic pinch effect, thermal effect, and electromigration effect caused by the pulse current. The effect of the pulse parameters on the mechanical properties of welded joints were consistent with that of the weld microstructure. The tensile strength and elongation of the optimal pulse current-aided laser-welded joint increased by 16.4% and 105%, respectively, compared with autogenous laser welding. PMID:28914825

Detection of Volatile Organic Compounds by Self-assembled Monolayer Coated Sensor Array with Concentration-independent Fingerprints

PubMed Central

Chang, Ye; Tang, Ning; Qu, Hemi; Liu, Jing; Zhang, Daihua; Zhang, Hao; Pang, Wei; Duan, Xuexin

2016-01-01

In this paper, we have modeled and analyzed affinities and kinetics of volatile organic compounds (VOCs) adsorption (and desorption) on various surface chemical groups using multiple self-assembled monolayers (SAMs) functionalized film bulk acoustic resonator (FBAR) array. The high-frequency and micro-scale resonator provides improved sensitivity in the detections of VOCs at trace levels. With the study of affinities and kinetics, three concentration-independent intrinsic parameters (monolayer adsorption capacity, adsorption energy constant and desorption rate) of gas-surface interactions are obtained to contribute to a multi-parameter fingerprint library of VOC analytes. Effects of functional group’s properties on gas-surface interactions are also discussed. The proposed sensor array with concentration-independent fingerprint library shows potential as a portable electronic nose (e-nose) system for VOCs discrimination and gas-sensitive materials selections. PMID:27045012

On the use of interaction error potentials for adaptive brain computer interfaces.

PubMed

Llera, A; van Gerven, M A J; Gómez, V; Jensen, O; Kappen, H J

2011-12-01

We propose an adaptive classification method for the Brain Computer Interfaces (BCI) which uses Interaction Error Potentials (IErrPs) as a reinforcement signal and adapts the classifier parameters when an error is detected. We analyze the quality of the proposed approach in relation to the misclassification of the IErrPs. In addition we compare static versus adaptive classification performance using artificial and MEG data. We show that the proposed adaptive framework significantly improves the static classification methods. Copyright © 2011 Elsevier Ltd. All rights reserved.

Spin-component-scaled Møller-Plesset (SCS-MP) perturbation theory: a generalization of the MP approach with improved properties.

PubMed

Fink, Reinhold F

2010-11-07

A rigorous perturbation theory is proposed, which has the same second order energy as the spin-component-scaled Møller-Plesset second order (SCS-MP2) method of Grimme [J. Chem. Phys. 118, 9095 (2003)]. This upgrades SCS-MP2 to a systematically improvable, true wave-function-based method. The perturbation theory is defined by an unperturbed Hamiltonian, Ĥ(0), that contains the ordinary Fock operator and spin operators Ŝ(2) that act either on the occupied or the virtual orbital spaces. Two choices for Ĥ(0) are discussed and the importance of a spin-pure Ĥ((0)) is underlined. Like the SCS-MP2 approach, the theory contains two parameters (c(os) and c(ss)) that scale the opposite-spin and the same-spin contributions to the second order perturbation energy. It is shown that these parameters can be determined from theoretical considerations by a Feenberg scaling approach or a fit of the wave functions from the perturbation theory to the exact one from a full configuration interaction calculation. The parameters c(os)=1.15 and c(ss)=0.75 are found to be optimal for a reasonable test set of molecules. The meaning of these parameters and the consequences following from a well defined improved MP method are discussed.

Acute effect of Vagus nerve stimulation parameters on cardiac chronotropic, inotropic, and dromotropic responses

NASA Astrophysics Data System (ADS)

Ojeda, David; Le Rolle, Virginie; Romero-Ugalde, Hector M.; Gallet, Clément; Bonnet, Jean-Luc; Henry, Christine; Bel, Alain; Mabo, Philippe; Carrault, Guy; Hernández, Alfredo I.

2017-11-01

Vagus nerve stimulation (VNS) is an established therapy for drug-resistant epilepsy and depression, and is considered as a potential therapy for other pathologies, including Heart Failure (HF) or inflammatory diseases. In the case of HF, several experimental studies on animals have shown an improvement in the cardiac function and a reverse remodeling of the cardiac cavity when VNS is applied. However, recent clinical trials have not been able to reproduce the same response in humans. One of the hypothesis to explain this lack of response is related to the way in which stimulation parameters are defined. The combined effect of VNS parameters is still poorly-known, especially in the case of VNS synchronously delivered with cardiac activity. In this paper, we propose a methodology to analyze the acute cardiovascular effects of VNS parameters individually, as well as their interactive effects. A Latin hypercube sampling method was applied to design a uniform experimental plan. Data gathered from this experimental plan was used to produce a Gaussian process regression (GPR) model in order to estimate unobserved VNS sequences. Finally, a Morris screening sensitivity analysis method was applied to each obtained GPR model. Results highlight dominant effects of pulse current, pulse width and number of pulses over frequency and delay and, more importantly, the degree of interactions between these parameters on the most important acute cardiovascular responses. In particular, high interacting effects between current and pulse width were found. Similar sensitivity profiles were observed for chronotropic, dromotropic and inotropic effects. These findings are of primary importance for the future development of closed-loop, personalized neuromodulator technologies.

Understanding and comparisons of different sampling approaches for the Fourier Amplitudes Sensitivity Test (FAST)

PubMed Central

Xu, Chonggang; Gertner, George

2013-01-01

Fourier Amplitude Sensitivity Test (FAST) is one of the most popular uncertainty and sensitivity analysis techniques. It uses a periodic sampling approach and a Fourier transformation to decompose the variance of a model output into partial variances contributed by different model parameters. Until now, the FAST analysis is mainly confined to the estimation of partial variances contributed by the main effects of model parameters, but does not allow for those contributed by specific interactions among parameters. In this paper, we theoretically show that FAST analysis can be used to estimate partial variances contributed by both main effects and interaction effects of model parameters using different sampling approaches (i.e., traditional search-curve based sampling, simple random sampling and random balance design sampling). We also analytically calculate the potential errors and biases in the estimation of partial variances. Hypothesis tests are constructed to reduce the effect of sampling errors on the estimation of partial variances. Our results show that compared to simple random sampling and random balance design sampling, sensitivity indices (ratios of partial variances to variance of a specific model output) estimated by search-curve based sampling generally have higher precision but larger underestimations. Compared to simple random sampling, random balance design sampling generally provides higher estimation precision for partial variances contributed by the main effects of parameters. The theoretical derivation of partial variances contributed by higher-order interactions and the calculation of their corresponding estimation errors in different sampling schemes can help us better understand the FAST method and provide a fundamental basis for FAST applications and further improvements. PMID:24143037

Understanding and comparisons of different sampling approaches for the Fourier Amplitudes Sensitivity Test (FAST).

PubMed

Xu, Chonggang; Gertner, George

2011-01-01

Fourier Amplitude Sensitivity Test (FAST) is one of the most popular uncertainty and sensitivity analysis techniques. It uses a periodic sampling approach and a Fourier transformation to decompose the variance of a model output into partial variances contributed by different model parameters. Until now, the FAST analysis is mainly confined to the estimation of partial variances contributed by the main effects of model parameters, but does not allow for those contributed by specific interactions among parameters. In this paper, we theoretically show that FAST analysis can be used to estimate partial variances contributed by both main effects and interaction effects of model parameters using different sampling approaches (i.e., traditional search-curve based sampling, simple random sampling and random balance design sampling). We also analytically calculate the potential errors and biases in the estimation of partial variances. Hypothesis tests are constructed to reduce the effect of sampling errors on the estimation of partial variances. Our results show that compared to simple random sampling and random balance design sampling, sensitivity indices (ratios of partial variances to variance of a specific model output) estimated by search-curve based sampling generally have higher precision but larger underestimations. Compared to simple random sampling, random balance design sampling generally provides higher estimation precision for partial variances contributed by the main effects of parameters. The theoretical derivation of partial variances contributed by higher-order interactions and the calculation of their corresponding estimation errors in different sampling schemes can help us better understand the FAST method and provide a fundamental basis for FAST applications and further improvements.

Promising New Photon Detection Concepts for High-Resolution Clinical and Preclinical PET

PubMed Central

Levin, Craig S.

2013-01-01

The ability of PET to visualize and quantify regions of low concentration of PET tracer representing subtle cellular and molecular signatures of disease depends on relatively complex biochemical, biologic, and physiologic factors that are challenging to control, as well as on instrumentation performance parameters that are, in principle, still possible to improve on. Thus, advances to the latter can somewhat offset barriers of the former. PET system performance parameters such as spatial resolution, contrast resolution, and photon sensitivity contribute significantly to PET’s ability to visualize and quantify lower concentrations of signal in the presence of background. In this report we present some technology innovations under investigation toward improving these PET system performance parameters. We focus particularly on a promising advance known as 3-dimensional position-sensitive detectors, which are detectors capable of distinguishing and measuring the position, energy, and arrival time of individual interactions of multi-interaction photon events in 3 dimensions. If successful, these new strategies enable enhancements such as the detection of fewer diseased cells in tissue or the ability to characterize lower-abundance molecular targets within cells. Translating these advanced capabilities to the clinic might allow expansion of PET’s roles in disease management, perhaps to earlier stages of disease. In preclinical research, such enhancements enable more sensitive and accurate studies of disease biology in living subjects. PMID:22302960

Investigation of the Effects of Inulin and β-Glucan on the Physical and Sensory Properties of Low-Fat Beef Burgers Containing Vegetable Oils: Optimisation of the Formulation Using D-Optimal Mixture Design

PubMed Central

Afshari, Roya; Khaksar, Ramin; Mohammadifar, Mohammad Amin; Amiri, Zohre; Komeili, Rozita; Khaneghah, Amin Mousavi

2015-01-01

Summary In this study, the D-optimal mixture design methodology was applied to determine the optimised proportions of inulin, β-glucan and breadcrumbs in formulation of low-fat beef burgers containing pre-emulsified canola and olive oil blend. Also, the effect of each of the ingredients individually as well as their interactions on cooking characteristics, texture, colour and sensory properties of low-fat beef burgers were investigated. The results of this study revealed that the increase of inulin content in the formulations of burgers led to lower cooking yield, moisture retention and increased lightness, overall acceptability, mouldability and desired textural parameters. In contrast, incorporation of β-glucan increased the cooking yield, moisture retention and decreased lightness, overall acceptability, mouldability and desired textural parameters of burger patties. The interaction between inulin and β-glucan improved the cooking characteristics of the burgers without significantly negative effect on the colour or sensory properties. The results of the study clearly stated that the optimum mixture for the burger formulation consisted of (in g per 100 g): inulin 3.1, β-glucan 2.2 and breadcrumbs 2.7. The texture parameters and cooking characteristics were improved by using the mixture of inulin, β-glucan and breadcrumbs, without any negative effects on the sensory properties of the burgers. PMID:27904378

Measuring Parameters of Massive Black Hole Binaries with Partially Aligned Spins

NASA Technical Reports Server (NTRS)

Lang, Ryan N.; Hughes, Scott A.; Cornish, Neil J.

2011-01-01

The future space-based gravitational wave detector LISA will be able to measure parameters of coalescing massive black hole binaries, often to extremely high accuracy. Previous work has demonstrated that the black hole spins can have a strong impact on the accuracy of parameter measurement. Relativistic spin-induced precession modulates the waveform in a manner which can break degeneracies between parameters, in principle significantly improving how well they are measured. Recent studies have indicated, however, that spin precession may be weak for an important subset of astrophysical binary black holes: those in which the spins are aligned due to interactions with gas. In this paper, we examine how well a binary's parameters can be measured when its spins are partially aligned and compare results using waveforms that include higher post-Newtonian harmonics to those that are truncated at leading quadrupole order. We find that the weakened precession can substantially degrade parameter estimation, particularly for the "extrinsic" parameters sky position and distance. Absent higher harmonics, LISA typically localizes the sky position of a nearly aligned binary about an order of magnitude less accurately than one for which the spin orientations are random. Our knowledge of a source's sky position will thus be worst for the gas-rich systems which are most likely to produce electromagnetic counterparts. Fortunately, higher harmonics of the waveform can make up for this degradation. By including harmonics beyond the quadrupole in our waveform model, we find that the accuracy with which most of the binary's parameters are measured can be substantially improved. In some cases, the improvement is such that they are measured almost as well as when the binary spins are randomly aligned.

Prediction of Environmental Impact of High-Energy Materials with Atomistic Computer Simulations

DTIC Science & Technology

2010-11-01

from a training set of compounds. Other methods include Quantitative Struc- ture-Activity Relationship ( QSAR ) and Quantitative Structure-Property...26 28 the development of QSPR/ QSAR models, in contrast to boiling points and critical parameters derived from empirical correlations, to improve...Quadratic Configuration Interaction Singles Doubles QSAR Quantitative Structure-Activity Relationship QSPR Quantitative Structure-Property

Potential for geophysical experiments in large scale tests.

USGS Publications Warehouse

Dieterich, J.H.

1981-01-01

Potential research applications for large-specimen geophysical experiments include measurements of scale dependence of physical parameters and examination of interactions with heterogeneities, especially flaws such as cracks. In addition, increased specimen size provides opportunities for improved recording resolution and greater control of experimental variables. Large-scale experiments using a special purpose low stress (100MPa).-Author

Incorporating time-delays in S-System model for reverse engineering genetic networks.

PubMed

Chowdhury, Ahsan Raja; Chetty, Madhu; Vinh, Nguyen Xuan

2013-06-18

In any gene regulatory network (GRN), the complex interactions occurring amongst transcription factors and target genes can be either instantaneous or time-delayed. However, many existing modeling approaches currently applied for inferring GRNs are unable to represent both these interactions simultaneously. As a result, all these approaches cannot detect important interactions of the other type. S-System model, a differential equation based approach which has been increasingly applied for modeling GRNs, also suffers from this limitation. In fact, all S-System based existing modeling approaches have been designed to capture only instantaneous interactions, and are unable to infer time-delayed interactions. In this paper, we propose a novel Time-Delayed S-System (TDSS) model which uses a set of delay differential equations to represent the system dynamics. The ability to incorporate time-delay parameters in the proposed S-System model enables simultaneous modeling of both instantaneous and time-delayed interactions. Furthermore, the delay parameters are not limited to just positive integer values (corresponding to time stamps in the data), but can also take fractional values. Moreover, we also propose a new criterion for model evaluation exploiting the sparse and scale-free nature of GRNs to effectively narrow down the search space, which not only reduces the computation time significantly but also improves model accuracy. The evaluation criterion systematically adapts the max-min in-degrees and also systematically balances the effect of network accuracy and complexity during optimization. The four well-known performance measures applied to the experimental studies on synthetic networks with various time-delayed regulations clearly demonstrate that the proposed method can capture both instantaneous and delayed interactions correctly with high precision. The experiments carried out on two well-known real-life networks, namely IRMA and SOS DNA repair network in Escherichia coli show a significant improvement compared with other state-of-the-art approaches for GRN modeling.

Modelling non-linear effects of dark energy

NASA Astrophysics Data System (ADS)

Bose, Benjamin; Baldi, Marco; Pourtsidou, Alkistis

2018-04-01

We investigate the capabilities of perturbation theory in capturing non-linear effects of dark energy. We test constant and evolving w models, as well as models involving momentum exchange between dark energy and dark matter. Specifically, we compare perturbative predictions at 1-loop level against N-body results for four non-standard equations of state as well as varying degrees of momentum exchange between dark energy and dark matter. The interaction is modelled phenomenologically using a time dependent drag term in the Euler equation. We make comparisons at the level of the matter power spectrum and the redshift space monopole and quadrupole. The multipoles are modelled using the Taruya, Nishimichi and Saito (TNS) redshift space spectrum. We find perturbation theory does very well in capturing non-linear effects coming from dark sector interaction. We isolate and quantify the 1-loop contribution coming from the interaction and from the non-standard equation of state. We find the interaction parameter ξ amplifies scale dependent signatures in the range of scales considered. Non-standard equations of state also give scale dependent signatures within this same regime. In redshift space the match with N-body is improved at smaller scales by the addition of the TNS free parameter σv. To quantify the importance of modelling the interaction, we create mock data sets for varying values of ξ using perturbation theory. This data is given errors typical of Stage IV surveys. We then perform a likelihood analysis using the first two multipoles on these sets and a ξ=0 modelling, ignoring the interaction. We find the fiducial growth parameter f is generally recovered even for very large values of ξ both at z=0.5 and z=1. The ξ=0 modelling is most biased in its estimation of f for the phantom w=‑1.1 case.

Ensemble urban flood simulation in comparison with laboratory-scale experiments: Impact of interaction models for manhole, sewer pipe, and surface flow

NASA Astrophysics Data System (ADS)

Noh, Seong Jin; Lee, Seungsoo; An, Hyunuk; Kawaike, Kenji; Nakagawa, Hajime

2016-11-01

An urban flood is an integrated phenomenon that is affected by various uncertainty sources such as input forcing, model parameters, complex geometry, and exchanges of flow among different domains in surfaces and subsurfaces. Despite considerable advances in urban flood modeling techniques, limited knowledge is currently available with regard to the impact of dynamic interaction among different flow domains on urban floods. In this paper, an ensemble method for urban flood modeling is presented to consider the parameter uncertainty of interaction models among a manhole, a sewer pipe, and surface flow. Laboratory-scale experiments on urban flood and inundation are performed under various flow conditions to investigate the parameter uncertainty of interaction models. The results show that ensemble simulation using interaction models based on weir and orifice formulas reproduces experimental data with high accuracy and detects the identifiability of model parameters. Among interaction-related parameters, the parameters of the sewer-manhole interaction show lower uncertainty than those of the sewer-surface interaction. Experimental data obtained under unsteady-state conditions are more informative than those obtained under steady-state conditions to assess the parameter uncertainty of interaction models. Although the optimal parameters vary according to the flow conditions, the difference is marginal. Simulation results also confirm the capability of the interaction models and the potential of the ensemble-based approaches to facilitate urban flood simulation.

Measurement of the Michel parameter {rho} in normal muon decay

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

Tu, X.; Amann, J.F.; Bolton, R.D.

1995-07-10

A new measurement of the Michel parameter {rho} in normal muon decay has been performed using the MEGA positron spectrometer. Over 500 million triggers were recorded and the data are currently being analyzed. The previous result has a precision on the value of {rho}{plus_minus}0.0026. The present experiment expects to improve the precision to {plus_minus}0.0008 or better. The improved result will be a precise test of the standard model of electroweak interactions for a purely leptonic process. It also will provide a better constraint on the {ital W}{sub {ital R}}{minus}{ital W}{sub {ital L}} mixing angle in the left-right symmetric models. {copyright}more » {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.« less

Accounting for Intraligand Interactions in Flexible Ligand Docking with a PMF-Based Scoring Function.

PubMed

Lizunov, A Y; Gonchar, A L; Zaitseva, N I; Zosimov, V V

2015-10-26

We analyzed the frequency with which intraligand contacts occurred in a set of 1300 protein-ligand complexes [ Plewczynski et al. J. Comput. Chem. 2011 , 32 , 742 - 755 .]. Our analysis showed that flexible ligands often form intraligand hydrophobic contacts, while intraligand hydrogen bonds are rare. The test set was also thoroughly investigated and classified. We suggest a universal method for enhancement of a scoring function based on a potential of mean force (PMF-based score) by adding a term accounting for intraligand interactions. The method was implemented via in-house developed program, utilizing an Algo_score scoring function [ Ramensky et al. Proteins: Struct., Funct., Genet. 2007 , 69 , 349 - 357 .] based on the Tarasov-Muryshev PMF [ Muryshev et al. J. Comput.-Aided Mol. Des. 2003 , 17 , 597 - 605 .]. The enhancement of the scoring function was shown to significantly improve the docking and scoring quality for flexible ligands in the test set of 1300 protein-ligand complexes [ Plewczynski et al. J. Comput. Chem. 2011 , 32 , 742 - 755 .]. We then investigated the correlation of the docking results with two parameters of intraligand interactions estimation. These parameters are the weight of intraligand interactions and the minimum number of bonds between the ligand atoms required to take their interaction into account.

Searching for dark matter-dark energy interactions: Going beyond the conformal case

NASA Astrophysics Data System (ADS)

van de Bruck, Carsten; Mifsud, Jurgen

2018-01-01

We consider several cosmological models which allow for nongravitational direct couplings between dark matter and dark energy. The distinguishing cosmological features of these couplings can be probed by current cosmological observations, thus enabling us to place constraints on these specific interactions which are composed of the conformal and disformal coupling functions. We perform a global analysis in order to independently constrain the conformal, disformal, and mixed interactions between dark matter and dark energy by combining current data from: Planck observations of the cosmic microwave background radiation anisotropies, a combination of measurements of baryon acoustic oscillations, a supernova type Ia sample, a compilation of Hubble parameter measurements estimated from the cosmic chronometers approach, direct measurements of the expansion rate of the Universe today, and a compilation of growth of structure measurements. We find that in these coupled dark-energy models, the influence of the local value of the Hubble constant does not significantly alter the inferred constraints when we consider joint analyses that include all cosmological probes. Moreover, the parameter constraints are remarkably improved with the inclusion of the growth of structure data set measurements. We find no compelling evidence for an interaction within the dark sector of the Universe.

Value of Computed Tomographic Perfusion-Based Patient Selection for Intra-Arterial Acute Ischemic Stroke Treatment.

PubMed

Borst, Jordi; Berkhemer, Olvert A; Roos, Yvo B W E M; van Bavel, Ed; van Zwam, Wim H; van Oostenbrugge, Robert J; van Walderveen, Marianne A A; Lingsma, Hester F; van der Lugt, Aad; Dippel, Diederik W J; Yoo, Albert J; Marquering, Henk A; Majoie, Charles B L M

2015-12-01

The utility of computed tomographic perfusion (CTP)-based patient selection for intra-arterial treatment of acute ischemic stroke has not been proven in randomized trials and requires further study in a cohort that was not selected based on CTP. Our objective was to study the relationship between CTP-derived parameters and outcome and treatment effect in patients with acute ischemic stroke because of a proximal intracranial arterial occlusion. We included 175 patients who underwent CTP in the Multicenter Randomized Clinical Trial of Endovascular Treatment for Acute Ischemic Stroke in The Netherlands (MR CLEAN). Association of CTP-derived parameters (ischemic-core volume, penumbra volume, and percentage ischemic core) with outcome was estimated with multivariable ordinal logistic regression as an adjusted odds ratio for a shift in the direction of a better outcome on the modified Rankin Scale. Interaction between CTP-derived parameters and treatment effect was determined using multivariable ordinal logistic regression. Interaction with treatment effect was also tested for mismatch (core <70 mL; penumbra core >1.2; penumbra core >10 mL). The adjusted odds ratio for improved functional outcome for ischemic core, percentage ischemic core, and penumbra were 0.79 per 10 mL (95% confidence interval: 0.71-0.89; P<0.001), 0.82 per 10% (95% confidence interval: 0.66-0.90; P=0.002), and 0.97 per 10 mL (96% confidence interval: 0.92-1.01; P=0.15), respectively. No significant interaction between any of the CTP-derived parameters and treatment effect was observed. We observed no significant interaction between mismatch and treatment effect. CTP seems useful for predicting functional outcome, but cannot reliably identify patients who will not benefit from intra-arterial therapy. © 2015 American Heart Association, Inc.

Improvement of metabolic parameters in healthy older adult men following a fasting calorie restriction intervention.

PubMed

Teng, Nur Islami Mohd Fahmi; Shahar, Suzana; Rajab, Nor Fadilah; Manaf, Zahara Abdul; Johari, Mohamad Hanapi; Ngah, Wan Zurinah Wan

2013-12-01

Calorie restriction and intermittent fasting are two dietary interventions that can improve aging. Religious fasting also suggested having similar benefit; however, such studies are still scarce. Thus, this study aimed to determine the effect of fasting calorie restriction (FCR) on metabolic parameters and DNA damage among healthy older adult men. A randomized controlled study was done on men, aged 50-70 years in Klang Valley, Malaysia. Subjects were divided into two groups; FCR (reduction of 300-500 kcal/d combined with 2 days/week of Muslim Sunnah Fasting) and control. Assessment was ascertained at three time point; baseline, weeks 6 and 12. Blood samples were analyzed for lipid profile, DNA damage and malondialdehyde (MDA). The FCR group reduced their energy intake for approximately 18% upon completion of the study. A significant interaction effect was found in body weight, body mass index, fat percentage, fat mass, blood pressure, total cholesterol, low-density lipoprotein cholesterol and the ratio of total cholesterol/high-density lipoprotein cholesterol (p < 0.05). A significant improvement (p < 0.001) in total DNA rejoining cells and MDA (p < 0.05) was also observed in the FCR group. FCR improved metabolic parameters and DNA damage in healthy older adult men. Therefore, there is a need to further examine the mechanism of FCR.

Influence of detector pixel size, TOF resolution and DOI on image quality in MR-compatible whole-body PET.

PubMed

Thoen, Hendrik; Keereman, Vincent; Mollet, Pieter; Van Holen, Roel; Vandenberghe, Stefaan

2013-09-21

The optimization of a whole-body PET system remains a challenging task, as the imaging performance is influenced by a complex interaction of different design parameters. However, it is not always clear which parameters have the largest impact on image quality and are most eligible for optimization. To determine this, we need to be able to assess their influence on image quality. We performed Monte-Carlo simulations of a whole-body PET scanner to predict the influence on image quality of three detector parameters: the TOF resolution, the transverse pixel size and depth-of-interaction (DOI)-correction. The inner diameter of the PET scanner was 65 cm, small enough to allow physical integration into a simultaneous PET-MR system. Point sources were used to evaluate the influence of transverse pixel size and DOI-correction on spatial resolution as function of radial distance. To evaluate the influence on contrast recovery and pixel noise a cylindrical phantom of 35 cm diameter was used, representing a large patient. The phantom contained multiple hot lesions with 5 mm diameter. These lesions were placed at radial distances of 50, 100 and 150 mm from the center of the field-of-view, to be able to study the effects at different radial positions. The non-prewhitening (NPW) observer was used for objective analysis of the detectability of the hot lesions in the cylindrical phantom. Based on this analysis the NPW-SNR was used to quantify the relative improvements in image quality due to changes of the variable detector parameters. The image quality of a whole-body PET scanner can be improved significantly by reducing the transverse pixel size from 4 to 2.6 mm and improving the TOF resolution from 600 to 400 ps and further from 400 to 200 ps. Compared to pixel size, the TOF resolution has the larger potential to increase image quality for the simulated phantom. The introduction of two layer DOI-correction only leads to a modest improvement for the spheres at radial distance of 150 mm from the center of the transaxial FOV.

Effects of raw material extrusion and steam conditioning on feed pellet quality and nutrient digestibility of growing meat rabbits.

PubMed

Liao, Kuoyao; Cai, Jingyi; Shi, Zhujun; Tian, Gang; Yan, Dong; Chen, Delin

2017-06-01

This study was conducted to investigate the effects of raw material extrusion and steam conditioning on feed pellet quality and nutrient digestibility of growing meat rabbits, in order to determine appropriate rabbit feed processing methods and processing parameters. In Exp. 1, an orthogonal design was adopted. Barrel temperature, material moisture content and feed rate were selected as test factors, and acid detergent fiber (ADF) content was selected as an evaluation index to research the optimum extrusion parameters. In Exp. 2, a two-factor design was adopted. Four kinds of rabbit feeds were processed and raw material extrusion adopted optimum extrusion parameters of Exp. 1. A total of 40 healthy and 42-day-old rabbits with similar weight were used in a randomized design, which consisted of 4 groups and 10 replicates in each group (1 rabbits in each replicate). The adaptation period lasted for 7 d, and the digestion trial lasted for 4 d. The results showed as follows: 1) ADF was significantly affected by barrel temperature ( P  < 0.05); the optimum extrusion parameters were barrel temperature 125 °C, moisture content 16% and feed rate 9 Hz. 2) Raw material extrusion and steam conditioning both significantly decreased powder percentage, pulverization ratio and protein solubility ( P  < 0.05), significantly improved hardness and starch gelatinization degree of rabbit feed ( P  < 0.05). They both had significant interaction effects on the processing quality of rabbit feed ( P  < 0.05). 3) Extrusion significantly improved the apparent digestibility of dry matter and total energy ( P  < 0.05). Extrusion and steam conditioning both significantly improved the apparent digestibility of crude fiber (CF), ADF and NDF ( P  < 0.05), but they had no interaction effects on the apparent digestibility of rabbit feed. Thus, using extrusion and steam conditioning technology at the same time in the weaning rabbits feed processing can improve the pellet quality and nutrient apparent digestibility of rabbit feed.

Computer simulations of alkali-acetate solutions: Accuracy of the forcefields in difference concentrations

NASA Astrophysics Data System (ADS)

Ahlstrand, Emma; Zukerman Schpector, Julio; Friedman, Ran

2017-11-01

When proteins are solvated in electrolyte solutions that contain alkali ions, the ions interact mostly with carboxylates on the protein surface. Correctly accounting for alkali-carboxylate interactions is thus important for realistic simulations of proteins. Acetates are the simplest carboxylates that are amphipathic, and experimental data for alkali acetate solutions are available and can be compared with observables obtained from simulations. We carried out molecular dynamics simulations of alkali acetate solutions using polarizable and non-polarizable forcefields and examined the ion-acetate interactions. In particular, activity coefficients and association constants were studied in a range of concentrations (0.03, 0.1, and 1M). In addition, quantum-mechanics (QM) based energy decomposition analysis was performed in order to estimate the contribution of polarization, electrostatics, dispersion, and QM (non-classical) effects on the cation-acetate and cation-water interactions. Simulations of Li-acetate solutions in general overestimated the binding of Li+ and acetates. In lower concentrations, the activity coefficients of alkali-acetate solutions were too high, which is suggested to be due to the simulation protocol and not the forcefields. Energy decomposition analysis suggested that improvement of the forcefield parameters to enable accurate simulations of Li-acetate solutions can be achieved but may require the use of a polarizable forcefield. Importantly, simulations with some ion parameters could not reproduce the correct ion-oxygen distances, which calls for caution in the choice of ion parameters when protein simulations are performed in electrolyte solutions.

Sensitivity of GRETINA position resolution to hole mobility

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

Prasher, V. S.; Cromaz, M.; Merchan, E.

The sensitivity of the position resolution of the gamma-ray tracking array GRETINA to the hole charge-carrier mobility parameter is investigated. The χ 2 results from a fit of averaged signal (“superpulse”) data exhibit a shallow minimum for hole mobilities 15% lower than the currently adopted values. Calibration data on position resolution is analyzed, together with simulations that isolate the hole mobility dependence of signal decomposition from other effects such as electronics cross-talk. Our results effectively exclude hole mobility as a dominant parameter for improving the position resolution for reconstruction of gamma-ray interaction points in GRETINA.

Sensitivity of GRETINA position resolution to hole mobility

DOE PAGES

Prasher, V. S.; Cromaz, M.; Merchan, E.; ...

2017-02-01

The sensitivity of the position resolution of the gamma-ray tracking array GRETINA to the hole charge-carrier mobility parameter is investigated. The χ 2 results from a fit of averaged signal (“superpulse”) data exhibit a shallow minimum for hole mobilities 15% lower than the currently adopted values. Calibration data on position resolution is analyzed, together with simulations that isolate the hole mobility dependence of signal decomposition from other effects such as electronics cross-talk. Our results effectively exclude hole mobility as a dominant parameter for improving the position resolution for reconstruction of gamma-ray interaction points in GRETINA.

Thermal and volumetric properties of complex aqueous electrolyte solutions using the Pitzer formalism - The PhreeSCALE code

NASA Astrophysics Data System (ADS)

Lach, Adeline; Boulahya, Faïza; André, Laurent; Lassin, Arnault; Azaroual, Mohamed; Serin, Jean-Paul; Cézac, Pierre

2016-07-01

The thermal and volumetric properties of complex aqueous solutions are described according to the Pitzer equation, explicitly taking into account the speciation in the aqueous solutions. The thermal properties are the apparent relative molar enthalpy (Lϕ) and the apparent molar heat capacity (Cp,ϕ). The volumetric property is the apparent molar volume (Vϕ). Equations describing these properties are obtained from the temperature or pressure derivatives of the excess Gibbs energy and make it possible to calculate the dilution enthalpy (∆HD), the heat capacity (cp) and the density (ρ) of aqueous solutions up to high concentrations. Their implementation in PHREEQC V.3 (Parkhurst and Appelo, 2013) is described and has led to a new numerical tool, called PhreeSCALE. It was tested first, using a set of parameters (specific interaction parameters and standard properties) from the literature for two binary systems (Na2SO4-H2O and MgSO4-H2O), for the quaternary K-Na-Cl-SO4 system (heat capacity only) and for the Na-K-Ca-Mg-Cl-SO4-HCO3 system (density only). The results obtained with PhreeSCALE are in agreement with the literature data when the same standard solution heat capacity (Cp0) and volume (V0) values are used. For further applications of this improved computation tool, these standard solution properties were calculated independently, using the Helgeson-Kirkham-Flowers (HKF) equations. By using this kind of approach, most of the Pitzer interaction parameters coming from literature become obsolete since they are not coherent with the standard properties calculated according to the HKF formalism. Consequently a new set of interaction parameters must be determined. This approach was successfully applied to the Na2SO4-H2O and MgSO4-H2O binary systems, providing a new set of optimized interaction parameters, consistent with the standard solution properties derived from the HKF equations.

Dynamic effect of total solid content, low substrate/inoculum ratio and particle size on solid-state anaerobic digestion.

PubMed

Motte, J-C; Escudié, R; Bernet, N; Delgenes, J-P; Steyer, J-P; Dumas, C

2013-09-01

Among all the process parameters of solid-state anaerobic digestion (SS-AD), total solid content (TS), inoculation (S/X ratio) and size of the organic solid particles can be optimized to improve methane yield and process stability. To evaluate the effects of each parameter and their interactions on methane production, a three level Box-Behnken experimental design was implemented in SS-AD batch tests degrading wheat straw by adjusting: TS content from 15% to 25%, S/X ratio (in volatile solids) between 28 and 47 and particle size with a mean diameter ranging from 0.1 to 1.4mm. A dynamic analysis of the methane production indicates that the S/X ratio has only an effect during the start-up phase of the SS-AD. During the growing phase, TS content becomes the main parameter governing the methane production and its strong interaction with the particle size suggests the important role of water compartmentation on SS-AD. Copyright © 2013 Elsevier Ltd. All rights reserved.

Interactive Reliability Model for Whisker-toughened Ceramics

NASA Technical Reports Server (NTRS)

Palko, Joseph L.

1993-01-01

Wider use of ceramic matrix composites (CMC) will require the development of advanced structural analysis technologies. The use of an interactive model to predict the time-independent reliability of a component subjected to multiaxial loads is discussed. The deterministic, three-parameter Willam-Warnke failure criterion serves as the theoretical basis for the reliability model. The strength parameters defining the model are assumed to be random variables, thereby transforming the deterministic failure criterion into a probabilistic criterion. The ability of the model to account for multiaxial stress states with the same unified theory is an improvement over existing models. The new model was coupled with a public-domain finite element program through an integrated design program. This allows a design engineer to predict the probability of failure of a component. A simple structural problem is analyzed using the new model, and the results are compared to existing models.

Optimisation of process parameters on thin shell part using response surface methodology (RSM)

NASA Astrophysics Data System (ADS)

Faiz, J. M.; Shayfull, Z.; Nasir, S. M.; Fathullah, M.; Rashidi, M. M.

2017-09-01

This study is carried out to focus on optimisation of process parameters by simulation using Autodesk Moldflow Insight (AMI) software. The process parameters are taken as the input in order to analyse the warpage value which is the output in this study. There are some significant parameters that have been used which are melt temperature, mould temperature, packing pressure, and cooling time. A plastic part made of Polypropylene (PP) has been selected as the study part. Optimisation of process parameters is applied in Design Expert software with the aim to minimise the obtained warpage value. Response Surface Methodology (RSM) has been applied in this study together with Analysis of Variance (ANOVA) in order to investigate the interactions between parameters that are significant to the warpage value. Thus, the optimised warpage value can be obtained using the model designed using RSM due to its minimum error value. This study comes out with the warpage value improved by using RSM.

Enhanced squeezing of a collective spin via control of its qudit subsystems.

PubMed

Norris, Leigh M; Trail, Collin M; Jessen, Poul S; Deutsch, Ivan H

2012-10-26

Unitary control of qudits can improve the collective spin squeezing of an atomic ensemble. Preparing the atoms in a state with large quantum fluctuations in magnetization strengthens the entangling Faraday interaction. The resulting increase in interatomic entanglement can be converted into metrologically useful spin squeezing. Further control can squeeze the internal atomic spin without compromising entanglement, providing an overall multiplicative factor in the collective squeezing. We model the effects of optical pumping and study the tradeoffs between enhanced entanglement and decoherence. For realistic parameters we see improvements of ~10 dB.

A New Framework for Adptive Sampling and Analysis During Long-Term Monitoring and Remedial Action Management

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

Minsker, Barbara

2005-06-01

Yonas Demissie, a research assistant supported by the project, has successfully created artificial data and assimilated it into coupled Modflow and artificial neural network models. His initial findings show that the neural networks help correct errors in the Modflow models. Abhishek Singh has used test cases from the literature to show that performing model calibration with an interactive genetic algorithm results in significantly improved parameter values. Meghna Babbar, the third research assistant supported by the project, has found similar results when applying an interactive genetic algorithms to long-term monitoring design. She has also developed new types of interactive genetic algorithmsmore » that significantly improve performance. Gayathri Gopalakrishnan, the last research assistant who is partially supported by the project, has shown that sampling branches of phytoremediation trees is an accurate approach to estimating soil and groundwater contaminations in areas surrounding the trees at the Argonne 317/319 site.« less

Stepwise Adaptations to Low Temperature as Revealed by Multiple Mutants of Psychrophilic α-Amylase from Antarctic Bacterium*

PubMed Central

Cipolla, Alexandre; D'Amico, Salvino; Barumandzadeh, Roya; Matagne, André; Feller, Georges

2011-01-01

The mutants Mut5 and Mut5CC from a psychrophilic α-amylase bear representative stabilizing interactions found in the heat-stable porcine pancreatic α-amylase but lacking in the cold-active enzyme from an Antarctic bacterium. From an evolutionary perspective, these mutants can be regarded as structural intermediates between the psychrophilic and the mesophilic enzymes. We found that these engineered interactions improve all the investigated parameters related to protein stability as follows: compactness; kinetically driven stability; thermodynamic stability; resistance toward chemical denaturation, and the kinetics of unfolding/refolding. Concomitantly to this improved stability, both mutants have lost the kinetic optimization to low temperature activity displayed by the parent psychrophilic enzyme. These results provide strong experimental support to the hypothesis assuming that the disappearance of stabilizing interactions in psychrophilic enzymes increases the amplitude of concerted motions required by catalysis and the dynamics of active site residues at low temperature, leading to a higher activity. PMID:21900238

Enhanced effect of temporal variation of the fine structure constant and the strong interaction in 229Th.

PubMed

Flambaum, V V

2006-09-01

The relative effects of the variation of the fine structure constant alpha = e2/variant Planck's over 2pi c and the dimensionless strong interaction parameter m(q)/LambdaQCD are enhanced by 5-6 orders of magnitude in a very narrow ultraviolet transition between the ground and the first excited states in the 229Th nucleus. It may be possible to investigate this transition with laser spectroscopy. Such an experiment would have the potential of improving the sensitivity to temporal variation of the fundamental constants by many orders of magnitude.

How CMB and large-scale structure constrain chameleon interacting dark energy

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

Boriero, Daniel; Das, Subinoy; Wong, Yvonne Y.Y., E-mail: boriero@physik.uni-bielefeld.de, E-mail: subinoy@iiap.res.in, E-mail: yvonne.y.wong@unsw.edu.au

2015-07-01

We explore a chameleon type of interacting dark matter-dark energy scenario in which a scalar field adiabatically traces the minimum of an effective potential sourced by the dark matter density. We discuss extensively the effect of this coupling on cosmological observables, especially the parameter degeneracies expected to arise between the model parameters and other cosmological parameters, and then test the model against observations of the cosmic microwave background (CMB) anisotropies and other cosmological probes. We find that the chameleon parameters α and β, which determine respectively the slope of the scalar field potential and the dark matter-dark energy coupling strength,more » can be constrained to α < 0.17 and β < 0.19 using CMB data and measurements of baryon acoustic oscillations. The latter parameter in particular is constrained only by the late Integrated Sachs-Wolfe effect. Adding measurements of the local Hubble expansion rate H{sub 0} tightens the bound on α by a factor of two, although this apparent improvement is arguably an artefact of the tension between the local measurement and the H{sub 0} value inferred from Planck data in the minimal ΛCDM model. The same argument also precludes chameleon models from mimicking a dark radiation component, despite a passing similarity between the two scenarios in that they both delay the epoch of matter-radiation equality. Based on the derived parameter constraints, we discuss possible signatures of the model for ongoing and future large-scale structure surveys.« less

Disturbance of DNA conformation by the binding of testosterone-based platinum drugs via groove-face and intercalative interactions: a molecular dynamics simulation study

PubMed Central

2013-01-01

Background To explore novel platinum-based anticancer agents that are distinct from the structure and interaction mode of the traditional cisplatin by forming the bifunctional intrastrand 1,2 GpG adduct, the monofunctional platinum + DNA adducts with extensive non-covalent interactions had been studied. It was reported that the monofunctional testosterone-based platinum(II) agents present the high anticancer activity. Moreover, it was also found that the testosterone-based platinum agents could cause the DNA helix to undergo significant unwinding and bending over the non-testosterone-based platinum agents. However, the interaction mechanisms of these platinum agents with DNA at the atomic level are not yet clear so far. Results In the present work, we used molecular dynamics (MD) simulations and DNA conformational dynamics calculations to study the DNA distortion properties of the testosterone-based platinum + DNA, the improved testosterone-based platinum + DNA and the non-testosterone-based platinum + DNA adducts. The results show that the intercalative interaction of the improved flexible testosterone-based platinum agent with DNA molecule could cause larger DNA conformational distortion than the groove-face interaction of the rigid testosterone-based platinum agent with DNA molecule. Further investigations for the non-testosterone-based platinum agent reveal the occurrence of insignificant change of DNA conformation due to the absence of testosterone ligand in such agent. Based on the DNA dynamics analysis, the DNA base motions relating to DNA groove parameter changes and hydrogen bond destruction of DNA base pairs were also discussed in this work. Conclusions The flexible linker in the improved testosterone-based platinum agent causes an intercalative interaction with DNA in the improved testosterone-based platinum + DNA adduct, which is different from the groove-face interaction caused by a rigid linker in the testosterone-based platinum agent. The present investigations provide useful information of DNA conformation affected by a testosterone-based platinum complex at the atomic level. PMID:23517640

Effects of Ignoring Item Interaction on Item Parameter Estimation and Detection of Interacting Items

ERIC Educational Resources Information Center

Chen, Cheng-Te; Wang, Wen-Chung

2007-01-01

This study explores the effects of ignoring item interaction on item parameter estimation and the efficiency of using the local dependence index Q[subscript 3] and the SAS NLMIXED procedure to detect item interaction under the three-parameter logistic model and the generalized partial credit model. Through simulations, it was found that ignoring…

Effects of two successive parity-invariant point interactions on one-dimensional quantum transmission: Resonance conditions for the parameter space

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

Konno, Kohkichi, E-mail: kohkichi@tomakomai-ct.ac.jp; Nagasawa, Tomoaki, E-mail: nagasawa@tomakomai-ct.ac.jp; Takahashi, Rohta, E-mail: takahashi@tomakomai-ct.ac.jp

We consider the scattering of a quantum particle by two independent, successive parity-invariant point interactions in one dimension. The parameter space for the two point interactions is given by the direct product of two tori, which is described by four parameters. By investigating the effects of the two point interactions on the transmission probability of plane wave, we obtain the conditions for the parameter space under which perfect resonant transmission occur. The resonance conditions are found to be described by symmetric and anti-symmetric relations between the parameters.

Interactions of galaxies outside clusters and massive groups

NASA Astrophysics Data System (ADS)

Yadav, Jaswant K.; Chen, Xuelei

2018-06-01

We investigate the dependence of physical properties of galaxies on small- and large-scale density environment. The galaxy population consists of mainly passively evolving galaxies in comparatively low-density regions of Sloan Digital Sky Survey (SDSS). We adopt (i) local density, ρ _{20}, derived using adaptive smoothing kernel, (ii) projected distance, r_p, to the nearest neighbor galaxy and (iii) the morphology of the nearest neighbor galaxy as various definitions of environment parameters of every galaxy in our sample. In order to detect long-range interaction effects, we group galaxy interactions into four cases depending on morphology of the target and neighbor galaxies. This study builds upon an earlier study by Park and Choi (2009) by including improved definitions of target and neighbor galaxies, thus enabling us to better understand the effect of "the nearest neighbor" interaction on the galaxy. We report that the impact of interaction on galaxy properties is detectable at least up to the pair separation corresponding to the virial radius of (the neighbor) galaxies. This turns out to be mostly between 210 and 360 h^{-1}kpc for galaxies included in our study. We report that early type fraction for isolated galaxies with r_p > r_{vir,nei} is almost ignorant of the background density and has a very weak density dependence for closed pairs. Star formation activity of a galaxy is found to be crucially dependent on neighbor galaxy morphology. We find star formation activity parameters and structure parameters of galaxies to be independent of the large-scale background density. We also exhibit that changing the absolute magnitude of the neighbor galaxies does not affect significantly the star formation activity of those target galaxies whose morphology and luminosities are fixed.

An Interactive Astronaut-Robot System with Gesture Control

PubMed Central

Liu, Jinguo; Luo, Yifan; Ju, Zhaojie

2016-01-01

Human-robot interaction (HRI) plays an important role in future planetary exploration mission, where astronauts with extravehicular activities (EVA) have to communicate with robot assistants by speech-type or gesture-type user interfaces embedded in their space suits. This paper presents an interactive astronaut-robot system integrating a data-glove with a space suit for the astronaut to use hand gestures to control a snake-like robot. Support vector machine (SVM) is employed to recognize hand gestures and particle swarm optimization (PSO) algorithm is used to optimize the parameters of SVM to further improve its recognition accuracy. Various hand gestures from American Sign Language (ASL) have been selected and used to test and validate the performance of the proposed system. PMID:27190503

Interactive videogame as rehabilitation tool of patients with chronic respiratory diseases: preliminary results of a feasibility study.

PubMed

Mazzoleni, Stefano; Montagnani, Giulia; Vagheggini, Guido; Buono, Lorenzo; Moretti, Francesca; Dario, Paolo; Ambrosino, Nicolino

2014-10-01

To evaluate the effectiveness of an interactive videogame (IV) system in addition to a supervised pulmonary rehabilitation programme (PRP) in patients with chronic respiratory diseases. Randomised Controlled Trial comparing standard PRP (20 patients, control group: CG), and PRP + sessions of interactive videogame-aided exercises (20 patients, experimental group: EG). Lung and respiratory muscle function, arterial blood gases, exercise capacity, dyspnoea, health status and health-related quality of life (HRQL) and emotional response were measured before and after PRP. A questionnaire on acceptability of the PRP was administered. Exercise capacity, dyspnoea and HRQL significantly improved in both groups after the PRP, whereas the EG showed a greater improvement in six-minute walk test and transitional dyspnoea index than the CG. No difference in psychological status or acceptability of PRP was observed between the two groups. The addition of IV training was more effective for improving some parameters of exercise tolerance and dyspnoea, although did not result in better psychological status nor it was better accepted than the standard PRP in patients with chronic respiratory diseases. Copyright © 2014 Elsevier Ltd. All rights reserved.

Water interactions with hydrophobic groups: Assessment and recalibration of semiempirical molecular orbital methods

NASA Astrophysics Data System (ADS)

Marion, Antoine; Monard, Gérald; Ruiz-López, Manuel F.; Ingrosso, Francesca

2014-07-01

In this work, we present a study of the ability of different semiempirical methods to describe intermolecular interactions in water solution. In particular, we focus on methods based on the Neglect of Diatomic Differential Overlap approximation. Significant improvements of these methods have been reported in the literature in the past years regarding the description of non-covalent interactions. In particular, a broad range of methodologies has been developed to deal with the properties of hydrogen-bonded systems, with varying degrees of success. In contrast, the interactions between water and a molecule containing hydrophobic groups have been little analyzed. Indeed, by considering the potential energy surfaces obtained using different semiempirical Hamiltonians for the intermolecular interactions of model systems, we found that none of the available methods provides an entirely satisfactory description of both hydrophobic and hydrophilic interactions in water. In addition, a vibrational analysis carried out in a model system for these interactions, a methane clathrate cluster, showed that some recent methods cannot be used to carry out studies of vibrational properties. Following a procedure established in our group [M. I. Bernal-Uruchurtu, M. T. C. Martins-Costa, C. Millot, and M. F. Ruiz-López, J. Comput. Chem. 21, 572 (2000); W. Harb, M. I. Bernal-Uruchurtu, and M. F. Ruiz-López, Theor. Chem. Acc. 112, 204 (2004)], we developed new parameters for the core-core interaction terms based on fitting potential energy curves obtained at the MP2 level for our model system. We investigated the transferability of the new parameters to describe a system, having both hydrophilic and hydrophobic groups, interacting with water. We found that only by introducing two different sets of parameters for hydrophilic and hydrophobic hydrogen atom types we are able to match the features of the ab initio calculated properties. Once this assumption is made, a good agreement with the MP2 reference is achieved. The results reported in this work provide therefore a direction for future developments of semiempirical approaches that are still required to investigate chemical processes in biomolecules and in large disordered systems.

Psychosocial and Psychophysiological Effects of Human-Animal Interactions: The Possible Role of Oxytocin

PubMed Central

Beetz, Andrea; Uvnäs-Moberg, Kerstin; Julius, Henri; Kotrschal, Kurt

2012-01-01

During the last decade it has become more widely accepted that pet ownership and animal assistance in therapy and education may have a multitude of positive effects on humans. Here, we review the evidence from 69 original studies on human-animal interactions (HAI) which met our inclusion criteria with regard to sample size, peer-review, and standard scientific research design. Among the well-documented effects of HAI in humans of different ages, with and without special medical, or mental health conditions are benefits for: social attention, social behavior, interpersonal interactions, and mood; stress-related parameters such as cortisol, heart rate, and blood pressure; self-reported fear and anxiety; and mental and physical health, especially cardiovascular diseases. Limited evidence exists for positive effects of HAI on: reduction of stress-related parameters such as epinephrine and norepinephrine; improvement of immune system functioning and pain management; increased trustworthiness of and trust toward other persons; reduced aggression; enhanced empathy and improved learning. We propose that the activation of the oxytocin system plays a key role in the majority of these reported psychological and psychophysiological effects of HAI. Oxytocin and HAI effects largely overlap, as documented by research in both, humans and animals, and first studies found that HAI affects the oxytocin system. As a common underlying mechanism, the activation of the oxytocin system does not only provide an explanation, but also allows an integrative view of the different effects of HAI. PMID:22866043

Reduction of Helicopter Blade-Vortex Interaction Noise by Active Rotor Control Technology

NASA Technical Reports Server (NTRS)

Yu, Yung H.; Gmelin, Bernd; Splettstoesser, Wolf; Brooks, Thomas F.; Philippe, Jean J.; Prieur, Jean

1997-01-01

Helicopter blade-vortex interaction noise is one of the most severe noise sources and is very important both in community annoyance and military detection. Research over the decades has substantially improved basic physical understanding of the mechanisms generating rotor blade-vortex interaction noise and also of controlling techniques, particularly using active rotor control technology. This paper reviews active rotor control techniques currently available for rotor blade vortex interaction noise reduction, including higher harmonic pitch control, individual blade control, and on-blade control technologies. Basic physical mechanisms of each active control technique are reviewed in terms of noise reduction mechanism and controlling aerodynamic or structural parameters of a blade. Active rotor control techniques using smart structures/materials are discussed, including distributed smart actuators to induce local torsional or flapping deformations, Published by Elsevier Science Ltd.

Influence of the Interaction Between Graphite and Polar Surfaces of ZnO on the Formation of Schottky Contact

NASA Astrophysics Data System (ADS)

Yatskiv, R.; Grym, J.

2018-03-01

We show that the interaction between graphite and polar surfaces of ZnO affects electrical properties of graphite/ZnO Schottky junctions. A strong interaction of the Zn-face with the graphite contact causes interface imperfections and results in the formation of laterally inhomogeneous Schottky contacts. On the contrary, high quality Schottky junctions form on the O-face, where the interaction is significantly weaker. Charge transport through the O-face ZnO/graphite junctions is well described by the thermionic emission model in both forward and reverse directions. We further demonstrate that the parameters of the graphite/ZnO Schottky diodes can be significantly improved when a thin layer of ZnO2 forms at the interface between graphite and ZnO after hydrogen peroxide surface treatment.

An Improved Method to Control the Critical Parameters of a Multivariable Control System

NASA Astrophysics Data System (ADS)

Subha Hency Jims, P.; Dharmalingam, S.; Wessley, G. Jims John

2017-10-01

The role of control systems is to cope with the process deficiencies and the undesirable effect of the external disturbances. Most of the multivariable processes are highly iterative and complex in nature. Aircraft systems, Modern Power Plants, Refineries, Robotic systems are few such complex systems that involve numerous critical parameters that need to be monitored and controlled. Control of these important parameters is not only tedious and cumbersome but also is crucial from environmental, safety and quality perspective. In this paper, one such multivariable system, namely, a utility boiler has been considered. A modern power plant is a complex arrangement of pipework and machineries with numerous interacting control loops and support systems. In this paper, the calculation of controller parameters based on classical tuning concepts has been presented. The controller parameters thus obtained and employed has controlled the critical parameters of a boiler during fuel switching disturbances. The proposed method can be applied to control the critical parameters like elevator, aileron, rudder, elevator trim rudder and aileron trim, flap control systems of aircraft systems.

Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical Effects on Surface Tension and Lipid Properties.

PubMed

Wennberg, Christian L; Murtola, Teemu; Hess, Berk; Lindahl, Erik

2013-08-13

The accuracy of electrostatic interactions in molecular dynamics advanced tremendously with the introduction of particle-mesh Ewald (PME) summation almost 20 years ago. Lattice summation electrostatics is now the de facto standard for most types of biomolecular simulations, and in particular, for lipid bilayers, it has been a critical improvement due to the large charges typically present in zwitterionic lipid headgroups. In contrast, Lennard-Jones interactions have continued to be handled with increasingly longer cutoffs, partly because few alternatives have been available despite significant difficulties in tuning cutoffs and parameters to reproduce lipid properties. Here, we present a new Lennard-Jones PME implementation applied to lipid bilayers. We confirm that long-range contributions are well approximated by dispersion corrections in simple systems such as pentadecane (which makes parameters transferable), but for inhomogeneous and anisotropic systems such as lipid bilayers there are large effects on surface tension, resulting in up to 5.5% deviations in area per lipid and order parameters-far larger than many differences for which reparameterization has been attempted. We further propose an approximation for combination rules in reciprocal space that significantly reduces the computational cost of Lennard-Jones PME and makes accurate treatment of all nonbonded interactions competitive with simulations employing long cutoffs. These results could potentially have broad impact on important applications such as membrane proteins and free energy calculations.

Interactions between drugs and polymers influencing hot melt extrusion.

PubMed

Li, Yongcheng; Pang, Huishi; Guo, Zhefei; Lin, Ling; Dong, Yixuan; Li, Ge; Lu, Ming; Wu, Chuangbin

2014-02-01

Hot melt extrusion (HME) as a technique for producing amorphous solid dispersion (ASD) has been widely used in pharmaceutical research. The biggest challenge for the application of HME is the thermal degradation of drug, poor physical stability of ASD and precipitation of drug during dissolution. Interactions between drugs and polymers may play an important role in overcoming these barriers. In this review, influence of drug-polymer interactions on HME and the methods for characterizing the drug-polymer interactions were reviewed. Strong drug-polymer interactions, especially ionic interactions and hydrogen bonds, are helpful to improving the thermal stability of drug during HME, enhancing the physical stability of ASD during storage and maintaining supersaturated solution after dissolution in gastrointestinal tract. The interactions can be quantitatively and qualitatively characterized by many analysing methods. As many factors collectively determine the properties of HME products, drug-polymer interactions play an extremely important role. However, the action mechanisms of drug-polymer interactions need intensive investigation to provide more useful information for optimizing the formulation and the process parameters of HME. © 2013 Royal Pharmaceutical Society.

Verbal collision avoidance messages during simulated driving: perceived urgency, alerting effectiveness and annoyance.

PubMed

Baldwin, Carryl L

2011-04-01

Matching the perceived urgency of an alert with the relative hazard level of the situation is critical for effective alarm response. Two experiments describe the impact of acoustic and semantic parameters on ratings of perceived urgency, annoyance and alerting effectiveness and on alarm response speed. Within a simulated driving context, participants rated and responded to collision avoidance system (CAS) messages spoken by a female or male voice (experiments 1 and 2, respectively). Results indicated greater perceived urgency and faster alarm response times as intensity increased from -2 dB signal to noise (S/N) ratio to +10 dB S/N, although annoyance ratings increased as well. CAS semantic content interacted with alarm intensity, indicating that at lower intensity levels participants paid more attention to the semantic content. Results indicate that both acoustic and semantic parameters independently and interactively impact CAS alert perceptions in divided attention conditions and this work can inform auditory alarm design for effective hazard matching. Matching the perceived urgency of an alert with the relative hazard level of the situation is critical for effective alarm response. Here, both acoustic and semantic parameters independently and interactively impacted CAS alert perceptions in divided attention conditions. This work can inform auditory alarm design for effective hazard matching. STATEMENT OF RELEVANCE: Results indicate that both acoustic parameters and semantic content can be used to design collision warnings with a range of urgency levels. Further, these results indicate that verbal warnings tailored to a specific hazard situation may improve hazard-matching capabilities without substantial trade-offs in perceived annoyance.

Thermodynamics of antibody-antigen interaction revealed by mutation analysis of antibody variable regions.

PubMed

Akiba, Hiroki; Tsumoto, Kouhei

2015-07-01

Antibodies (immunoglobulins) bind specific molecules (i.e. antigens) with high affinity and specificity. In order to understand their mechanisms of recognition, interaction analysis based on thermodynamic and kinetic parameters, as well as structure determination is crucial. In this review, we focus on mutational analysis which gives information about the role of each amino acid residue in antibody-antigen interaction. Taking anti-hen egg lysozyme antibodies and several anti-small molecule antibodies, the energetic contribution of hot-spot and non-hot-spot residues is discussed in terms of thermodynamics. Here, thermodynamics of the contribution from aromatic, charged and hydrogen bond-forming amino acids are discussed, and their different characteristics have been elucidated. The information gives fundamental understanding of the antibody-antigen interaction. Furthermore, the consequences of antibody engineering are analysed from thermodynamic viewpoints: humanization to reduce immunogenicity and rational design to improve affinity. Amino acid residues outside hot-spots in the interface play important roles in these cases, and thus thermodynamic and kinetic parameters give much information about the antigen recognition. Thermodynamic analysis of mutant antibodies thus should lead to advanced strategies to design and select antibodies with high affinity. © The Authors 2015. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

Three-dimensional FEM model of FBGs in PANDA fibers with experimentally determined model parameters

NASA Astrophysics Data System (ADS)

Lindner, Markus; Hopf, Barbara; Koch, Alexander W.; Roths, Johannes

2017-04-01

A 3D-FEM model has been developed to improve the understanding of multi-parameter sensing with Bragg gratings in attached or embedded polarization maintaining fibers. The material properties of the fiber, especially Young's modulus and Poisson's ratio of the fiber's stress applying parts, are crucial for accurate simulations, but are usually not provided by the manufacturers. A methodology is presented to determine the unknown parameters by using experimental characterizations of the fiber and iterative FEM simulations. The resulting 3D-Model is capable of describing the change in birefringence of the free fiber when exposed to longitudinal strain. In future studies the 3D-FEM model will be employed to study the interaction of PANDA fibers with the surrounding materials in which they are embedded.

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

Da Rio, Nicola; Robberto, Massimo, E-mail: ndario@rssd.esa.int

We present the Tool for Astrophysical Data Analysis (TA-DA), a new software aimed to greatly simplify and improve the analysis of stellar photometric data in comparison with theoretical models, and allow the derivation of stellar parameters from multi-band photometry. Its flexibility allows one to address a number of such problems: from the interpolation of stellar models, or sets of stellar physical parameters in general, to the computation of synthetic photometry in arbitrary filters or units; from the analysis of observed color-magnitude diagrams to a Bayesian derivation of stellar parameters (and extinction) based on multi-band data. TA-DA is available as amore » pre-compiled Interactive Data Language widget-based application; its graphical user interface makes it considerably user-friendly. In this paper, we describe the software and its functionalities.« less

Transitions of interaction outcomes in a uni-directional consumer-resource system

USGS Publications Warehouse

Wang, Y.; DeAngelis, D.L.

2011-01-01

A uni-directional consumer-resource system of two species is analyzed. Our aim is to understand the mechanisms that determine how the interaction outcomes depend on the context of the interaction; that is, on the model parameters. The dynamic behavior of the model is described and, in particular, it is demonstrated that no periodic orbits exist. Then the parameter (factor) space is shown to be divided into four regions, which correspond to the four forms of interaction outcomes; i.e. mutualism, commensalism, parasitism and amensalism. It is shown that the interaction outcomes of the system transition smoothly among these four forms when the parameters of the system are varied continuously. Varying each parameter individually or varying pairs of parameters can also lead to smooth transitions between the interaction outcomes. The analysis leads to both conditions for which each species achieves its maximal density, and situations in which periodic oscillations of the interaction outcomes emerge. ?? 2011 Elsevier Ltd.

Quantitative evaluation of water quality in the coastal zone by remote sensing

NASA Technical Reports Server (NTRS)

James, W. P.

1971-01-01

Remote sensing as a tool in a waste management program is discussed. By monitoring both the pollution sources and the environmental quality, the interaction between the components of the exturaine system was observed. The need for in situ sampling is reduced with the development of improved calibrated, multichannel sensors. Remote sensing is used for: (1) pollution source determination, (2) mapping the influence zone of the waste source on water quality parameters, and (3) estimating the magnitude of the water quality parameters. Diffusion coefficients and circulation patterns can also be determined by remote sensing, along with subtle changes in vegetative patterns and density.

An improved wave rotor refrigerator using an outside gas flow for recycling the expansion work

NASA Astrophysics Data System (ADS)

Zhao, J.; Hu, D.

2017-03-01

To overcome the bottleneck of traditional gas wave refrigeration, an improved wave rotor refrigerator (WRR) cycle has been proposed, in which the expansion work was recycled during the process of refrigeration. Thermodynamic analysis of the two cycles shows that the refrigeration efficiency of the improved WRR cycle has been greatly increased compared with the traditional WRR. The performance of an improved WRR was investigated by adjusting the major operational parameters, such as the rotational speed of the wave rotor, port size, and inflow overpressure. The experimental results show that pressure loss can be reduced by nearly 40 % in this improved refrigeration system. Meanwhile, a two-dimensional numerical simulation was performed to understand the wave interactions that take place inside the rotor channels.

Materials cohesion and interaction forces.

PubMed

Rosenholm, Jarl B; Peiponen, Kai-Erik; Gornov, Evgeny

2008-09-01

The most important methods to determine the cohesive interactions of materials and adhesive interactions between different substances are reviewed. The term cohesion is generalized as representing the unifying interaction forces of a single material and adhesion forces between different substances due to attraction. The aim is to interlink a number of frequently used interaction parameters in order to promote the understanding of materials research executed within different scientific (Material, Colloid, Sol-Gel and Nano) communities. The modern interdisciplinary research requires a removal of the historical obstacles represented by widely differing nomenclature used for the same material properties. The interaction parameters of different models are reviewed and representative numerical values computed from tabulated thermodynamic and spectroscopic material constants. The results are compared with published values. The models are grouped to represent single and two component systems, respectively. The latter group includes models for films on substrates and work of adhesion between liquids and solids. In most cases rather rough approximations have been employed, mostly relating to van der Waals substances for which the gas state is common reference state. In order to improve the predictability of the key Hamaker constant, a novel model for interpreting the dielectric spectrum is presented. The interrelation between thermodynamic, electronic, spectroscopic and dielectric parameters is illustrated by model calculations on typical inorganic materials of current interest as model compounds. The ionic solids are represented by NaCl and KCl, while ZnO, FeO, Fe(2)O(3), Fe(3)O(4), Al(2)O(3), SiO(2), TiO(2), ZrO(2), SnO, SnO(2) represent ceramic oxides and semiconductors. The model compounds thus illustrate the effect of bond type (covalent or ionic) and valence (charge number and sign) of the constituent elements. However, since the focus is placed on a phenomenological analysis, the number of examples remains self-evidently incomplete.

Protein tyrosine phosphatases: Ligand interaction analysis and optimisation of virtual screening.

PubMed

Ghattas, Mohammad A; Atatreh, Noor; Bichenkova, Elena V; Bryce, Richard A

2014-07-01

Docking-based virtual screening is an established component of structure-based drug discovery. Nevertheless, scoring and ranking of computationally docked ligand libraries still suffer from many false positives. Identifying optimal docking parameters for a target protein prior to virtual screening can improve experimental hit rates. Here, we examine protocols for virtual screening against the important but challenging class of drug target, protein tyrosine phosphatases. In this study, common interaction features were identified from analysis of protein-ligand binding geometries of more than 50 complexed phosphatase crystal structures. It was found that two interactions were consistently formed across all phosphatase inhibitors: (1) a polar contact with the conserved arginine residue, and (2) at least one interaction with the P-loop backbone amide. In order to investigate the significance of these features on phosphatase-ligand binding, a series of seeded virtual screening experiments were conducted on three phosphatase enzymes, PTP1B, Cdc25b and IF2. It was observed that when the conserved arginine and P-loop amide interactions were used as pharmacophoric constraints during docking, enrichment of the virtual screen significantly increased in the three studied phosphatases, by up to a factor of two in some cases. Additionally, the use of such pharmacophoric constraints considerably improved the ability of docking to predict the inhibitor's bound pose, decreasing RMSD to the crystallographic geometry by 43% on average. Constrained docking improved enrichment of screens against both open and closed conformations of PTP1B. Incorporation of an ordered water molecule in PTP1B screening was also found to generally improve enrichment. The knowledge-based computational strategies explored here can potentially inform structure-based design of new phosphatase inhibitors using docking-based virtual screening. Copyright © 2014 Elsevier Inc. All rights reserved.

Accurate calculation and modeling of the adiabatic connection in density functional theory

NASA Astrophysics Data System (ADS)

Teale, A. M.; Coriani, S.; Helgaker, T.

2010-04-01

Using a recently implemented technique for the calculation of the adiabatic connection (AC) of density functional theory (DFT) based on Lieb maximization with respect to the external potential, the AC is studied for atoms and molecules containing up to ten electrons: the helium isoelectronic series, the hydrogen molecule, the beryllium isoelectronic series, the neon atom, and the water molecule. The calculation of AC curves by Lieb maximization at various levels of electronic-structure theory is discussed. For each system, the AC curve is calculated using Hartree-Fock (HF) theory, second-order Møller-Plesset (MP2) theory, coupled-cluster singles-and-doubles (CCSD) theory, and coupled-cluster singles-doubles-perturbative-triples [CCSD(T)] theory, expanding the molecular orbitals and the effective external potential in large Gaussian basis sets. The HF AC curve includes a small correlation-energy contribution in the context of DFT, arising from orbital relaxation as the electron-electron interaction is switched on under the constraint that the wave function is always a single determinant. The MP2 and CCSD AC curves recover the bulk of the dynamical correlation energy and their shapes can be understood in terms of a simple energy model constructed from a consideration of the doubles-energy expression at different interaction strengths. Differentiation of this energy expression with respect to the interaction strength leads to a simple two-parameter doubles model (AC-D) for the AC integrand (and hence the correlation energy of DFT) as a function of the interaction strength. The structure of the triples-energy contribution is considered in a similar fashion, leading to a quadratic model for the triples correction to the AC curve (AC-T). From a consideration of the structure of a two-level configuration-interaction (CI) energy expression of the hydrogen molecule, a simple two-parameter CI model (AC-CI) is proposed to account for the effects of static correlation on the AC. When parametrized in terms of the same input data, the AC-CI model offers improved performance over the corresponding AC-D model, which is shown to be the lowest-order contribution to the AC-CI model. The utility of the accurately calculated AC curves for the analysis of standard density functionals is demonstrated for the BLYP exchange-correlation functional and the interaction-strength-interpolation (ISI) model AC integrand. From the results of this analysis, we investigate the performance of our proposed two-parameter AC-D and AC-CI models when a simple density functional for the AC at infinite interaction strength is employed in place of information at the fully interacting point. The resulting two-parameter correlation functionals offer a qualitatively correct behavior of the AC integrand with much improved accuracy over previous attempts. The AC integrands in the present work are recommended as a basis for further work, generating functionals that avoid spurious error cancellations between exchange and correlation energies and give good accuracy for the range of densities and types of correlation contained in the systems studied here.

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

Marion, Antoine; Monard, Gérald; Ruiz-López, Manuel F., E-mail: Manuel.Ruiz@univ-lorraine.fr

In this work, we present a study of the ability of different semiempirical methods to describe intermolecular interactions in water solution. In particular, we focus on methods based on the Neglect of Diatomic Differential Overlap approximation. Significant improvements of these methods have been reported in the literature in the past years regarding the description of non-covalent interactions. In particular, a broad range of methodologies has been developed to deal with the properties of hydrogen-bonded systems, with varying degrees of success. In contrast, the interactions between water and a molecule containing hydrophobic groups have been little analyzed. Indeed, by considering themore » potential energy surfaces obtained using different semiempirical Hamiltonians for the intermolecular interactions of model systems, we found that none of the available methods provides an entirely satisfactory description of both hydrophobic and hydrophilic interactions in water. In addition, a vibrational analysis carried out in a model system for these interactions, a methane clathrate cluster, showed that some recent methods cannot be used to carry out studies of vibrational properties. Following a procedure established in our group [M. I. Bernal-Uruchurtu, M. T. C. Martins-Costa, C. Millot, and M. F. Ruiz-López, J. Comput. Chem. 21, 572 (2000); W. Harb, M. I. Bernal-Uruchurtu, and M. F. Ruiz-López, Theor. Chem. Acc. 112, 204 (2004)], we developed new parameters for the core-core interaction terms based on fitting potential energy curves obtained at the MP2 level for our model system. We investigated the transferability of the new parameters to describe a system, having both hydrophilic and hydrophobic groups, interacting with water. We found that only by introducing two different sets of parameters for hydrophilic and hydrophobic hydrogen atom types we are able to match the features of the ab initio calculated properties. Once this assumption is made, a good agreement with the MP2 reference is achieved. The results reported in this work provide therefore a direction for future developments of semiempirical approaches that are still required to investigate chemical processes in biomolecules and in large disordered systems.« less

Identifying mechanical property parameters of planetary soil using in-situ data obtained from exploration rovers

NASA Astrophysics Data System (ADS)

Ding, Liang; Gao, Haibo; Liu, Zhen; Deng, Zongquan; Liu, Guangjun

2015-12-01

Identifying the mechanical property parameters of planetary soil based on terramechanics models using in-situ data obtained from autonomous planetary exploration rovers is both an important scientific goal and essential for control strategy optimization and high-fidelity simulations of rovers. However, identifying all the terrain parameters is a challenging task because of the nonlinear and coupling nature of the involved functions. Three parameter identification methods are presented in this paper to serve different purposes based on an improved terramechanics model that takes into account the effects of slip, wheel lugs, etc. Parameter sensitivity and coupling of the equations are analyzed, and the parameters are grouped according to their sensitivity to the normal force, resistance moment and drawbar pull. An iterative identification method using the original integral model is developed first. In order to realize real-time identification, the model is then simplified by linearizing the normal and shearing stresses to derive decoupled closed-form analytical equations. Each equation contains one or two groups of soil parameters, making step-by-step identification of all the unknowns feasible. Experiments were performed using six different types of single-wheels as well as a four-wheeled rover moving on planetary soil simulant. All the unknown model parameters were identified using the measured data and compared with the values obtained by conventional experiments. It is verified that the proposed iterative identification method provides improved accuracy, making it suitable for scientific studies of soil properties, whereas the step-by-step identification methods based on simplified models require less calculation time, making them more suitable for real-time applications. The models have less than 10% margin of error comparing with the measured results when predicting the interaction forces and moments using the corresponding identified parameters.

Lecithin-gold hybrid nanocarriers as efficient and pH selective vehicles for oral delivery of diacerein-In-vitro and in-vivo study.

PubMed

Javed, Ibrahim; Hussain, Syed Zajif; Shahzad, Atif; Khan, Jahanzeb Muhammad; Ur-Rehman, Habib; Rehman, Mubashar; Usman, Faisal; Razi, Muhammad Tahir; Shah, Muhammad Raza; Hussain, Irshad

2016-05-01

We report the synthesis and evaluation of lecithin-gold hybrid nanocarriers for the oral delivery of drugs with improved pharmacokinetics, Au-drug interactive bioactivity and controlled drug releasing behavior at physiological pH inside human body. For this purpose, diacerein, a hydrophobic anti-arthritic drug, was loaded in lecithin NPs (LD NPs), which were further coated by Au NPs either by in-situ production of Au NPs on LD NPs or by employing pre-synthesized Au NPs. All LDAu NPs were found to release drug selectively at the physiological pH of 7.4 and showed 2.5 times increase in the oral bioavailability of diacerein. Pharmacological efficacy was significantly improved i.e., greater than the additive effect of diacerein and Au NPs alone. LDAu NPs started suppressing inflammation at first phase, whereas LD NPs showed activity in the second phase of inflammation. These results indicate the interaction of Au NPs with prostaglandins and histaminic mediators of first phase of carrageenan induced inflammation. Acute toxicity study showed no hepatic damage but the renal toxicity parameters were close to the upper safety limits. Toxicity parameters were dependent on surface engineering of LDAu NPs. Apart from enhancing the oral bioavailability of hydrophobic drugs and improving their anti-inflammatory activity, these hybrid nanocarriers may have potential applications in gold-based photothermal therapy and the tracing of inflammation at atherosclerotic and arthritic site. Copyright © 2016 Elsevier B.V. All rights reserved.

On improving the performance of nonphotochemical quenching in CP29 light-harvesting antenna complex

NASA Astrophysics Data System (ADS)

Berman, Gennady P.; Nesterov, Alexander I.; Sayre, Richard T.; Still, Susanne

2016-03-01

We model and simulate the performance of charge-transfer in nonphotochemical quenching (NPQ) in the CP29 light-harvesting antenna-complex associated with photosystem II (PSII). The model consists of five discrete excitonic energy states and two sinks, responsible for the potentially damaging processes and charge-transfer channels, respectively. We demonstrate that by varying (i) the parameters of the chlorophyll-based dimer, (ii) the resonant properties of the protein-solvent environment interaction, and (iii) the energy transfer rates to the sinks, one can significantly improve the performance of the NPQ. Our analysis suggests strategies for improving the performance of the NPQ in response to environmental changes, and may stimulate experimental verification.

A study on the role of powertrain system dynamics on vehicle driveability

NASA Astrophysics Data System (ADS)

Castellazzi, Luca; Tonoli, Andrea; Amati, Nicola; Galliera, Enrico

2017-07-01

Vehicle driveability describes the complex interactions between the driver and the vehicle, mainly related to longitudinal vibrations. Today, a relevant part of the driveability process optimisation is realised by means of track tests, which require a considerable effort due to the number of parameters (such as stiffness and damping components) affecting this behaviour. The drawback of this approach is that it is carried on at a stage when a design iteration becomes very expensive in terms of time and cost. The objective of this work is to propose a light and accurate tool to represent the relevant quantities involved in the driveability analysis, and to understand which are the main vehicle parameters that influence the torsional vibrations transmitted to the driver. Particular attention is devoted to the role of the tyre, the engine mount, the dual mass flywheel and their possible interactions. The presented nonlinear dynamic model has been validated in time and frequency domain and, through linearisation of its nonlinear components, allows to exploit modal and energy analysis. Objective indexes regarding the driving comfort are additionally considered in order to evaluate possible driveability improvements related to the sensitivity of powertrain parameters.

How does informational heterogeneity affect the quality of forecasts?

NASA Astrophysics Data System (ADS)

Gualdi, S.; De Martino, A.

2010-01-01

We investigate a toy model of inductive interacting agents aiming to forecast a continuous, exogenous random variable E. Private information on E is spread heterogeneously across agents. Herding turns out to be the preferred forecasting mechanism when heterogeneity is maximal. However in such conditions aggregating information efficiently is hard even in the presence of learning, as the herding ratio rises significantly above the efficient market expectation of 1 and remarkably close to the empirically observed values. We also study how different parameters (interaction range, learning rate, cost of information and score memory) may affect this scenario and improve efficiency in the hard phase.

Electron trajectory evaluation in laser-plasma interaction for effective output beam

NASA Astrophysics Data System (ADS)

Zobdeh, P.; Sadighi-Bonabi, R.; Afarideh, H.

2010-06-01

Using the ellipsoidal cavity model, the quasi-monoenergetic electron output beam in laser-plasma interaction is described. By the cavity regime the quality of electron beam is improved in comparison with those generated from other methods such as periodic plasma wave field, spheroidal cavity regime and plasma channel guided acceleration. Trajectory of electron motion is described as hyperbolic, parabolic or elliptic paths. We find that the self-generated electron bunch has a smaller energy width and more effective gain in energy spectrum. Initial condition for the ellipsoidal cavity is determined by laser-plasma parameters. The electron trajectory is influenced by its position, energy and cavity electrostatic potential.

Effects of Pilates exercises on sensory interaction, postural control and fatigue in patients with multiple sclerosis.

PubMed

Soysal Tomruk, Melda; Uz, Muhammed Zahid; Kara, Bilge; İdiman, Egemen

2016-05-01

Decreased postural control, sensory integration deficits and fatigue are important problems that cause functional impairments in patients with multiple sclerosis (pwMS). To examine the effect of modified clinical Pilates exercises on sensory interaction and balance, postural control and fatigue in pwMS. Eleven patients with multiple sclerosis and 12 healthy matched controls were recruited in this study. Limits of stability and postural stability tests were used to evaluate postural control by Biodex Balance System and sensory interaction assessed. Fatigue was assessed by Modified Fatigue Impact Scale. Pilates exercises were applied two times a week for 10 weeks and measurements were repeated to pwMS after exercise training. Postural control and fatigue (except psychosocial parameter) of pwMS were significantly worser than healthy controls (p<0.05). Significant improvements occurred in sensory interaction (eyes open, foam surface) and total, physical and cognitive scores of fatigue after 10-week modified clinical Pilates training (p<0.05). No significant changes were detected in postural control after the pilates exercises (p>0.05). Ten-week Pilates training is effective to improve sensory interaction and to decrease fatigue. Pilates exercises can be applied safely in ambulatory pwMS for enhance sensory interaction and balance and combat fatigue. More investigations are needed. Copyright © 2016 Elsevier B.V. All rights reserved.

A multi-mode real-time terrain parameter estimation method for wheeled motion control of mobile robots

NASA Astrophysics Data System (ADS)

Li, Yuankai; Ding, Liang; Zheng, Zhizhong; Yang, Qizhi; Zhao, Xingang; Liu, Guangjun

2018-05-01

For motion control of wheeled planetary rovers traversing on deformable terrain, real-time terrain parameter estimation is critical in modeling the wheel-terrain interaction and compensating the effect of wheel slipping. A multi-mode real-time estimation method is proposed in this paper to achieve accurate terrain parameter estimation. The proposed method is composed of an inner layer for real-time filtering and an outer layer for online update. In the inner layer, sinkage exponent and internal frictional angle, which have higher sensitivity than that of the other terrain parameters to wheel-terrain interaction forces, are estimated in real time by using an adaptive robust extended Kalman filter (AREKF), whereas the other parameters are fixed with nominal values. The inner layer result can help synthesize the current wheel-terrain contact forces with adequate precision, but has limited prediction capability for time-variable wheel slipping. To improve estimation accuracy of the result from the inner layer, an outer layer based on recursive Gauss-Newton (RGN) algorithm is introduced to refine the result of real-time filtering according to the innovation contained in the history data. With the two-layer structure, the proposed method can work in three fundamental estimation modes: EKF, REKF and RGN, making the method applicable for flat, rough and non-uniform terrains. Simulations have demonstrated the effectiveness of the proposed method under three terrain types, showing the advantages of introducing the two-layer structure.

A Bayesian-based multilevel factorial analysis method for analyzing parameter uncertainty of hydrological model

NASA Astrophysics Data System (ADS)

Liu, Y. R.; Li, Y. P.; Huang, G. H.; Zhang, J. L.; Fan, Y. R.

2017-10-01

In this study, a Bayesian-based multilevel factorial analysis (BMFA) method is developed to assess parameter uncertainties and their effects on hydrological model responses. In BMFA, Differential Evolution Adaptive Metropolis (DREAM) algorithm is employed to approximate the posterior distributions of model parameters with Bayesian inference; factorial analysis (FA) technique is used for measuring the specific variations of hydrological responses in terms of posterior distributions to investigate the individual and interactive effects of parameters on model outputs. BMFA is then applied to a case study of the Jinghe River watershed in the Loess Plateau of China to display its validity and applicability. The uncertainties of four sensitive parameters, including soil conservation service runoff curve number to moisture condition II (CN2), soil hydraulic conductivity (SOL_K), plant available water capacity (SOL_AWC), and soil depth (SOL_Z), are investigated. Results reveal that (i) CN2 has positive effect on peak flow, implying that the concentrated rainfall during rainy season can cause infiltration-excess surface flow, which is an considerable contributor to peak flow in this watershed; (ii) SOL_K has positive effect on average flow, implying that the widely distributed cambisols can lead to medium percolation capacity; (iii) the interaction between SOL_AWC and SOL_Z has noticeable effect on the peak flow and their effects are dependent upon each other, which discloses that soil depth can significant influence the processes of plant uptake of soil water in this watershed. Based on the above findings, the significant parameters and the relationship among uncertain parameters can be specified, such that hydrological model's capability for simulating/predicting water resources of the Jinghe River watershed can be improved.

Adaptive Control Parameters for Dispersal of Multi-Agent Mobile Ad Hoc Network (MANET) Swarms

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

Kurt Derr; Milos Manic

A mobile ad hoc network is a collection of independent nodes that communicate wirelessly with one another. This paper investigates nodes that are swarm robots with communications and sensing capabilities. Each robot in the swarm may operate in a distributed and decentralized manner to achieve some goal. This paper presents a novel approach to dynamically adapting control parameters to achieve mesh configuration stability. The presented approach to robot interaction is based on spring force laws (attraction and repulsion laws) to create near-optimal mesh like configurations. In prior work, we presented the extended virtual spring mesh (EVSM) algorithm for the dispersionmore » of robot swarms. This paper extends the EVSM framework by providing the first known study on the effects of adaptive versus static control parameters on robot swarm stability. The EVSM algorithm provides the following novelties: 1) improved performance with adaptive control parameters and 2) accelerated convergence with high formation effectiveness. Simulation results show that 120 robots reach convergence using adaptive control parameters more than twice as fast as with static control parameters in a multiple obstacle environment.« less

Efficient hierarchical trans-dimensional Bayesian inversion of magnetotelluric data

NASA Astrophysics Data System (ADS)

Xiang, Enming; Guo, Rongwen; Dosso, Stan E.; Liu, Jianxin; Dong, Hao; Ren, Zhengyong

2018-06-01

This paper develops an efficient hierarchical trans-dimensional (trans-D) Bayesian algorithm to invert magnetotelluric (MT) data for subsurface geoelectrical structure, with unknown geophysical model parameterization (the number of conductivity-layer interfaces) and data-error models parameterized by an auto-regressive (AR) process to account for potential error correlations. The reversible-jump Markov-chain Monte Carlo algorithm, which adds/removes interfaces and AR parameters in birth/death steps, is applied to sample the trans-D posterior probability density for model parameterization, model parameters, error variance and AR parameters, accounting for the uncertainties of model dimension and data-error statistics in the uncertainty estimates of the conductivity profile. To provide efficient sampling over the multiple subspaces of different dimensions, advanced proposal schemes are applied. Parameter perturbations are carried out in principal-component space, defined by eigen-decomposition of the unit-lag model covariance matrix, to minimize the effect of inter-parameter correlations and provide effective perturbation directions and length scales. Parameters of new layers in birth steps are proposed from the prior, instead of focused distributions centred at existing values, to improve birth acceptance rates. Parallel tempering, based on a series of parallel interacting Markov chains with successively relaxed likelihoods, is applied to improve chain mixing over model dimensions. The trans-D inversion is applied in a simulation study to examine the resolution of model structure according to the data information content. The inversion is also applied to a measured MT data set from south-central Australia.

Interactive autonomy and robotic skills

NASA Technical Reports Server (NTRS)

Kellner, A.; Maediger, B.

1994-01-01

Current concepts of robot-supported operations for space laboratories (payload servicing, inspection, repair, and ORU exchange) are mainly based on the concept of 'interactive autonomy' which implies autonomous behavior of the robot according to predefined timelines, predefined sequences of elementary robot operations and within predefined world models supplying geometrical and other information for parameter instantiation on the one hand, and the ability to override and change the predefined course of activities by human intervention on the other hand. Although in principle a very powerful and useful concept, in practice the confinement of the robot to the abstract world models and predefined activities appears to reduce the robot's stability within real world uncertainties and its applicability to non-predefined parts of the world, calling for frequent corrective interaction by the operator, which in itself may be tedious and time-consuming. Methods are presented to improve this situation by incorporating 'robotic skills' into the concept of interactive autonomy.

Prediction of interface residue based on the features of residue interaction network.

PubMed

Jiao, Xiong; Ranganathan, Shoba

2017-11-07

Protein-protein interaction plays a crucial role in the cellular biological processes. Interface prediction can improve our understanding of the molecular mechanisms of the related processes and functions. In this work, we propose a classification method to recognize the interface residue based on the features of a weighted residue interaction network. The random forest algorithm is used for the prediction and 16 network parameters and the B-factor are acting as the element of the input feature vector. Compared with other similar work, the method is feasible and effective. The relative importance of these features also be analyzed to identify the key feature for the prediction. Some biological meaning of the important feature is explained. The results of this work can be used for the related work about the structure-function relationship analysis via a residue interaction network model. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effects of selective attention on continuous opinions and discrete decisions

NASA Astrophysics Data System (ADS)

Si, Xia-Meng; Liu, Yun; Xiong, Fei; Zhang, Yan-Chao; Ding, Fei; Cheng, Hui

2010-09-01

Selective attention describes that individuals have a preference on information according to their involving motivation. Based on achievements of social psychology, we propose an opinion interacting model to improve the modeling of individuals’ interacting behaviors. There are two parameters governing the probability of agents interacting with opponents, i.e. individual relevance and time-openness. It is found that, large individual relevance and large time-openness advance the appearance of large clusters, but large individual relevance and small time-openness favor the lessening of extremism. We also put this new model into application to work out some factor leading to a successful product. Numerical simulations show that selective attention, especially individual relevance, cannot be ignored by launcher firms and information spreaders so as to attain the most successful promotion.

D3GB: An Interactive Genome Browser for R, Python, and WordPress.

PubMed

Barrios, David; Prieto, Carlos

2017-05-01

Genome browsers are useful not only for showing final results but also for improving analysis protocols, testing data quality, and generating result drafts. Its integration in analysis pipelines allows the optimization of parameters, which leads to better results. New developments that facilitate the creation and utilization of genome browsers could contribute to improving analysis results and supporting the quick visualization of genomic data. D3 Genome Browser is an interactive genome browser that can be easily integrated in analysis protocols and shared on the Web. It is distributed as an R package, a Python module, and a WordPress plugin to facilitate its integration in pipelines and the utilization of platform capabilities. It is compatible with popular data formats such as GenBank, GFF, BED, FASTA, and VCF, and enables the exploration of genomic data with a Web browser.

Competition among Li+, Na+, K+ and Rb+ Monovalent Ions for DNA in Molecular Dynamics Simulations using the Additive CHARMM36 and Drude Polarizable Force Fields

PubMed Central

Savelyev, Alexey; MacKerell, Alexander D.

2015-01-01

In the present study we report on interactions of and competition between monovalent ions for two DNA sequences in MD simulations. Efforts included the development and validation of parameters for interactions among the first-group monovalent cations, Li+, Na+, K+ and Rb+, and DNA in the Drude polarizable and additive CHARMM36 force fields (FF). The optimization process targeted gas-phase QM interaction energies of various model compounds with ions and osmotic pressures of bulk electrolyte solutions of chemically relevant ions. The optimized ionic parameters are validated against counterion condensation theory and buffer exchange-atomic emission spectroscopy measurements providing quantitative data on the competitive association of different monovalent ions with DNA. Comparison between experimental and MD simulation results demonstrates that, compared to the additive CHARMM36 model, the Drude FF provides an improved description of the general features of the ionic atmosphere around DNA and leads to closer agreement with experiment on the ionic competition within the ion atmosphere. Results indicate the importance of extended simulation systems on the order of 25 Å beyond the DNA surface to obtain proper convergence of ion distributions. PMID:25751286

SIMPLE estimate of the free energy change due to aliphatic mutations: superior predictions based on first principles.

PubMed

Bueno, Marta; Camacho, Carlos J; Sancho, Javier

2007-09-01

The bioinformatics revolution of the last decade has been instrumental in the development of empirical potentials to quantitatively estimate protein interactions for modeling and design. Although computationally efficient, these potentials hide most of the relevant thermodynamics in 5-to-40 parameters that are fitted against a large experimental database. Here, we revisit this longstanding problem and show that a careful consideration of the change in hydrophobicity, electrostatics, and configurational entropy between the folded and unfolded state of aliphatic point mutations predicts 20-30% less false positives and yields more accurate predictions than any published empirical energy function. This significant improvement is achieved with essentially no free parameters, validating past theoretical and experimental efforts to understand the thermodynamics of protein folding. Our first principle analysis strongly suggests that both the solute-solute van der Waals interactions in the folded state and the electrostatics free energy change of exposed aliphatic mutations are almost completely compensated by similar interactions operating in the unfolded ensemble. Not surprisingly, the problem of properly accounting for the solvent contribution to the free energy of polar and charged group mutations, as well as of mutations that disrupt the protein backbone remains open. 2007 Wiley-Liss, Inc.

Combustion behavior of different kinds of torrefied biomass and their blends with lignite.

PubMed

Toptas, Asli; Yildirim, Yeliz; Duman, Gozde; Yanik, Jale

2015-02-01

In this study, the combustion behavior of different kinds of torrefied biomass (lignocellulosic and animal wastes) and their blends with lignite was investigated via non-isothermal thermogravimetric method under air atmosphere. For comparison, combustion characteristics of raw biomasses were also determined. Torrefaction process improved the reactivity of char combustion step of biomasses. Characteristic combustion parameters for blends showed non-additivity behavior. It was found that the mixture of torrefied biomasses and lignite at a ratio of 1:1 had a lower ignition and burnout temperature than the coal-only sample. Although no interactions were observed between the lignite and torrefied biomass at initial step of combustion, a certain degree of interaction between the components occurred at char combustion step. Kinetic parameters of combustion were calculated by using the Coats Redfern model. Overall, this study showed that poultry litters can be used as a substitute fuel in coal/biomass co-firing systems by blending with lignocellulosic biomass. Copyright © 2014 Elsevier Ltd. All rights reserved.

Automated respiratory cycles selection is highly specific and improves respiratory mechanics analysis.

PubMed

Rigo, Vincent; Graas, Estelle; Rigo, Jacques

2012-07-01

Selected optimal respiratory cycles should allow calculation of respiratory mechanic parameters focusing on patient-ventilator interaction. New computer software automatically selecting optimal breaths and respiratory mechanics derived from those cycles are evaluated. Retrospective study. University level III neonatal intensive care unit. Ten mins synchronized intermittent mandatory ventilation and assist/control ventilation recordings from ten newborns. The ventilator provided respiratory mechanic data (ventilator respiratory cycles) every 10 secs. Pressure, flow, and volume waves and pressure-volume, pressure-flow, and volume-flow loops were reconstructed from continuous pressure-volume recordings. Visual assessment determined assisted leak-free optimal respiratory cycles (selected respiratory cycles). New software graded the quality of cycles (automated respiratory cycles). Respiratory mechanic values were derived from both sets of optimal cycles. We evaluated quality selection and compared mean values and their variability according to ventilatory mode and respiratory mechanic provenance. To assess discriminating power, all 45 "t" values obtained from interpatient comparisons were compared for each respiratory mechanic parameter. A total of 11,724 breaths are evaluated. Automated respiratory cycle/selected respiratory cycle selections agreement is high: 88% of maximal κ with linear weighting. Specificity and positive predictive values are 0.98 and 0.96, respectively. Averaged values are similar between automated respiratory cycle and ventilator respiratory cycle. C20/C alone is markedly decreased in automated respiratory cycle (1.27 ± 0.37 vs. 1.81 ± 0.67). Tidal volume apparent similarity disappears in assist/control: automated respiratory cycle tidal volume (4.8 ± 1.0 mL/kg) is significantly lower than for ventilator respiratory cycle (5.6 ± 1.8 mL/kg). Coefficients of variation decrease for all automated respiratory cycle parameters in all infants. "t" values from ventilator respiratory cycle data are two to three times higher than ventilator respiratory cycles. Automated selection is highly specific. Automated respiratory cycle reflects most the interaction of both ventilator and patient. Improving discriminating power of ventilator monitoring will likely help in assessing disease status and following trends. Averaged parameters derived from automated respiratory cycles are more precise and could be displayed by ventilators to improve real-time fine tuning of ventilator settings.

Improving Land-Surface Model Hydrology: Is an Explicit Aquifer Model Better than a Deeper Soil Profile?

NASA Technical Reports Server (NTRS)

Gulden, L. E.; Rosero, E.; Yang, Z.-L.; Rodell, Matthew; Jackson, C. S.; Niu, G.-Y.; Yeh, P. J.-F.; Famiglietti, J. S.

2007-01-01

Land surface models (LSMs) are computer programs, similar to weather and climate prediction models, which simulate the storage and movement of water (including soil moisture, snow, evaporation, and runoff) after it falls to the ground as precipitation. It is not currently possible to measure all of the variables of interest everywhere on Earth with sufficient accuracy. Hence LSMs have been developed to integrate the available information, including satellite observations, using powerful computers, in order to track water storage and redistribution. The maps are used to improve weather forecasts, support water resources and agricultural applications, and study the Earth's water cycle and climate variability. Recently, the models have begun to simulate groundwater storage. In this paper, we compare several possible approaches, and examine the pitfalls associated with trying to estimate aquifer parameters (such as porosity) that are required by the models. We find that explicit representation of groundwater, as opposed to the addition of deeper soil layers, considerably decreases the sensitivity of modeled terrestrial water storage to aquifer parameter choices. We also show that approximate knowledge of parameter values is not sufficient to guarantee realistic model performance: because interaction among parameters is significant, they must be prescribed as a harmonious set.

Improved Limits on Axionlike-Particle-Mediated P, T-Violating Interactions between Electrons and Nucleons from Electric Dipole Moments of Atoms and Molecules.

PubMed

Stadnik, Y V; Dzuba, V A; Flambaum, V V

2018-01-05

In the presence of P, T-violating interactions, the exchange of axionlike particles between electrons and nucleons in atoms and molecules induces electric dipole moments (EDMs) of atoms and molecules. We perform calculations of such axion-exchange-induced atomic EDMs using the relativistic Hartree-Fock-Dirac method including electron core polarization corrections. We present analytical estimates to explain the dependence of these induced atomic EDMs on the axion mass and atomic parameters. From the experimental bounds on the EDMs of atoms and molecules, including ^{133}Cs, ^{205}Tl, ^{129}Xe, ^{199}Hg, ^{171}Yb^{19}F, ^{180}Hf^{19}F^{+}, and ^{232}Th^{16}O, we constrain the P, T-violating scalar-pseudoscalar nucleon-electron and electron-electron interactions mediated by a generic axionlike particle of arbitrary mass. Our limits improve on existing laboratory bounds from other experiments by many orders of magnitude for m_{a}≳10^{-2}  eV. We also place constraints on CP violation in certain types of relaxion models.

Interaction-induced effects on Bose-Hubbard parameters

NASA Astrophysics Data System (ADS)

Kremer, Mark; Sachdeva, Rashi; Benseny, Albert; Busch, Thomas

2017-12-01

We study the effects of repulsive on-site interactions on the broadening of the localized Wannier functions used for calculating the parameters to describe ultracold atoms in optical lattices. For this, we replace the common single-particle Wannier functions, which do not contain any information about the interactions, by two-particle Wannier functions obtained from an exact solution which takes the interactions into account. We then use these interaction-dependent basis functions to calculate the Bose-Hubbard model parameters, showing that they are substantially different both at low and high lattice depths from the ones calculated using single-particle Wannier functions. Our results suggest that density effects are not negligible for many parameter ranges and need to be taken into account in metrology experiments.

Comparative studies on structures, mechanical properties, sensitivity, stabilities and detonation performance of CL-20/TNT cocrystal and composite explosives by molecular dynamics simulation.

PubMed

Hang, Gui-Yun; Yu, Wen-Li; Wang, Tao; Wang, Jin-Tao; Li, Zhen

2017-09-19

To investigate and compare the differences of structures and properties of CL-20/TNT cocrystal and composite explosives, the CL-20/TNT cocrystal and composite models were established. Molecular dynamics simulations were performed to investigate the structures, mechanical properties, sensitivity, stabilities and detonation performance of cocrystal and composite models with COMPASS force field in NPT ensemble. The lattice parameters, mechanical properties, binding energies, interaction energy of trigger bond, cohesive energy density and detonation parameters were determined and compared. The results show that, compared with pure CL-20, the rigidity and stiffness of cocrystal and composite models decreased, while plastic properties and ductility increased, so mechanical properties can be effectively improved by adding TNT into CL-20 and the cocrystal model has better mechanical properties. The interaction energy of the trigger bond and the cohesive energy density is in the order of CL-20/TNT cocrystal > CL-20/TNT composite > pure CL-20, i.e., cocrystal model is less sensitive than CL-20 and the composite model, and has the best safety parameters. Binding energies show that the cocrystal model has higher intermolecular interaction energy values than the composite model, thus illustrating the better stability of the cocrystal model. Detonation parameters vary as CL-20 > cocrystal > composite, namely, the energy density and power of cocrystal and composite model are weakened; however, the CL-20/TNT cocrystal explosive still has desirable energy density and detonation performance. This results presented in this paper help offer some helpful guidance to better understand the mechanism of CL-20/TNT cocrystal explosives and provide some theoretical assistance for cocrystal explosive design.

One-dimensional model of interacting-step fluctuations on vicinal surfaces: Analytical formulas and kinetic Monte-Carlo simulations

NASA Astrophysics Data System (ADS)

Patrone, Paul; Einstein, T. L.; Margetis, Dionisios

2011-03-01

We study a 1+1D, stochastic, Burton-Cabrera-Frank (BCF) model of interacting steps fluctuating on a vicinal crystal. The step energy accounts for entropic and nearest-neighbor elastic-dipole interactions. Our goal is to formulate and validate a self-consistent mean-field (MF) formalism to approximately solve the system of coupled, nonlinear stochastic differential equations (SDEs) governing fluctuations in surface motion. We derive formulas for the time-dependent terrace width distribution (TWD) and its steady-state limit. By comparison with kinetic Monte-Carlo simulations, we show that our MF formalism improves upon models in which step interactions are linearized. We also indicate how fitting parameters of our steady state MF TWD may be used to determine the mass transport regime and step interaction energy of certain experimental systems. PP and TLE supported by NSF MRSEC under Grant DMR 05-20471 at U. of Maryland; DM supported by NSF under Grant DMS 08-47587.

Real-time interactive projection system based on infrared structured-light method

NASA Astrophysics Data System (ADS)

Qiao, Xiaorui; Zhou, Qian; Ni, Kai; He, Liang; Wu, Guanhao; Mao, Leshan; Cheng, Xuemin; Ma, Jianshe

2012-11-01

Interactive technologies have been greatly developed in recent years, especially in projection field. However, at present, most interactive projection systems are based on special designed interactive pens or whiteboards, which is inconvenient and limits the improvement of user experience. In this paper, we introduced our recent progress on theoretically modeling a real-time interactive projection system. The system permits the user to easily operate or draw on the projection screen directly by fingers without any other auxiliary equipment. The projector projects infrared striping patterns onto the screen and the CCD captures the deformational image. We resolve the finger's position and track its movement by processing the deformational image in real-time. A new way to determine whether the finger touches the screen is proposed. The first deformational fringe on the fingertip and the first fringe at the finger shadow are the same one. The correspondence is obtained, so the location parameters can be decided by triangulation. The simulation results are given, and errors are analyzed.

Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field

PubMed Central

2015-01-01

Recently we presented a first-generation all-atom Drude polarizable force field for DNA based on the classical Drude oscillator model, focusing on optimization of key dihedral angles followed by extensive validation of the force field parameters. Presently, we describe the procedure for balancing the electrostatic interactions between ions, water, and DNA as required for development of the Drude force field for DNA. The proper balance of these interactions is shown to impact DNA stability and subtler conformational properties, including the conformational equilibrium between the BI and BII states, and the A and B forms of DNA. The parametrization efforts were simultaneously guided by gas-phase quantum mechanics (QM) data on small model compounds and condensed-phase experimental data on the hydration and osmotic properties of biologically relevant ions and their solutions, as well as theoretical predictions for ionic distribution around DNA oligomer. In addition, fine-tuning of the internal base parameters was performed to obtain the final DNA model. Notably, the Drude model is shown to more accurately reproduce counterion condensation theory predictions of DNA charge neutralization by the condensed ions as compared to the CHARMM36 additive DNA force field, indicating an improved physical description of the forces dictating the ionic solvation of DNA due to the explicit treatment of electronic polarizability. In combination with the polarizable DNA force field, the availability of Drude polarizable parameters for proteins, lipids, and carbohydrates will allow for simulation studies of heterogeneous biological systems. PMID:24874104

Optics measurement algorithms and error analysis for the proton energy frontier

NASA Astrophysics Data System (ADS)

Langner, A.; Tomás, R.

2015-03-01

Optics measurement algorithms have been improved in preparation for the commissioning of the LHC at higher energy, i.e., with an increased damage potential. Due to machine protection considerations the higher energy sets tighter limits in the maximum excitation amplitude and the total beam charge, reducing the signal to noise ratio of optics measurements. Furthermore the precision in 2012 (4 TeV) was insufficient to understand beam size measurements and determine interaction point (IP) β -functions (β*). A new, more sophisticated algorithm has been developed which takes into account both the statistical and systematic errors involved in this measurement. This makes it possible to combine more beam position monitor measurements for deriving the optical parameters and demonstrates to significantly improve the accuracy and precision. Measurements from the 2012 run have been reanalyzed which, due to the improved algorithms, result in a significantly higher precision of the derived optical parameters and decreased the average error bars by a factor of three to four. This allowed the calculation of β* values and demonstrated to be fundamental in the understanding of emittance evolution during the energy ramp.

Surface Peroneal Nerve Stimulation in Lower Limb Hemiparesis: Effect on Quantitative Gait Parameters

PubMed Central

Sheffler, Lynne R.; Taylor, Paul N.; Bailey, Stephanie Nogan; Gunzler, Douglas D.; Buurke, Jaap H.; IJzerman, Maarten J.; Chae, John

2015-01-01

Objective To evaluate possible mechanisms for functional improvement and compare ambulation training with surface peroneal nerve stimulation (PNS) versus usual care (UC) via quantitative gait analysis. Design Randomized controlled clinical trial. Setting Teaching hospital of academic medical center. Participants 110 chronic stroke survivors (> 12-wks post-stroke) with unilateral hemiparesis. Interventions Subjects were randomized to a surface PNS device or UC intervention. Subjects were treated for 12-wks and followed for 6-months post-treatment. Main Outcome Measures Spatiotemporal, kinematic, and kinetic parameters of gait. Results Cadence (F3,153=5.81, p=.012), stride length (F3,179=20.01, p<.001), walking speed (F3,167=18.2, p<.001), anterior posterior ground reaction force (F3,164=6.61, p=.004), peak hip power in pre-swing (F3,156=8.76, p<.001), and peak ankle power at push-off (F3,149=6.38, p=.005) all improved with respect to time. However, peak ankle DF in swing (F3,184=4.99, p=.031) worsened. In general, the greatest change for all parameters occurred during the treatment period. There was no significant treatment group by time interaction effects for any of the spatiotemporal, kinematic, or kinetic parameters. Conclusions Gait training with PNS and usual care was associated with improvements in peak hip power in pre-swing and peak ankle power at push-off, which may have resulted in improved cadence, stride length, and walking speed; however, there were no differences between treatment groups. Both treatment groups also experienced a decrease in peak ankle DF in swing, though the clinical implications of this finding are unclear. PMID:25802966

Kamlet-Taft solvent parameters, NMR spectroscopic analysis and thermoelectrochemistry of lithium-glyme solvate ionic liquids and their dilute solutions.

PubMed

Black, Jeffrey J; Dolan, Andrew; Harper, Jason B; Aldous, Leigh

2018-06-06

Solvate ionic liquids are a relatively new class of liquids produced by combining a coordinating solvent with a salt. They have a variety of uses and their suitability for such depends upon the ratio of salt to coordinating solvent. This work investigates the Kamlet-Taft solvent parameters of, NMR chemical shifts of nuclei in, and thermoelectrochemistry of a selected set of solvate ionic liquids produced from glymes (methyl terminated oligomers of ethylene glycol) and lithium bis(trifluoromethylsulfonyl)imide at two different compositions. The aim is to improve the understanding of the interactions occurring in these ionic liquids to help select suitable solvate ionic liquids for future applications.

Modified screening interaction potential on dust lattice waves in dusty plasma ring

NASA Astrophysics Data System (ADS)

He, Kerong; Chen, Hui; Liu, Sanqiu

2017-05-01

In the present paper, the modified screening interaction potential was adopted to investigate the dust lattice waves in dusty ring. Firstly, the influence of parameter ε on the modified screening interaction potential was analyzed; and it was found that the parameter ε has a long-range effect on the pairwise interaction between the particles. Secondly, the dispersion relations of longitudinal and transverse waves are obtained, and the effect of long-range action parameter ε, dimensionless lattice parameter α and dimensionless shielding parameter \\tilde{κ } on the dust lattice waves propagation in dusty ring are studied. Some interesting phenomena, such as the coupling of longitudinal and transverse waves, and instabilities of transverse waves are found, which are in good agreement with some previous works. Finally, the transverse wave instabilities and the relevant critical lattice parameter αc are presented and discussed.

Empirical parameterization of a model for predicting peptide helix/coil equilibrium populations.

PubMed Central

Andersen, N. H.; Tong, H.

1997-01-01

A modification of the Lifson-Roig formulation of helix/coil transitions is presented; it (1) incorporates end-capping and coulombic (salt bridges, hydrogen bonding, and side-chain interactions with charged termini and the helix dipole) effects, (2) helix-stabilizing hydrophobic clustering, (3) allows for different inherent termination probabilities of individual residues, and (4) differentiates helix elongation in the first versus subsequent turns of a helix. Each residue is characterized by six parameters governing helix formation. The formulation of the conditional probability of helix initiation and termination that we developed is essentially the same as one presented previously (Shalongo W, Stellwagen, E. 1995. Protein Sci 4:1161-1166) and nearly the mathematical equivalent of the new capping formulation incorporated in the model presented by Rohl et al. (1996. Protein Sci 5:2623-2637). Side-chain/side-chain interactions are, in most cases, incorporated as context dependent modifications of propagation rather than nucleation parameters. An alternative procedure for converting [theta]221 values to experimental fractional helicities () is presented. Tests of the program predictions suggest this method may have some advantages both for designed peptides and for the analysis of secondary structure preferences that could drive the formation of molten-globule intermediates on protein folding pathways. The model predicts the fractional helicity of 385 peptides with a root-mean-square deviation (RMSD) of 0.050 and locates (with precise definition of the termini in many cases) helices in proteins as well as competing methods. The propagation and nucleation parameters were derived from NMR data and from the CD data for a 79 peptide "learning set" for which an excellent fit resulted (RMSD = 0.0295). The current set of parameter corrections for capping boxes, helix dipole interactions, and side-chain/side-chain interactions (coulombic, hydrogen bonding and hydrophobic clustering), although still under development provide a significant improvement in both helix/coil equilibrium prediction for peptides and helix location in protein sequences. This is clearly evident in the rms deviations between CD measures and calculated values of fractional helicity for different classes of peptides before and after applying the corrections: for peptides lacking capping boxes and i/i + 3 and i/i + 4 side-chain/side-chain interactions RMSD = 0.044 (n = 164) versus RMSD = 0.054 (0.172 without the corrections, n = 221) for peptides that required context-dependent corrections of the parameters. If we restrict the analysis to N-acylated peptides with helix stabilizing side-chain/side-chain interactions (including N-capping boxes), the degree to which our corrections account for the stabilizing interaction can be judged from the change in helicity underestimation, (calc-CD): -0.15 +/- 0.10, which is reduced to -0.018 +/- 0.048 (n = 191) upon applying the corrections. PMID:9300492

Model-experiment interaction to improve representation of phosphorus limitation in land models

NASA Astrophysics Data System (ADS)

Norby, R. J.; Yang, X.; Cabugao, K. G. M.; Childs, J.; Gu, L.; Haworth, I.; Mayes, M. A.; Porter, W. S.; Walker, A. P.; Weston, D. J.; Wright, S. J.

2015-12-01

Carbon-nutrient interactions play important roles in regulating terrestrial carbon cycle responses to atmospheric and climatic change. None of the CMIP5 models has included routines to represent the phosphorus (P) cycle, although P is commonly considered to be the most limiting nutrient in highly productive, lowland tropical forests. Model simulations with the Community Land Model (CLM-CNP) show that inclusion of P coupling leads to a smaller CO2 fertilization effect and warming-induced CO2 release from tropical ecosystems, but there are important uncertainties in the P model, and improvements are limited by a dearth of data. Sensitivity analysis identifies the relative importance of P cycle parameters in determining P availability and P limitation, and thereby helps to define the critical measurements to make in field campaigns and manipulative experiments. To improve estimates of P supply, parameters that describe maximum amount of labile P in soil and sorption-desorption processes are necessary for modeling the amount of P available for plant uptake. Biochemical mineralization is poorly constrained in the model and will be improved through field observations that link root traits to mycorrhizal activity, phosphatase activity, and root depth distribution. Model representation of P demand by vegetation, which currently is set by fixed stoichiometry and allometric constants, requires a different set of data. Accurate carbon cycle modeling requires accurate parameterization of the photosynthetic machinery: Vc,max and Jmax. Relationships between the photosynthesis parameters and foliar nutrient (N and P) content are being developed, and by including analysis of covariation with other plant traits (e.g., specific leaf area, wood density), we can provide a basis for more dynamic, trait-enabled modeling. With this strong guidance from model sensitivity and uncertainty analysis, field studies are underway in Puerto Rico and Panama to collect model-relevant data on P supply and demand functions. New FACE and soil warming experiments in P-limited ecosystems in subtropical Australia, and tropical Brazil, Puerto Rico, and Panama will provide important benchmarks for the performance of P-enabled models under future conditions.

Power Law and Logarithmic Ricci Dark Energy Models in Hořava-Lifshitz Cosmology

NASA Astrophysics Data System (ADS)

Pasqua, Antonio; Chattopadhyay, Surajit; Khurshudyan, Martiros; Myrzakulov, Ratbay; Hakobyan, Margarit; Movsisyan, Artashes

2015-03-01

In this work, we studied the Power Law and the Logarithmic Entropy Corrected versions of the Ricci Dark Energy (RDE) model in a spatially non-flat universe and in the framework of Hořava-Lifshitz cosmology. For the two cases containing non-interacting and interacting RDE and Dark Matter (DM), we obtained the exact differential equation that determines the evolutionary form of the RDE energy density. Moreover, we obtained the expressions of the deceleration parameter q and, using a parametrization of the equation of state (EoS) parameter ω D given by the relation ω D ( z) = ω 0+ ω 1 z, we derived the expressions of both ω 0 and ω 1. We interestingly found that the expression of ω 0 is the same for both non-interacting and interacting case. The expression of ω 1 for the interacting case has strong dependence from the interacting parameter b 2. The parameters derived in this work are done in small redshift approximation and for low redshift expansion of the EoS parameter.

On improving the performance of nonphotochemical quenching in CP29 light-harvesting antenna complex

DOE PAGES

Berman, Gennady Petrovich; Nesterov, Alexander I.; Sayre, Richard Thomas; ...

2016-02-02

In this study, we model and simulate the performance of charge-transfer in nonphotochemical quenching (NPQ) in the CP29 light-harvesting antenna-complex associated with photosystem II (PSII). The model consists of five discrete excitonic energy states and two sinks, responsible for the potentially damaging processes and charge-transfer channels, respectively. We demonstrate that by varying (i) the parameters of the chlorophyll-based dimer, (ii) the resonant properties of the protein-solvent environment interaction, and (iii) the energy transfer rates to the sinks, one can significantly improve the performance of the NPQ. In conclusion, our analysis suggests strategies for improving the performance of the NPQ inmore » response to environmental changes, and may stimulate experimental verification.« less

Effects of microbial phytase, produced by solid-state fermentation, on the performance and nutrient utilisation of broilers fed maize- and wheat-based diets.

PubMed

Wu, Y B; Ravindran, V; Hendriks, W H

2003-12-01

1. The influence of a microbial phytase on the performance, toe ash contents and nutrient utilisation of male broilers fed diets based on maize and wheat was investigated. The experiment was conducted as 2 x 2 x 2 factorial arrangement of treatments. Within the factorial, two diet types (maize-soy or wheat-soy) containing two levels of non-phytate phosphorus (3.0 or 4.5 g/kg) were evaluated and each level of non-phytate phosphorus was supplemented with 0 or 500 PU phytase/kg diet. Each of the 8 dietary treatments were fed to 6 pens of 8 birds from d 1 to 21 post-hatching. 2. Main effects of diet type and phytase were observed for all parameters. Main effect of non-phytate phosphorus was significant only for feed/gain and toe ash contents. Phytase addition improved weight gains irrespective of diet type or non-phytate phosphorus level, but the magnitude of improvement in the phosphorus-deficient wheat-soy diet was greater, resulting in a diet type x non-phytate phosphorus interaction. Responses in toe ash contents were noted only in phosphorus-deficient diets, as indicated by a non-phytate phosphorus x phytase interaction. 3. Phytase addition improved apparent metabolisable energy values of wheat-based diets, but had little effect on the apparent metabolisable energy of maize-based diets as shown by a diet type x phytase interaction. The apparent metabolisable energy was not influenced by dietary non-phytate P. 4. Phytase improved ileal nitrogen digestibility in both diet types, but the responses to added phytase tended to be higher in wheat-based diets, as shown by a diet type x phytase interaction. 5. Increasing the dietary non-phytate phosphorus level reduced phosphorus digestibility and increased excreta phosphorus content. Addition of phytase improved phosphorus digestibility, but the increments were higher in low phosphorus diets resulting in a non-phytate phosphorus x phytase interaction. Phytase addition tended to lower the excreta phosphorus content, but the effects were greater in birds fed low phosphorus diets, as shown by a non-phytate phosphorus x phytase interaction.

Computer simulations of rapid granular flows of spheres interacting with a flat, frictional boundary

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

Louge, M.Y.

This paper employs computer simulations to test the theory of Jenkins [J. Applied Mech. [bold 59], 120 (1992)] for the interaction between a rapid granular flow of spheres and a flat, frictional wall. This paper examines the boundary conditions that relate the shear stress and energy flux at the wall to the normal stress, slip velocity, and fluctuation energy, and to the parameters that characterize a collision. It is found that while the theory captures the trends of the boundary conditions at low friction, it does not anticipate their behavior at large friction. A critical evaluation of Jenkins' assumptions suggestsmore » where his theory may be improved.« less

Evidence for Mikheyev-Smirnov-Wolfenstein effects in solar neutrino flavor transitions

NASA Astrophysics Data System (ADS)

Fogli, G. L.; Lisi, E.; Marrone, A.; Palazzo, A.

2004-03-01

We point out that the recent data from the Sudbury Neutrino Observatory, together with other relevant measurements from solar and reactor neutrino experiments, convincingly show that the flavor transitions of solar neutrinos are affected by Mikheyev-Smirnov-Wolfenstein (MSW) effects. More precisely, one can safely reject the null hypothesis of no MSW interaction energy in matter, despite the fact that the interaction amplitude (formally treated as a free parameter) is still weakly constrained by the current phenomenology. Such a constraint can be improved, however, by future data from the KamLAND experiment. In the standard MSW case, we also perform an updated analysis of two-family active oscillations of solar and reactor neutrinos.

Identifying and analyzing methods for reducing the energy consumption of helicopters

NASA Technical Reports Server (NTRS)

Davis, S. J.; Rosenstein, H. J.

1976-01-01

Reductions in helicopter energy consumption can be accomplished through the use of advanced technology in the areas of powerplant design, improved rotor efficiency, reduced parasite drag, and reduced structural empty weight. Baseline helicopters incorporating technology were designed for a short range (200 n mi) and a very short haul (100 n mi) mission scenario. Parametric analyses were then conducted to determine the impact of technology improvement. Many of the parameters varied are interrelated. A summary of such interactions is presented, and some additional sensitivity values were added so that energy reduction and DOC as affected by the major technological factors or operational modes are clearly defined.

Identification of Optimum Magnetic Behavior of NanoCrystalline CmFeAl Type Heusler Alloy Powders Using Response Surface Methodology

NASA Astrophysics Data System (ADS)

Srivastava, Y.; Srivastava, S.; Boriwal, L.

2016-09-01

Mechanical alloying is a novelistic solid state process that has received considerable attention due to many advantages over other conventional processes. In the present work, Co2FeAl healer alloy powder, prepared successfully from premix basic powders of Cobalt (Co), Iron (Fe) and Aluminum (Al) in stoichiometric of 60Co-26Fe-14Al (weight %) by novelistic mechano-chemical route. Magnetic properties of mechanically alloyed powders were characterized by vibrating sample magnetometer (VSM). 2 factor 5 level design matrix was applied to experiment process. Experimental results were used for response surface methodology. Interaction between the input process parameters and the response has been established with the help of regression analysis. Further analysis of variance technique was applied to check the adequacy of developed model and significance of process parameters. Test case study was performed with those parameters, which was not selected for main experimentation but range was same. Response surface methodology, the process parameters must be optimized to obtain improved magnetic properties. Further optimum process parameters were identified using numerical and graphical optimization techniques.

Imposition of physical parameters in dissipative particle dynamics

NASA Astrophysics Data System (ADS)

Mai-Duy, N.; Phan-Thien, N.; Tran-Cong, T.

2017-12-01

In the mesoscale simulations by the dissipative particle dynamics (DPD), the motion of a fluid is modelled by a set of particles interacting in a pairwise manner, and it has been shown to be governed by the Navier-Stokes equation, with its physical properties, such as viscosity, Schmidt number, isothermal compressibility, relaxation and inertia time scales, in fact its whole rheology resulted from the choice of the DPD model parameters. In this work, we will explore the response of a DPD fluid with respect to its parameter space, where the model input parameters can be chosen in advance so that (i) the ratio between the relaxation and inertia time scales is fixed; (ii) the isothermal compressibility of water at room temperature is enforced; and (iii) the viscosity and Schmidt number can be specified as inputs. These impositions are possible with some extra degrees of freedom in the weighting functions for the conservative and dissipative forces. Numerical experiments show an improvement in the solution quality over conventional DPD parameters/weighting functions, particularly for the number density distribution and computed stresses.

Computation of energy interaction parameters as well as electric dipole intensity parameters for the absorption spectral study of the interaction of Pr(III) with L-phenylalanine, L-glycine, L-alanine and L-aspartic acid in the presence and absence of Ca 2+ in organic solvents

NASA Astrophysics Data System (ADS)

Moaienla, T.; Singh, Th. David; Singh, N. Rajmuhon; Devi, M. Indira

2009-10-01

Studying the absorption difference and comparative absorption spectra of the interaction of Pr(III) and Nd(III) with L-phenylalanine, L-glycine, L-alanine and L-aspartic acid in the presence and absence of Ca 2+ in organic solvents, various energy interaction parameters like Slater-Condon ( FK), Racah ( Ek), Lande factor ( ξ4f), nephelauxetic ratio ( β), bonding ( b1/2), percentage-covalency ( δ) have been evaluated applying partial and multiple regression analysis. The values of oscillator strength ( P) and Judd-Ofelt electric dipole intensity parameter Tλ ( λ = 2, 4, 6) for different 4f-4f transitions have been computed. On analysis of the variation of the various energy interaction parameters as well as the changes in the oscillator strength ( P) and Tλ values reveal the mode of binding with different ligands.

Developing strategies for predicting hyperkalemia in potassium-increasing drug-drug interactions.

PubMed

Eschmann, Emmanuel; Beeler, Patrick Emanuel; Schneemann, Markus; Blaser, Jürg

2017-01-01

To compare different strategies predicting hyperkalemia (serum potassium level ≥5.5 mEq/l) in hospitalized patients for whom medications triggering potassium-increasing drug-drug interactions (DDIs) were ordered. We investigated 5 strategies that combined prediction triggered at onset of DDI versus continuous monitoring and taking into account an increasing number of patient parameters. The considered patient parameters were identified using generalized additive models, and the thresholds of the prediction strategies were calculated by applying Youden's J statistic to receiver operation characteristic curves. Half of the data served as the calibration set, half as the validation set. We identified 132 incidences of hyperkalemia induced by 8413 potentially severe potassium-increasing DDIs among 76 467 patients. The positive predictive value (PPV) of those strategies predicting hyperkalemia at the onset of DDI ranged from 1.79% (undifferentiated anticipation of hyperkalemia due to the DDI) to 3.02% (additionally considering the baseline serum potassium) and 3.10% (including further patient parameters). Continuous monitoring significantly increased the PPV to 8.25% (considering the current serum potassium) and 9.34% (additional patient parameters). Continuous monitoring of the risk for hyperkalemia based on current potassium level shows a better predictive power than predictions triggered at the onset of DDI. This contrasts with efforts to improve DDI alerts by taking into account more patient parameters at the time of ordering. © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Algorithm sensitivity analysis and parameter tuning for tissue image segmentation pipelines

PubMed Central

Kurç, Tahsin M.; Taveira, Luís F. R.; Melo, Alba C. M. A.; Gao, Yi; Kong, Jun; Saltz, Joel H.

2017-01-01

Abstract Motivation: Sensitivity analysis and parameter tuning are important processes in large-scale image analysis. They are very costly because the image analysis workflows are required to be executed several times to systematically correlate output variations with parameter changes or to tune parameters. An integrated solution with minimum user interaction that uses effective methodologies and high performance computing is required to scale these studies to large imaging datasets and expensive analysis workflows. Results: The experiments with two segmentation workflows show that the proposed approach can (i) quickly identify and prune parameters that are non-influential; (ii) search a small fraction (about 100 points) of the parameter search space with billions to trillions of points and improve the quality of segmentation results (Dice and Jaccard metrics) by as much as 1.42× compared to the results from the default parameters; (iii) attain good scalability on a high performance cluster with several effective optimizations. Conclusions: Our work demonstrates the feasibility of performing sensitivity analyses, parameter studies and auto-tuning with large datasets. The proposed framework can enable the quantification of error estimations and output variations in image segmentation pipelines. Availability and Implementation: Source code: https://github.com/SBU-BMI/region-templates/. Contact: teodoro@unb.br Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28062445

Algorithm sensitivity analysis and parameter tuning for tissue image segmentation pipelines.

PubMed

Teodoro, George; Kurç, Tahsin M; Taveira, Luís F R; Melo, Alba C M A; Gao, Yi; Kong, Jun; Saltz, Joel H

2017-04-01

Sensitivity analysis and parameter tuning are important processes in large-scale image analysis. They are very costly because the image analysis workflows are required to be executed several times to systematically correlate output variations with parameter changes or to tune parameters. An integrated solution with minimum user interaction that uses effective methodologies and high performance computing is required to scale these studies to large imaging datasets and expensive analysis workflows. The experiments with two segmentation workflows show that the proposed approach can (i) quickly identify and prune parameters that are non-influential; (ii) search a small fraction (about 100 points) of the parameter search space with billions to trillions of points and improve the quality of segmentation results (Dice and Jaccard metrics) by as much as 1.42× compared to the results from the default parameters; (iii) attain good scalability on a high performance cluster with several effective optimizations. Our work demonstrates the feasibility of performing sensitivity analyses, parameter studies and auto-tuning with large datasets. The proposed framework can enable the quantification of error estimations and output variations in image segmentation pipelines. Source code: https://github.com/SBU-BMI/region-templates/ . teodoro@unb.br. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Effects of Raindrop Shape Parameter on the Simulation of Plum Rains

NASA Astrophysics Data System (ADS)

Mei, H.; Zhou, L.; Li, X.; Huang, X.; Guo, W.

2017-12-01

The raindrop shape parameter of particle distribution is generally set as constant in a Double-moment Bulk Microphysics Scheme (DBMS) using Gama distribution function though which suggest huge differences in time and space according to observations. Based on Milbrandt 2-mon(MY) DBMS, four cases during Plum Rains season are simulated coupled with four empirical relationships between shape parameter (μr) and slope parameter of raindrop which have been concluded from observations of raindrop distributions. The analysis of model results suggest that μr have some influences on rainfall. Introducing the diagnostic formulas of μr may have some improvement on systematic biases of 24h accumulated rainfall and show some correction ability on local characteristics of rainfall distribution. Besides,the tendency to improve strong rainfall could be sensitive to μr. With the improvement of the diagnosis of μr using the empirically diagnostic formulas, μr increases generally in the middle- and lower-troposphere and decreases with the stronger rainfall. Its conclued that, the decline in raindrop water content and the increased raindrop mass-weighted average terminal velocity directly related to μr are the direct reasons of variations in the precipitation.On the other side, the environmental conditions including relative humidity and dynamical parameters are the key indirectly causes which has close relationships with the changes in cloud particles and rainfall distributions.Furthermore,the differences in the scale of improvement between the weak and heavy rainfall mainly come from the distinctions of response features about their variable fields respectively. The extent of variation in the features of cloud particles in warm clouds of heavy rainfall differs greatly from that of weak rainfall, though they share the same trend of variation. On the conditions of weak rainfall, the response of physical characteristics to μr performed consistent trends and some linear features. However, environmental conditions of relative humidity and dynamical parameters perform strong and vertically deep adjustments in the heavy precipitation with vigorous cloud systems. In this case, the microphysical processes and environmental conditions experience complex interactions with each other and no significant laws could be concluded.

Impact of initial surface parameters on the final quality of laser micro-polished surfaces

NASA Astrophysics Data System (ADS)

Chow, Michael; Bordatchev, Evgueni V.; Knopf, George K.

2012-03-01

Laser micro-polishing (LμP) is a new laser-based microfabrication technology for improving surface quality during a finishing operation and for producing parts and surfaces with near-optical surface quality. The LμP process uses low power laser energy to melt a thin layer of material on the previously machined surface. The polishing effect is achieved as the molten material in the laser-material interaction zone flows from the elevated regions to the local minimum due to surface tension. This flow of molten material then forms a thin ultra-smooth layer on the top surface. The LμP is a complex thermo-dynamic process where the melting, flow and redistribution of molten material is significantly influenced by a variety of process parameters related to the laser, the travel motions and the material. The goal of this study is to analyze the impact of initial surface parameters on the final surface quality. Ball-end micromilling was used for preparing initial surface of samples from H13 tool steel that were polished using a Q-switched Nd:YAG laser. The height and width of micromilled scallops (waviness) were identified as dominant parameter affecting the quality of the LμPed surface. By adjusting process parameters, the Ra value of a surface, having a waviness period of 33 μm and a peak-to-valley value of 5.9 μm, was reduced from 499 nm to 301 nm, improving the final surface quality by 39.7%.

qPIPSA: Relating enzymatic kinetic parameters and interaction fields

PubMed Central

Gabdoulline, Razif R; Stein, Matthias; Wade, Rebecca C

2007-01-01

Background The simulation of metabolic networks in quantitative systems biology requires the assignment of enzymatic kinetic parameters. Experimentally determined values are often not available and therefore computational methods to estimate these parameters are needed. It is possible to use the three-dimensional structure of an enzyme to perform simulations of a reaction and derive kinetic parameters. However, this is computationally demanding and requires detailed knowledge of the enzyme mechanism. We have therefore sought to develop a general, simple and computationally efficient procedure to relate protein structural information to enzymatic kinetic parameters that allows consistency between the kinetic and structural information to be checked and estimation of kinetic constants for structurally and mechanistically similar enzymes. Results We describe qPIPSA: quantitative Protein Interaction Property Similarity Analysis. In this analysis, molecular interaction fields, for example, electrostatic potentials, are computed from the enzyme structures. Differences in molecular interaction fields between enzymes are then related to the ratios of their kinetic parameters. This procedure can be used to estimate unknown kinetic parameters when enzyme structural information is available and kinetic parameters have been measured for related enzymes or were obtained under different conditions. The detailed interaction of the enzyme with substrate or cofactors is not modeled and is assumed to be similar for all the proteins compared. The protein structure modeling protocol employed ensures that differences between models reflect genuine differences between the protein sequences, rather than random fluctuations in protein structure. Conclusion Provided that the experimental conditions and the protein structural models refer to the same protein state or conformation, correlations between interaction fields and kinetic parameters can be established for sets of related enzymes. Outliers may arise due to variation in the importance of different contributions to the kinetic parameters, such as protein stability and conformational changes. The qPIPSA approach can assist in the validation as well as estimation of kinetic parameters, and provide insights into enzyme mechanism. PMID:17919319

Maintaining Supersaturation of Nimodipine by PVP with or without the Presence of Sodium Lauryl Sulfate and Sodium Taurocholate.

PubMed

Pui, Yipshu; Chen, Yuejie; Chen, Huijun; Wang, Shan; Liu, Chengyu; Tonnis, Wouter; Chen, Linc; Serno, Peter; Bracht, Stefan; Qian, Feng

2018-05-30

Amorphous solid dispersion (ASD) is one of the most versatile supersaturating drug delivery systems to improve the dissolution rate and oral bioavailability of poorly water-soluble drugs. PVP based ASD formulation of nimodipine (NMD) has been marketed and effectively used in clinic for nearly 30 years, yet the mechanism by which PVP maintains the supersaturation and subsequently improves the bioavailability of NMD was rarely investigated. In this research, we first studied the molecular interactions between NMD and PVP by solution NMR, using CDCl 3 as the solvent, and the drug-polymer Flory-Huggins interaction parameter. No strong specific interaction between PVP and NMD was detected in the nonaqueous state. However, we observed that aqueous supersaturation of NMD could be significantly maintained by PVP, presumably due to the hydrophobic interactions between the hydrophobic moieties of PVP and NMD in aqueous medium. This hypothesis was supported by dynamic light scattering (DLS) and supersaturation experiments in the presence of different surfactants. DLS revealed the formation of NMD/PVP aggregates when NMD was supersaturated, suggesting the formation of hydrophobic interactions between the drug and polymer. The addition of surfactants, sodium lauryl sulfate (SLS) or sodium taurocholate (NaTC), into PVP maintained that NMD supersaturation demonstrated different effects: SLS could only improve NMD supersaturation with concentration above its critical aggregation concentration (CAC) value while not with lower concentration. Nevertheless, NaTC could prolong NMD supersaturation independent of concentration, with lower concentration outperformed higher concentration. We attribute these observations to PVP-surfactant interactions and the formation of PVP/surfactant complexes. In summary, despite the lack of specific interactions in the nonaqueous state, NMD aqueous supersaturation in the presence of PVP was attained by hydrophobic interactions between the hydrophobic moieties of NMD and PVP. This hydrophobic interaction could be disrupted by surfactants, which interact with PVP competitively, thus hindering the capability of PVP to maintain NMD supersaturation. Therefore, caution is needed when evaluating such ASDs in vitro and in vivo when various surfactants are present either in the formulation or in the surrounding medium.

Improving the hadron physics of non-Standard-Model decays: example bounds on R-parity violation

NASA Astrophysics Data System (ADS)

Daub, J. T.; Dreiner, H. K.; Hanhart, C.; Kubis, B.; Meißner, U.-G.

2013-01-01

Using the example of selected decays driven by R-parity-violating supersymmetric operators, we demonstrate how strong final-state interactions can be controlled quantitatively with high precision, thus allowing for a more accurate extraction of effective parameters from data. In our examples we focus on the lepton-flavor-violating decays τ → μπ + π - . InR-parityviolationthesecanariseduetotheproductoftwocouplings. We find bounds that are an order of magnitude stronger than previous ones.

A designed experiment in stitched/RTM composites

NASA Technical Reports Server (NTRS)

Dickinson, Larry C.

1993-01-01

The damage tolerance of composite laminates can be significantly improved by the addition of through-the-thickness fibrous reinforcement such as stitching. However, there are numerous stitching parameters which can be independently varied, and their separate and combined effects on mechanical properties need to be determined. A statistically designed experiment (a 2(sup 5-1) fractional factorial, also known as a Taguchi L16 test matrix) used to evaluate five important parameters is described. The effects and interactions of stitch thread material, stitch thread strength, stitch row spacing and stitch pitch are examined for both thick (48 ply) and thin (16 ply) carbon/epoxy (AS4/E905L) composites. Tension, compression and compression after impact tests are described. Preliminary results of completed tension testing are discussed. Larger threads decreased tensile strength. Panel thickness was found not to be an important stitching parameter for tensile properties. Tensile modulus was unaffected by stitching.

Conditional High-Order Boltzmann Machines for Supervised Relation Learning.

PubMed

Huang, Yan; Wang, Wei; Wang, Liang; Tan, Tieniu

2017-09-01

Relation learning is a fundamental problem in many vision tasks. Recently, high-order Boltzmann machine and its variants have shown their great potentials in learning various types of data relation in a range of tasks. But most of these models are learned in an unsupervised way, i.e., without using relation class labels, which are not very discriminative for some challenging tasks, e.g., face verification. In this paper, with the goal to perform supervised relation learning, we introduce relation class labels into conventional high-order multiplicative interactions with pairwise input samples, and propose a conditional high-order Boltzmann Machine (CHBM), which can learn to classify the data relation in a binary classification way. To be able to deal with more complex data relation, we develop two improved variants of CHBM: 1) latent CHBM, which jointly performs relation feature learning and classification, by using a set of latent variables to block the pathway from pairwise input samples to output relation labels and 2) gated CHBM, which untangles factors of variation in data relation, by exploiting a set of latent variables to multiplicatively gate the classification of CHBM. To reduce the large number of model parameters generated by the multiplicative interactions, we approximately factorize high-order parameter tensors into multiple matrices. Then, we develop efficient supervised learning algorithms, by first pretraining the models using joint likelihood to provide good parameter initialization, and then finetuning them using conditional likelihood to enhance the discriminant ability. We apply the proposed models to a series of tasks including invariant recognition, face verification, and action similarity labeling. Experimental results demonstrate that by exploiting supervised relation labels, our models can greatly improve the performance.

Density functional theory and molecular dynamics study of the uranyl ion (UO₂)²⁺.

PubMed

Rodríguez-Jeangros, Nicolás; Seminario, Jorge M

2014-03-01

The detection of uranium is very important, especially in water and, more importantly, in the form of uranyl ion (UO₂)²⁺, which is one of its most abundant moieties. Here, we report analyses and simulations of uranyl in water using ab initio modified force fields for water with improved parameters and charges of uranyl. We use a TIP4P model, which allows us to obtain accurate water properties such as the boiling point and the second and third shells of water molecules in the radial distribution function thanks to a fictitious charge that corrects the 3-point models by reproducing the exact dipole moment of the water molecule. We also introduced non-bonded interaction parameters for the water-uranyl intermolecular force field. Special care was taken in testing the effect of a range of uranyl charges on the structure of uranyl-water complexes. Atomic charges of the solvated ion in water were obtained using density functional theory (DFT) calculations taking into account the presence of nitrate ions in the solution, forming a neutral ensemble. DFT-based force fields were calculated in such a way that water properties, such as the boiling point or the pair distribution function stand. Finally, molecular dynamics simulations of a water box containing uranyl cations and nitrate anions are performed at room temperature. The three peaks in the oxygen-oxygen radial distribution function for water were found to be kept in the presence of uranyl thanks to the improvement of interaction parameters and charges. Also, we found three shells of water molecules surrounding the uranyl ion instead of two as was previously thought.

Group contribution methodology based on the statistical associating fluid theory for heteronuclear molecules formed from Mie segments.

PubMed

Papaioannou, Vasileios; Lafitte, Thomas; Avendaño, Carlos; Adjiman, Claire S; Jackson, George; Müller, Erich A; Galindo, Amparo

2014-02-07

A generalization of the recent version of the statistical associating fluid theory for variable range Mie potentials [Lafitte et al., J. Chem. Phys. 139, 154504 (2013)] is formulated within the framework of a group contribution approach (SAFT-γ Mie). Molecules are represented as comprising distinct functional (chemical) groups based on a fused heteronuclear molecular model, where the interactions between segments are described with the Mie (generalized Lennard-Jonesium) potential of variable attractive and repulsive range. A key feature of the new theory is the accurate description of the monomeric group-group interactions by application of a high-temperature perturbation expansion up to third order. The capabilities of the SAFT-γ Mie approach are exemplified by studying the thermodynamic properties of two chemical families, the n-alkanes and the n-alkyl esters, by developing parameters for the methyl, methylene, and carboxylate functional groups (CH3, CH2, and COO). The approach is shown to describe accurately the fluid-phase behavior of the compounds considered with absolute average deviations of 1.20% and 0.42% for the vapor pressure and saturated liquid density, respectively, which represents a clear improvement over other existing SAFT-based group contribution approaches. The use of Mie potentials to describe the group-group interaction is shown to allow accurate simultaneous descriptions of the fluid-phase behavior and second-order thermodynamic derivative properties of the pure fluids based on a single set of group parameters. Furthermore, the application of the perturbation expansion to third order for the description of the reference monomeric fluid improves the predictions of the theory for the fluid-phase behavior of pure components in the near-critical region. The predictive capabilities of the approach stem from its formulation within a group-contribution formalism: predictions of the fluid-phase behavior and thermodynamic derivative properties of compounds not included in the development of group parameters are demonstrated. The performance of the theory is also critically assessed with predictions of the fluid-phase behavior (vapor-liquid and liquid-liquid equilibria) and excess thermodynamic properties of a variety of binary mixtures, including polymer solutions, where very good agreement with the experimental data is seen, without the need for adjustable mixture parameters.

Analytical study on the generalized Davydov model in the alpha helical proteins

NASA Astrophysics Data System (ADS)

Wang, Pan; Xiao, Shu-Hong; Chen, Li; Yang, Gang

2017-06-01

In this paper, we investigate the dynamics of a generalized Davydov model derived from an infinite chain of alpha helical protein molecules which contain three hydrogen bonding spines running almost parallel to the helical axis. Through the introduction of the auxiliary function, the bilinear form, one-, two- and three-soliton solutions for the generalized Davydov model are obtained firstly. Propagation and interactions of solitons have been investigated analytically and graphically. The amplitude of the soliton is only related to the complex parameter μ and real parameter 𝜃 with a range of [0, 2π]. The velocity of the soliton is only related to the complex parameter μ, real parameter 𝜃, lattice parameter 𝜀, and physical parameters β1, β3 and β4. Overtaking and head-on interactions of two and three solitons are presented. The common in the interactions of three solitons is the directions of the solitons change after the interactions. The soliton derived in this paper is expected to have potential applications in the alpha helical proteins.

Parametrization and Benchmark of Long-Range Corrected DFTB2 for Organic Molecules

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

Vuong, Van Quan; Akkarapattiakal Kuriappan, Jissy; Kubillus, Maximilian

In this paper, we present the parametrization and benchmark of long-range corrected second-order density functional tight binding (DFTB), LC-DFTB2, for organic and biological molecules. The LC-DFTB2 model not only improves fundamental orbital energy gaps but also ameliorates the DFT self-interaction error and overpolarization problem, and further improves charge-transfer excited states significantly. Electronic parameters for the construction of the DFTB2 Hamiltonian as well as repulsive potentials were optimized for molecules containing C, H, N, and O chemical elements. We use a semiautomatic parametrization scheme based on a genetic algorithm. With the new parameters, LC-DFTB2 describes geometries and vibrational frequencies of organicmore » molecules similarly well as third-order DFTB3/3OB, the de facto standard parametrization based on a GGA functional. Finally, LC-DFTB2 performs well also for atomization and reaction energies, however, slightly less satisfactorily than DFTB3/3OB.« less

Parametrization and Benchmark of Long-Range Corrected DFTB2 for Organic Molecules

DOE PAGES

Vuong, Van Quan; Akkarapattiakal Kuriappan, Jissy; Kubillus, Maximilian; ...

2017-12-12

In this paper, we present the parametrization and benchmark of long-range corrected second-order density functional tight binding (DFTB), LC-DFTB2, for organic and biological molecules. The LC-DFTB2 model not only improves fundamental orbital energy gaps but also ameliorates the DFT self-interaction error and overpolarization problem, and further improves charge-transfer excited states significantly. Electronic parameters for the construction of the DFTB2 Hamiltonian as well as repulsive potentials were optimized for molecules containing C, H, N, and O chemical elements. We use a semiautomatic parametrization scheme based on a genetic algorithm. With the new parameters, LC-DFTB2 describes geometries and vibrational frequencies of organicmore » molecules similarly well as third-order DFTB3/3OB, the de facto standard parametrization based on a GGA functional. Finally, LC-DFTB2 performs well also for atomization and reaction energies, however, slightly less satisfactorily than DFTB3/3OB.« less

Modeling the Hot Tensile Flow Behaviors at Ultra-High-Strength Steel and Construction of Three-Dimensional Continuous Interaction Space for Forming Parameters

NASA Astrophysics Data System (ADS)

Quan, Guo-zheng; Zhan, Zong-yang; Wang, Tong; Xia, Yu-feng

2017-01-01

The response of true stress to strain rate, temperature and strain is a complex three-dimensional (3D) issue, and the accurate description of such constitutive relationships significantly contributes to the optimum process design. To obtain the true stress-strain data of ultra-high-strength steel, BR1500HS, a series of isothermal hot tensile tests were conducted in a wide temperature range of 973-1,123 K and a strain rate range of 0.01-10 s-1 on a Gleeble 3800 testing machine. Then the constitutive relationships were modeled by an optimally constructed and well-trained backpropagation artificial neural network (BP-ANN). The evaluation of BP-ANN model revealed that it has admirable performance in characterizing and predicting the flow behaviors of BR1500HS. A comparison on improved Arrhenius-type constitutive equation and BP-ANN model shows that the latter has higher accuracy. Consequently, the developed BP-ANN model was used to predict abundant stress-strain data beyond the limited experimental conditions. Then a 3D continuous interaction space for temperature, strain rate, strain and stress was constructed based on these predicted data. The developed 3D continuous interaction space for hot working parameters contributes to fully revealing the intrinsic relationships of BR1500HS steel.

Identifying key sources of uncertainty in the modelling of greenhouse gas emissions from wastewater treatment.

PubMed

Sweetapple, Christine; Fu, Guangtao; Butler, David

2013-09-01

This study investigates sources of uncertainty in the modelling of greenhouse gas emissions from wastewater treatment, through the use of local and global sensitivity analysis tools, and contributes to an in-depth understanding of wastewater treatment modelling by revealing critical parameters and parameter interactions. One-factor-at-a-time sensitivity analysis is used to screen model parameters and identify those with significant individual effects on three performance indicators: total greenhouse gas emissions, effluent quality and operational cost. Sobol's method enables identification of parameters with significant higher order effects and of particular parameter pairs to which model outputs are sensitive. Use of a variance-based global sensitivity analysis tool to investigate parameter interactions enables identification of important parameters not revealed in one-factor-at-a-time sensitivity analysis. These interaction effects have not been considered in previous studies and thus provide a better understanding wastewater treatment plant model characterisation. It was found that uncertainty in modelled nitrous oxide emissions is the primary contributor to uncertainty in total greenhouse gas emissions, due largely to the interaction effects of three nitrogen conversion modelling parameters. The higher order effects of these parameters are also shown to be a key source of uncertainty in effluent quality. Copyright © 2013 Elsevier Ltd. All rights reserved.

Transient Inverse Calibration of Site-Wide Groundwater Model to Hanford Operational Impacts from 1943 to 1996--Alternative Conceptual Model Considering Interaction with Uppermost Basalt Confined Aquifer

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

Vermeul, Vincent R.; Cole, Charles R.; Bergeron, Marcel P.

2001-08-29

The baseline three-dimensional transient inverse model for the estimation of site-wide scale flow parameters, including their uncertainties, using data on the transient behavior of the unconfined aquifer system over the entire historical period of Hanford operations, has been modified to account for the effects of basalt intercommunication between the Hanford unconfined aquifer and the underlying upper basalt confined aquifer. Both the baseline and alternative conceptual models (ACM-1) considered only the groundwater flow component and corresponding observational data in the 3-Dl transient inverse calibration efforts. Subsequent efforts will examine both groundwater flow and transport. Comparisons of goodness of fit measures andmore » parameter estimation results for the ACM-1 transient inverse calibrated model with those from previous site-wide groundwater modeling efforts illustrate that the new 3-D transient inverse model approach will strengthen the technical defensibility of the final model(s) and provide the ability to incorporate uncertainty in predictions related to both conceptual model and parameter uncertainty. These results, however, indicate that additional improvements are required to the conceptual model framework. An investigation was initiated at the end of this basalt inverse modeling effort to determine whether facies-based zonation would improve specific yield parameter estimation results (ACM-2). A description of the justification and methodology to develop this zonation is discussed.« less

Effects of simvastatin, ezetimibe and simvastatin/ezetimibe on mitochondrial function and leukocyte/endothelial cell interactions in patients with hypercholesterolemia.

PubMed

Hernandez-Mijares, Antonio; Bañuls, Celia; Rovira-Llopis, Susana; Diaz-Morales, Noelia; Escribano-Lopez, Irene; de Pablo, Carmen; Alvarez, Angeles; Veses, Silvia; Rocha, Milagros; Victor, Victor M

2016-04-01

Cholesterol-lowering therapy has been related with several beneficial effects; however, its influence on oxidative stress and endothelial function is not fully elucidated. To investigate the effect of simvastatin and ezetimibe on mitochondrial function and leukocyte-endothelium interactions in polymorphonuclear cells of hyperlipidemic patients. Thirty-nine hyperlipidemic patients were randomly assigned to one of two groups: one received simvastatin (40 mg/day) and the other received ezetimibe (10 mg/day) for 4 weeks, after which both groups were administered combined therapy for an additional 4-week period. Lipid profile, mitochondrial parameters (oxygen consumption, reactive oxygen species (ROS) and membrane potential), glutathione levels, superoxide dismutase activity, catalase activity and leukocyte/endothelial cell interactions and adhesion molecules -VCAM-1, ICAM-1, E-selectin, were evaluated. An improvement in lipid profile was observed after administration of simvastatin or ezetimibe alone (LDLc: -40.2 vs -19.6%, respectively), though this effect was stronger with the former (p < 0.001), and a further reduction was registered when the two were combined (LDLc: -50.7% vs -56.8%, respectively). In addition to this, simvastatin, ezetimibe and simvastatin + ezetimibe significantly increased oxygen consumption, membrane potential and glutathione content, and decreased levels of ROS, thereby improving mitochondrial function. Furthermore, simvastatin + ezetimibe increased catalase activity. In addition, simvastatin and simvastatin/ezetimibe improved leukocyte/endothelium interactions by decreasing leukocyte rolling and adhesion and increasing leukocyte rolling velocity. Finally, simvastatin, ezetimibe and simvastatin + ezetimibe reduced levels of the adhesion molecule ICAM-1, and ezetimibe + simvastatin significantly decreased levels of E-selectin. Co-administration of simvastatin and ezetimibe has an additive cholesterol-lowering effect and beneficial consequences for mitochondrial function and leukocyte/endothelium interactions in leukocytes of hypercholesterolemic patients. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Machine learning action parameters in lattice quantum chromodynamics

NASA Astrophysics Data System (ADS)

Shanahan, Phiala E.; Trewartha, Daniel; Detmold, William

2018-05-01

Numerical lattice quantum chromodynamics studies of the strong interaction are important in many aspects of particle and nuclear physics. Such studies require significant computing resources to undertake. A number of proposed methods promise improved efficiency of lattice calculations, and access to regions of parameter space that are currently computationally intractable, via multi-scale action-matching approaches that necessitate parametric regression of generated lattice datasets. The applicability of machine learning to this regression task is investigated, with deep neural networks found to provide an efficient solution even in cases where approaches such as principal component analysis fail. The high information content and complex symmetries inherent in lattice QCD datasets require custom neural network layers to be introduced and present opportunities for further development.

Groundwater budgets for Detrital, Hualapai, and Sacramento Valleys, Mohave County, Arizona, 2007-08

USGS Publications Warehouse

Garner, Bradley D.; Truini, Margot

2011-01-01

Figures 9, 10, and 11 from this report present water budgets for Detritial, Hualapai, and Sacramento Valleys in Northwestern Arizona. These figures show average values for each water-budget component. Uncertainty is discussed but not shown on these report figures. As an aid to readers, these figures have been implemented as interactive, web-based figures here. Water-budget parameters can be varied within reasonable bounds of uncertainty and the effects those changes have on the water budget will be shown as they are varied. This can aid in understanding sensitivity-which parameters most or least affect the water budgets-and also could provide a generally improved sense of the hydrologic cycle represented in these water budgets.

Development of a real-time clinical decision support system upon the web mvc-based architecture for prostate cancer treatment

PubMed Central

2011-01-01

Background A real-time clinical decision support system (RTCDSS) with interactive diagrams enables clinicians to instantly and efficiently track patients' clinical records (PCRs) and improve their quality of clinical care. We propose a RTCDSS to process online clinical informatics from multiple databases for clinical decision making in the treatment of prostate cancer based on Web Model-View-Controller (MVC) architecture, by which the system can easily be adapted to different diseases and applications. Methods We designed a framework upon the Web MVC-based architecture in which the reusable and extractable models can be conveniently adapted to other hospital information systems and which allows for efficient database integration. Then, we determined the clinical variables of the prostate cancer treatment based on participating clinicians' opinions and developed a computational model to determine the pretreatment parameters. Furthermore, the components of the RTCDSS integrated PCRs and decision factors for real-time analysis to provide evidence-based diagrams upon the clinician-oriented interface for visualization of treatment guidance and health risk assessment. Results The resulting system can improve quality of clinical treatment by allowing clinicians to concurrently analyze and evaluate the clinical markers of prostate cancer patients with instantaneous clinical data and evidence-based diagrams which can automatically identify pretreatment parameters. Moreover, the proposed RTCDSS can aid interactions between patients and clinicians. Conclusions Our proposed framework supports online clinical informatics, evaluates treatment risks, offers interactive guidance, and provides real-time reference for decision making in the treatment of prostate cancer. The developed clinician-oriented interface can assist clinicians in conveniently presenting evidence-based information to patients and can be readily adapted to an existing hospital information system and be easily applied in other chronic diseases. PMID:21385459

Text Mining Effectively Scores and Ranks the Literature for Improving Chemical-Gene-Disease Curation at the Comparative Toxicogenomics Database

PubMed Central

Johnson, Robin J.; Lay, Jean M.; Lennon-Hopkins, Kelley; Saraceni-Richards, Cynthia; Sciaky, Daniela; Murphy, Cynthia Grondin; Mattingly, Carolyn J.

2013-01-01

The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) is a public resource that curates interactions between environmental chemicals and gene products, and their relationships to diseases, as a means of understanding the effects of environmental chemicals on human health. CTD provides a triad of core information in the form of chemical-gene, chemical-disease, and gene-disease interactions that are manually curated from scientific articles. To increase the efficiency, productivity, and data coverage of manual curation, we have leveraged text mining to help rank and prioritize the triaged literature. Here, we describe our text-mining process that computes and assigns each article a document relevancy score (DRS), wherein a high DRS suggests that an article is more likely to be relevant for curation at CTD. We evaluated our process by first text mining a corpus of 14,904 articles triaged for seven heavy metals (cadmium, cobalt, copper, lead, manganese, mercury, and nickel). Based upon initial analysis, a representative subset corpus of 3,583 articles was then selected from the 14,094 articles and sent to five CTD biocurators for review. The resulting curation of these 3,583 articles was analyzed for a variety of parameters, including article relevancy, novel data content, interaction yield rate, mean average precision, and biological and toxicological interpretability. We show that for all measured parameters, the DRS is an effective indicator for scoring and improving the ranking of literature for the curation of chemical-gene-disease information at CTD. Here, we demonstrate how fully incorporating text mining-based DRS scoring into our curation pipeline enhances manual curation by prioritizing more relevant articles, thereby increasing data content, productivity, and efficiency. PMID:23613709

Development of a real-time clinical decision support system upon the Web MVC-based architecture for prostate cancer treatment.

PubMed

Lin, Hsueh-Chun; Wu, Hsi-Chin; Chang, Chih-Hung; Li, Tsai-Chung; Liang, Wen-Miin; Wang, Jong-Yi Wang

2011-03-08

A real-time clinical decision support system (RTCDSS) with interactive diagrams enables clinicians to instantly and efficiently track patients' clinical records (PCRs) and improve their quality of clinical care. We propose a RTCDSS to process online clinical informatics from multiple databases for clinical decision making in the treatment of prostate cancer based on Web Model-View-Controller (MVC) architecture, by which the system can easily be adapted to different diseases and applications. We designed a framework upon the Web MVC-based architecture in which the reusable and extractable models can be conveniently adapted to other hospital information systems and which allows for efficient database integration. Then, we determined the clinical variables of the prostate cancer treatment based on participating clinicians' opinions and developed a computational model to determine the pretreatment parameters. Furthermore, the components of the RTCDSS integrated PCRs and decision factors for real-time analysis to provide evidence-based diagrams upon the clinician-oriented interface for visualization of treatment guidance and health risk assessment. The resulting system can improve quality of clinical treatment by allowing clinicians to concurrently analyze and evaluate the clinical markers of prostate cancer patients with instantaneous clinical data and evidence-based diagrams which can automatically identify pretreatment parameters. Moreover, the proposed RTCDSS can aid interactions between patients and clinicians. Our proposed framework supports online clinical informatics, evaluates treatment risks, offers interactive guidance, and provides real-time reference for decision making in the treatment of prostate cancer. The developed clinician-oriented interface can assist clinicians in conveniently presenting evidence-based information to patients and can be readily adapted to an existing hospital information system and be easily applied in other chronic diseases.

Interspecies interactions are an integral determinant of microbial community dynamics

PubMed Central

Aziz, Fatma A. A.; Suzuki, Kenshi; Ohtaki, Akihiro; Sagegami, Keita; Hirai, Hidetaka; Seno, Jun; Mizuno, Naoko; Inuzuka, Yuma; Saito, Yasuhisa; Tashiro, Yosuke; Hiraishi, Akira; Futamata, Hiroyuki

2015-01-01

This study investigated the factors that determine the dynamics of bacterial communities in a complex system using multidisciplinary methods. Since natural and engineered microbial ecosystems are too complex to study, six types of synthetic microbial ecosystems (SMEs) were constructed under chemostat conditions with phenol as the sole carbon and energy source. Two to four phenol-degrading, phylogenetically and physiologically different bacterial strains were used in each SME. Phylogeny was based on the nucleotide sequence of 16S rRNA genes, while physiologic traits were based on kinetic and growth parameters on phenol. Two indices, J parameter and “interspecies interaction,” were compared to predict which strain would become dominant in an SME. The J parameter was calculated from kinetic and growth parameters. On the other hand, “interspecies interaction,” a new index proposed in this study, was evaluated by measuring the specific growth activity, which was determined on the basis of relative growth of a strain with or without the supernatant prepared from other bacterial cultures. Population densities of strains used in SMEs were enumerated by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase and were compared to predictions made from J parameter and interspecies interaction calculations. In 4 of 6 SEMs tested the final dominant strain shown by real-time qPCR analyses coincided with the strain predicted by both the J parameter and the interspecies interaction. However, in SMEII-2 and SMEII-3 the final dominant Variovorax strains coincided with prediction of the interspecies interaction but not the J parameter. These results demonstrate that the effects of interspecies interactions within microbial communities contribute to determining the dynamics of the microbial ecosystem. PMID:26539177

On unravelling mechanism of interplay between cloud and large scale circulation: a grey area in climate science

NASA Astrophysics Data System (ADS)

De, S.; Agarwal, N. K.; Hazra, Anupam; Chaudhari, Hemantkumar S.; Sahai, A. K.

2018-04-01

The interaction between cloud and large scale circulation is much less explored area in climate science. Unfolding the mechanism of coupling between these two parameters is imperative for improved simulation of Indian summer monsoon (ISM) and to reduce imprecision in climate sensitivity of global climate model. This work has made an effort to explore this mechanism with CFSv2 climate model experiments whose cloud has been modified by changing the critical relative humidity (CRH) profile of model during ISM. Study reveals that the variable CRH in CFSv2 has improved the nonlinear interactions between high and low frequency oscillations in wind field (revealed as internal dynamics of monsoon) and modulates realistically the spatial distribution of interactions over Indian landmass during the contrasting monsoon season compared to the existing CRH profile of CFSv2. The lower tropospheric wind error energy in the variable CRH simulation of CFSv2 appears to be minimum due to the reduced nonlinear convergence of error to the planetary scale range from long and synoptic scales (another facet of internal dynamics) compared to as observed from other CRH experiments in normal and deficient monsoons. Hence, the interplay between cloud and large scale circulation through CRH may be manifested as a change in internal dynamics of ISM revealed from scale interactive quasi-linear and nonlinear kinetic energy exchanges in frequency as well as in wavenumber domain during the monsoon period that eventually modify the internal variance of CFSv2 model. Conversely, the reduced wind bias and proper modulation of spatial distribution of scale interaction between the synoptic and low frequency oscillations improve the eastward and northward extent of water vapour flux over Indian landmass that in turn give feedback to the realistic simulation of cloud condensates attributing improved ISM rainfall in CFSv2.

Systematic study of rapidity dispersion parameter in high energy nucleus-nucleus interactions

NASA Astrophysics Data System (ADS)

Bhattacharyya, Swarnapratim; Haiduc, Maria; Neagu, Alina Tania; Firu, Elena

2014-03-01

A systematic study of rapidity dispersion parameter as a quantitative measure of clustering of particles has been carried out in the interactions of 16O, 28Si and 32S projectiles at 4.5 A GeV/c with heavy (AgBr) and light (CNO) groups of targets present in the nuclear emulsion. For all the interactions, the total ensemble of events has been divided into four overlapping multiplicity classes depending on the number of shower particles. For all the interactions and for each multiplicity class, the rapidity dispersion parameter values indicate the occurrence of clusterization during the multiparticle production at Dubna energy. The measured rapidity dispersion parameter values are found to decrease with the increase of average multiplicity for all the interactions. The dependence of rapidity dispersion parameter on the average multiplicity can be successfully described by a relation D(η) = a + b + c2. The experimental results have been compared with the results obtained from the analysis of Monte Carlo simulated (MC-RAND) events. MC-RAND events show weaker clusterization among the pions in comparison to the experimental data.

Evaluation of the simultaneous effects of processing parameters on the iron and zinc solubility of infant sorghum porridge by response surface methodology.

PubMed

Kayodé, A P Polycarpe; Nout, Martinus J R; Bakker, Evert J; Van Boekel, Martinus A J S

2006-06-14

The purpose of this study was to improve the micronutrient quality of indigenous African infant flour using traditional techniques available in the region. Response surface methodology was used to study the effect of duration of soaking, germination, and fermentation on phytate and phenolic compounds (PC), pH, viscosity, and the in vitro solubility (IVS) of iron and zinc in infant sorghum flour. The phytate and the PC concentrations of the flour were significantly modified as a result of the duration of germination and fermentation and their mutual interaction. These modifications were accompanied by a significant increase in % IVS Zn after 24 h of sprouting. Except for the interaction of soaking and fermentation, none of the processing parameters exerted a significant effect on the % IVS Fe. The viscosity of the porridge prepared with the flour decreased significantly with the duration of germination, making it possible to produce a porridge with high energy and nutrient density. The use of germination in combination with fermentation is recommended in the processing of cereals for infant feeding in developing countries.

Correlation of experimentally measured atomic scale properties of EUV photoresist to modeling performance: an exploration

NASA Astrophysics Data System (ADS)

Kandel, Yudhishthir; Chandonait, Jonathan; Melvin, Lawrence S.; Marokkey, Sajan; Yan, Qiliang; Grzeskowiak, Steven; Painter, Benjamin; Denbeaux, Gregory

2017-03-01

Extreme ultraviolet (EUV) lithography at 13.5 nm stands at the crossroads of next generation patterning technology for high volume manufacturing of integrated circuits. Photo resist models that form the part of overall pattern transform model for lithography play a vital role in supporting this effort. The physics and chemistry of these resists must be understood to enable the construction of accurate models for EUV Optical Proximity Correction (OPC). In this study, we explore the possibility of improving EUV photo-resist models by directly correlating the parameters obtained from experimentally measured atomic scale physical properties; namely, the effect of interaction of EUV photons with photo acid generators in standard chemically amplified EUV photoresist, and associated electron energy loss events. Atomic scale physical properties will be inferred from the measurements carried out in Electron Resist Interaction Chamber (ERIC). This study will use measured physical parameters to establish a relationship with lithographically important properties, such as line edge roughness and CD variation. The data gathered from these measurements is used to construct OPC models of the resist.

Interaction of femtosecond laser pulses with plants: towards distinguishing weeds and crops using plasma temperature

NASA Astrophysics Data System (ADS)

Kunz, Jeremy N.; Voronine, Dmitri V.; Ko, Brian A.; Lee, Ho Wai Howard; Rana, Aman; Bagavathiannan, Muthukumar V.; Sokolov, Alexei V.; Scully, Marlan O.

2017-05-01

The ability to distinguish between crops and weeds using sensors from a distance will greatly benefit the farming community through improved and efficient scouting for weeds, reduced herbicide input costs and improved profitability. In the present study, we examined the utility of femtosecond laser-induced breakdown spectroscopy (LIBS) for plant species differentiation. Greenhouse-grown plants of dallisgrass, wheat, soybean and bell pepper were evaluated using LIBS under an ambient environment. LIBS experiments were performed on the leaf samples of different plant species using a femtosecond laser system with an inexpensive lightweight detector. Temperatures of laser-induced plasma in plants depend on many parameters and were determined for each of the study species by the constituent elements interacting with femtosecond laser pulses. Using elemental calcium transitions in plant tissue samples to measure plasma temperatures, we report consistent differences among the four study species, with average values ranging from 5090 ± 168 K (soybean) to 5647 ± 223 K (dallisgrass).

Quantum metrology and estimation of Unruh effect

PubMed Central

Wang, Jieci; Tian, Zehua; Jing, Jiliang; Fan, Heng

2014-01-01

We study the quantum metrology for a pair of entangled Unruh-Dewitt detectors when one of them is accelerated and coupled to a massless scalar field. Comparing with previous schemes, our model requires only local interaction and avoids the use of cavities in the probe state preparation process. We show that the probe state preparation and the interaction between the accelerated detector and the external field have significant effects on the value of quantum Fisher information, correspondingly pose variable ultimate limit of precision in the estimation of Unruh effect. We find that the precision of the estimation can be improved by a larger effective coupling strength and a longer interaction time. Alternatively, the energy gap of the detector has a range that can provide us a better precision. Thus we may adjust those parameters and attain a higher precision in the estimation. We also find that an extremely high acceleration is not required in the quantum metrology process. PMID:25424772

The improvement of the effectiveness of using natural gas in hot-water boilers by means of condensing economizers

NASA Astrophysics Data System (ADS)

Vnukov, A. K.; Rozanova, F. A.

2013-07-01

The paper describes the results of the study of the mathematical model of a condensing economizer (CE) interacting with the technological parameter of the particular district heating station. This model has been developed by the authors. It is shown that the CE, due to condensation of water vapor and augmentation of convective heat exchange between products of natural gas combustion, makes it possible to save up to 8% of fuel.

New procedure for the determination of Hansen solubility parameters by means of inverse gas chromatography.

PubMed

Adamska, K; Bellinghausen, R; Voelkel, A

2008-06-27

The Hansen solubility parameter (HSP) seems to be a useful tool for the thermodynamic characterization of different materials. Unfortunately, estimation of the HSP values can cause some problems. In this work different procedures by using inverse gas chromatography have been presented for calculation of pharmaceutical excipients' solubility parameter. The new procedure proposed, based on the Lindvig et al. methodology, where experimental data of Flory-Huggins interaction parameter are used, can be a reasonable alternative for the estimation of HSP values. The advantage of this method is that the values of Flory-Huggins interaction parameter chi for all test solutes are used for further calculation, thus diverse interactions between test solute and material are taken into consideration.

Mesoscale mechanics of twisting carbon nanotube yarns.

PubMed

Mirzaeifar, Reza; Qin, Zhao; Buehler, Markus J

2015-03-12

Fabricating continuous macroscopic carbon nanotube (CNT) yarns with mechanical properties close to individual CNTs remains a major challenge. Spinning CNT fibers and ribbons for enhancing the weak interactions between the nanotubes is a simple and efficient method for fabricating high-strength and tough continuous yarns. Here we investigate the mesoscale mechanics of twisting CNT yarns using full atomistic and coarse grained molecular dynamics simulations, considering concurrent mechanisms at multiple length-scales. To investigate the mechanical response of such a complex structure without losing insights into the molecular mechanism, we applied a multiscale strategy. The full atomistic results are used for training a coarse grained model for studying larger systems consisting of several CNTs. The mesoscopic model parameters are updated as a function of the twist angle, based on the full atomistic results, in order to incorporate the atomistic scale deformation mechanisms in larger scale simulations. By bridging across two length scales, our model is capable of accurately predicting the mechanical behavior of twisted yarns while the atomistic level deformations in individual nanotubes are integrated into the model by updating the parameters. Our results focused on studying a bundle of close packed nanotubes provide novel mechanistic insights into the spinning of CNTs. Our simulations reveal how twisting a bundle of CNTs improves the shear interaction between the nanotubes up to a certain level due to increasing the interaction surface. Furthermore, twisting the bundle weakens the intertube interactions due to excessive deformation in the cross sections of individual CNTs in the bundle.

Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications

PubMed Central

2015-01-01

We report the parametrization of the approximate density functional tight binding method, DFTB3, for sulfur and phosphorus. The parametrization is done in a framework consistent with our previous 3OB set established for O, N, C, and H, thus the resulting parameters can be used to describe a broad set of organic and biologically relevant molecules. The 3d orbitals are included in the parametrization, and the electronic parameters are chosen to minimize errors in the atomization energies. The parameters are tested using a fairly diverse set of molecules of biological relevance, focusing on the geometries, reaction energies, proton affinities, and hydrogen bonding interactions of these molecules; vibrational frequencies are also examined, although less systematically. The results of DFTB3/3OB are compared to those from DFT (B3LYP and PBE), ab initio (MP2, G3B3), and several popular semiempirical methods (PM6 and PDDG), as well as predictions of DFTB3 with the older parametrization (the MIO set). In general, DFTB3/3OB is a major improvement over the previous parametrization (DFTB3/MIO), and for the majority cases tested here, it also outperforms PM6 and PDDG, especially for structural properties, vibrational frequencies, hydrogen bonding interactions, and proton affinities. For reaction energies, DFTB3/3OB exhibits major improvement over DFTB3/MIO, due mainly to significant reduction of errors in atomization energies; compared to PM6 and PDDG, DFTB3/3OB also generally performs better, although the magnitude of improvement is more modest. Compared to high-level calculations, DFTB3/3OB is most successful at predicting geometries; larger errors are found in the energies, although the results can be greatly improved by computing single point energies at a high level with DFTB3 geometries. There are several remaining issues with the DFTB3/3OB approach, most notably its difficulty in describing phosphate hydrolysis reactions involving a change in the coordination number of the phosphorus, for which a specific parametrization (3OB/OPhyd) is developed as a temporary solution; this suggests that the current DFTB3 methodology has limited transferability for complex phosphorus chemistry at the level of accuracy required for detailed mechanistic investigations. Therefore, fundamental improvements in the DFTB3 methodology are needed for a reliable method that describes phosphorus chemistry without ad hoc parameters. Nevertheless, DFTB3/3OB is expected to be a competitive QM method in QM/MM calculations for studying phosphorus/sulfur chemistry in condensed phase systems, especially as a low-level method that drives the sampling in a dual-level QM/MM framework. PMID:24803865

Evaluation of helicopter noise due to b blade-vortex interaction for five tip configurations. [conducted in the Langley V/STOL tunnel

NASA Technical Reports Server (NTRS)

Hoad, D. R.

1979-01-01

The effect of tip shape modification on blade vortex interaction induced helicopter blade slap noise was investigated. Simulated flight and descent velocities which have been shown to produce blade slap were tested. Aerodynamic performance parameters of the rotor system were monitored to ensure properly matched flight conditions among the tip shapes. The tunnel was operated in the open throat configuration with treatment to improve the acoustic characteristics of the test chamber. Four promising tips were used along with a standard square tip as a baseline configuration. A detailed acoustic evaluation on the same rotor system of the relative applicability of the various tip configurations for blade slap noise reduction is provided.

Control of Screening of a Charged Particle in Electrolytic Aqueous Paul Trap

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

Park, Jae Hyun nmn; Krstic, Predrag S

2011-01-01

Individual charged particles could be trapped and confined in the combined radio-frequency and DC quadrupole electric field of an aqueous Paul trap. Viscosity of water improves confinement and extends the range of the trap parameters which characterize the stability of the trap. Electrolyte, if present in aqueous solution, may screen the charged particle and thus partially or fully suppress electrophoretic interaction with the applied filed, possibly reducing it to a generally much weaker dielectrophoretic interaction with an induced dipole. Applying molecular dynamics simulation we show that the quadrupole field has a different affects at the electrolyte ions and at muchmore » heavier charged particle, effectively eliminating the screening effect and reinstating the electrophoretic confinement.« less

Control Of Screening Of A Charged Particle In Electrolytic Aqueous Paul Trap

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

Park, Jae Hyun; Krstic, Predrag S.

2011-06-01

Individual charged particles could be trapped and confined by the combined radio-frequency and DC quadrupole electric field of an aqueous Paul trap. Viscosity of water improves confinement and extends the range of the trap parameters which characterize the stability of the trap. Electrolyte, if present in aqueous solution, may screen the charged particle and thus partially or fully suppress electrophoretic interaction with the applied filed, possibly reducing it to a generally much weaker dielectrophoretic interaction with an induced dipole. Applying molecular dynamics simulation we show that the quadrupole field has a different effect at the electrolyte ions and at muchmore » heavier charged particle, effectively eliminating the screening by electrolyte ions and reinstating the electrophoretic confinement.« less

The interaction between foliar GA3 application and arbuscular mycorrhizal fungi inoculation improves growth in salinized tomato (Solanum lycopersicum L.) plants by modifying the hormonal balance.

PubMed

Khalloufi, Mouna; Martínez-Andújar, Cristina; Lachaâl, Mokhtar; Karray-Bouraoui, Najoua; Pérez-Alfocea, Francisco; Albacete, Alfonso

2017-07-01

The agriculture industry is frequently affected by various abiotic stresses limiting plant productivity. To decrease the negative effect of salinity and improve growth performance, some strategies have been used, such as exogenous application of plant growth regulators (i.e. gibberellic acid, GA 3 ), or arbuscular mycorrhizal fungi (AMF) inoculation. To gain insights about the cross-talk effect of exogenous GA 3 application and AMF inoculation on growth under salinity conditions, tomato plants (Solanum lycopersicum, cv. TT-115) were inoculated or not with the AMF Rhizophagus irregularis and exposed to different treatments during two weeks: 0M GA 3 +0mM NaCl, 10 -6 M GA 3 +0mM NaCl, 0M GA 3 +100mM NaCl and 10 -6 M GA 3 +100mM NaCl. Results have revealed that AMF inoculation or GA 3 application alone, but especially their interaction, resulted in growth improvement under salinity conditions. The growth improvement observed in AMF-inoculated tomato plants under salinity conditions was mainly associated to ionic factors (higherK concentration and K/Na ratio) while the alleviating effect of GA 3 application and its interaction with AMF appear to be due to changes in the hormonal balance. Foliar GA 3 application was found to increase the active gibberellins (GAs), resulting in a positive correlation between GA 3 and the growth-related parameters. Furthermore, cytokinins, indoleacetic acid and abscisic acid concentrations increased in AMF inoculated or GA 3 treated plants but, notably, in AMF plants treated with GA 3 , which showed improved growth under salinity conditions. This suggests that there is an interactive positive effect between GAs and AMF which alleviates growth impairment under salinity conditions by modifying the hormonal balance of the plant. Copyright © 2017 Elsevier GmbH. All rights reserved.

Genotype × environment interaction analysis of North American shrub willow yield trials confirms superior performance of triploid hybrids

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

Fabio, Eric S.; Volk, Timothy A.; Miller, Raymond O.

Development of dedicated bioenergy crop production systems will require accurate yield estimates, which will be important for determining many of the associated environmental and economic impacts of their production. Shrub willow (Salix spp) is being promoted in areas of the USA and Canada due to its adaption to cool climates and wide genetic diversity available for breeding improvement. Willow breeding in North America is in an early stage, and selection of elite genotypes for commercialization will require testing across broad geographic regions to gain an understanding of how shrub willow interacts with the environment. We analyzed a dataset of first-rotationmore » shrub willow yields of 16 genotypes across 10 trial environments in the USA and Canada for genotype-by-environment interactions using the additive main effects and multiplicative interactions (AMMI) model. Mean genotype yields ranged from 5.22 to 8.58 oven-dry Mg ha -1 yr -1. Analysis of the main effect of genotype showed that one round of breeding improved yields by as much as 20% over check cultivars and that triploid hybrids, most notably Salix viminalis × S. miyabeana, exhibited superior yields. We also found important variability in genotypic response to environments, which suggests specific adaptability could be exploited among 16 genotypes for yield gains. Strong positive correlations were found between environment main effects and AMMI parameters and growing environment temperatures. These findings demonstrate yield improvements are possible in one generation and will be important for developing cultivar recommendations and for future breeding efforts.« less

Genotype × environment interaction analysis of North American shrub willow yield trials confirms superior performance of triploid hybrids

DOE PAGES

Fabio, Eric S.; Volk, Timothy A.; Miller, Raymond O.; ...

2016-01-30

Development of dedicated bioenergy crop production systems will require accurate yield estimates, which will be important for determining many of the associated environmental and economic impacts of their production. Shrub willow (Salix spp) is being promoted in areas of the USA and Canada due to its adaption to cool climates and wide genetic diversity available for breeding improvement. Willow breeding in North America is in an early stage, and selection of elite genotypes for commercialization will require testing across broad geographic regions to gain an understanding of how shrub willow interacts with the environment. We analyzed a dataset of first-rotationmore » shrub willow yields of 16 genotypes across 10 trial environments in the USA and Canada for genotype-by-environment interactions using the additive main effects and multiplicative interactions (AMMI) model. Mean genotype yields ranged from 5.22 to 8.58 oven-dry Mg ha -1 yr -1. Analysis of the main effect of genotype showed that one round of breeding improved yields by as much as 20% over check cultivars and that triploid hybrids, most notably Salix viminalis × S. miyabeana, exhibited superior yields. We also found important variability in genotypic response to environments, which suggests specific adaptability could be exploited among 16 genotypes for yield gains. Strong positive correlations were found between environment main effects and AMMI parameters and growing environment temperatures. These findings demonstrate yield improvements are possible in one generation and will be important for developing cultivar recommendations and for future breeding efforts.« less

Environmental enrichment and social interaction improve cognitive function and decrease reactive oxidative species in normal adult mice.

PubMed

Doulames, Vanessa; Lee, Sangmook; Shea, Thomas B

2014-05-01

Environmental stimulation and increased social interactions stimulate cognitive performance, while decrease in these parameters can exacerbate cognitive decline as a function of illness, injury, or age. We examined the impact of environmental stimulation and social interactions on cognitive performance in healthy adult C57B1/6J mice. Mice were housed for 1 month individually or in groups of three (to prevent or allow social interaction) in either a standard environment (SE) or an enlarged cage containing nesting material and items classically utilized to stimulate exploration and activity ("enriched environment"; EE). Cognitive performance was tested by Y maze navigation and Novel Object Recognition (NOR; which compares the relative amount of time mice spent investigating a novel vs. a familiar object). Mice maintained for 1 month under isolated conditions in the SE statistically declined in performance versus baseline in the Y maze (p < 0.02; ANOVA). Performance under all other conditions did not change from baseline. Maintenance in groups in the SE statistically improved NOR (p < 0.01), whereas maintenance in isolation in the SE did not alter performance from baseline. Maintenance in the EE statistically improved performance in NOR for mice housed in groups and individually (p < 0.01). Maintenance under isolated conditions slightly increased reactive oxygen/nitrogen species (ROS/RNS) in brain. Environmental enrichment did not influence ROS/RNS. These findings indicate that environmental and social enrichment can positively influence cognitive performance in healthy adult mice, and support the notion that proactive approaches may delay age-related cognitive decline.

Equations of state for real gases on the nuclear scale

NASA Astrophysics Data System (ADS)

Vovchenko, Volodymyr

2017-07-01

The formalism to augment the classical models of the equation of state for real gases with quantum statistical effects is presented. It allows an arbitrary excluded volume procedure to model repulsive interactions, and an arbitrary density-dependent mean field to model attractive interactions. Variations on the excluded volume mechanism include van der Waals (VDW) and Carnahan-Starling models, while the mean fields are based on VDW, Redlich-Kwong-Soave, Peng-Robinson, and Clausius equations of state. The VDW parameters of the nucleon-nucleon interaction are fitted in each model to the properties of the ground state of nuclear matter, and the following range of values is obtained: a =330 -430 MeV fm3 and b =2.5 -4.4 fm3 . In the context of the excluded volume approach, the fits to the nuclear ground state disfavor the values of the effective hard-core radius of a nucleon significantly smaller than 0.5 fm , at least for the nuclear matter region of the phase diagram. Modifications to the standard VDW repulsion and attraction terms allow one to improve significantly the value of the nuclear incompressibility factor K0, bringing it closer to empirical estimates. The generalization to include the baryon-baryon interactions into the hadron resonance gas model is performed. The behavior of the baryon-related lattice QCD observables at zero chemical potential is shown to be strongly correlated to the nuclear matter properties: an improved description of the nuclear incompressibility also yields an improved description of the lattice data at μ =0 .

Antagonistic and synergistic interactions among predators.

PubMed

Huxel, Gary R

2007-08-01

The structure and dynamics of food webs are largely dependent upon interactions among consumers and their resources. However, interspecific interactions such as intraguild predation and interference competition can also play a significant role in the stability of communities. The role of antagonistic/synergistic interactions among predators has been largely ignored in food web theory. These mechanisms influence predation rates, which is one of the key factors regulating food web structure and dynamics, thus ignoring them can potentially limit understanding of food webs. Using nonlinear models, it is shown that critical aspects of multiple predator food web dynamics are antagonistic/synergistic interactions among predators. The influence of antagonistic/synergistic interactions on coexistence of predators depended largely upon the parameter set used and the degree of feeding niche differentiation. In all cases when there was no effect of antagonism or synergism (a ( ij )=1.00), the predators coexisted. Using the stable parameter set, coexistence occurred across the range of antagonism/synergism used. However, using the chaotic parameter strong antagonism resulted in the extinction of one or both species, while strong synergism tended to coexistence. Whereas using the limit cycle parameter set, coexistence was strongly dependent on the degree of feeding niche overlap. Additionally increasing the degree of feeding specialization of the predators on the two prey species increased the amount of parameter space in which coexistence of the two predators occurred. Bifurcation analyses supported the general pattern of increased stability when the predator interaction was synergistic and decreased stability when it was antagonistic. Thus, synergistic interactions should be more common than antagonistic interactions in ecological systems.

Inference of genetic network of Xenopus frog egg: improved genetic algorithm.

PubMed

Wu, Shinq-Jen; Chou, Chia-Hsien; Wu, Cheng-Tao; Lee, Tsu-Tian

2006-01-01

An improved genetic algorithm (IGA) is proposed to achieve S-system gene network modeling of Xenopus frog egg. Via the time-courses training datasets from Michaelis-Menten model, the optimal parameters are learned. The S-system can clearly describe activative and inhibitory interaction between genes as generating and consuming process. We concern the mitotic control in cell-cycle of Xenopus frog egg to realize cyclin-Cdc2 and Cdc25 for MPF activity. The proposed IGA can achieve global search with migration and keep the best chromosome with elitism operation. The generated gene regulatory networks can provide biological researchers for further experiments in Xenopus frog egg cell cycle control.

Ghost Dark Energy with Sign-changeable Interaction Term

NASA Astrophysics Data System (ADS)

Zadeh, M. Abdollahi; Sheykhi, A.; Moradpour, H.

2017-11-01

Regarding the Veneziano ghost of QCD and its generalized form, we consider a Friedmann-Robertson-Walker (FRW) universe filled by a pressureless matter and a dark energy component interacting with each other through a mutual sign-changeable interaction of positive coupling constant. Our study shows that, at the late time, for the deceleration parameter we have q → -1, while the equation of state parameter of the interacting ghost dark energy (GDE) does not cross the phantom line, namely ω D ≥ -1. We also extend our study to the generalized ghost dark energy (GGDE) model and show that, at late time, the equation of state parameter of the interacting GGDE also respects the phantom line in both flat and non-flat universes. Moreover, we find out that, unlike the non-flat universe, we have q → -1 at late time for flat FRW universe. In order to make the behavior of the underlying models more clear, the deceleration parameter q as well as the equation of state parameter w D for flat and closed universes have been plotted against the redshift parameter, z. All of the studied cases admit a transition in the expansion history of universe from a deceleration phase to an accelerated one around z ≈ 0.6.

Reconstruction of interaction rate in holographic dark energy

NASA Astrophysics Data System (ADS)

Mukherjee, Ankan

2016-11-01

The present work is based on the holographic dark energy model with Hubble horizon as the infrared cut-off. The interaction rate between dark energy and dark matter has been reconstructed for three different parameterizations of the deceleration parameter. Observational constraints on the model parameters have been obtained by maximum likelihood analysis using the observational Hubble parameter data (OHD), type Ia supernovab data (SNe), baryon acoustic oscillation data (BAO) and the distance prior of cosmic microwave background (CMB) namely the CMB shift parameter data (CMBShift). The interaction rate obtained in the present work remains always positive and increases with expansion. It is very similar to the result obtained by Sen and Pavon [1] where the interaction rate has been reconstructed for a parametrization of the dark energy equation of state. Tighter constraints on the interaction rate have been obtained in the present work as it is based on larger data sets. The nature of the dark energy equation of state parameter has also been studied for the present models. Though the reconstruction is done from different parametrizations, the overall nature of the interaction rate is very similar in all the cases. Different information criteria and the Bayesian evidence, which have been invoked in the context of model selection, show that the these models are at close proximity of each other.

Chain alignment for improved properties - Optimization of PLA and PHB-V by crystallization and reinforcement

NASA Astrophysics Data System (ADS)

Moser, K.; Bergmann, B.; Diemert, J.; Elsner, P.

2014-05-01

In this paper two promising ways to improve the material characteristics of PLA and PHB-V are presented by showing their positive effects on mechanical, optical, and thermal properties. The optimization is achieved by increasing the crystallization from the melt of the polymer chains and the other by means of a reinforcement of the matrices by bio-based materials. In the case of crystallization specific nucleating agents and optimized process parameters promote optimized crystallization conditions and lead particularly in toughness to significant improvements. In addition to crystallization the introduction of cellulose-based reinforcing materials is also a good alternative to improve the ductility of a biopolymer matrix considerably. Due to their polar surface structure cellulose fibres are favouring a very good interaction to the also polar biopolymers. In addition, the polar surfaces of both materials results in very homogeneous dispersion within the compound.

Lower limb power rehabilitation (LLPR) using interactive video game for improvement of balance function in older people.

PubMed

Chen, Po-Yin; Wei, Shun-Hwa; Hsieh, Wan-Ling; Cheen, Jang-Rong; Chen, Liang-Kung; Kao, Chung-Lan

2012-01-01

Declined balance functions have adverse effects on elderly population. Lower limbs muscle power training is currently an emerging concept in rehabilitation on individuals with decreased balance and mobility. In this prospective, controlled study, we used a human-computer interactive video-game-based rehabilitation device (LLPR) for training of lower limb muscle power in the elderly. Forty (aged >65 years) individuals were recruited from the community. Twenty participants in the exercise group received 30-min training, twice a week, using the LLPR system. The LLPR system allows participants to perform fast speed sit-to-stand (STS) movements. Twenty age-matched participants in the control group performed slow speed STS movements, as well as strengthening and balance exercises, with the same frequency and duration. The results were compared after 12 sessions (6 weeks) of training. The mechanical and time parameters during STS movement were measured using the LLPR system. Modified falls efficacy scale (MFES), Tinetti Performance-Oriented Mobility Assessment (POMA), function reach test, five times sit to stand (FTSS) and Timed Up and Go (TUG) were administered to participants as clinical assessments. Results showed that in the exercise group, all the mechanical and time parameters showed significant improvement. In control group, only the maximal vertical ground reaction force (MVGRF) improved significantly. For clinical assessments (balance, mobility, and self-confidence), exercise group showed significantly better scores. The STS movements in video-game-based training mimic real life situations which may help to transfer the training effects into daily activities. The effectiveness of lower limb muscle training is worthy of further investigation. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Interaction between morphine and noradrenergic system of basolateral amygdala on anxiety and memory in the elevated plus-maze test based on a test-retest paradigm.

PubMed

Valizadegan, Farhad; Oryan, Shahrbanoo; Nasehi, Mohammad; Zarrindast, Mohammad Reza

2013-05-01

The amygdala is the key brain structure for anxiety and emotional memory storage. We examined the involvement of β-adrenoreceptors in the basolateral amygdala (BLA) and their interaction with morphine in modulating these behaviors. The elevated plus-maze has been employed for investigating anxiety and memory. Male Wistar rats were used for this test. We injected morphine (4, 5, and 6 mg/kg) intraperitoneally, while salbutamol (albuterol) (1, 2, and 4 μg/rat) and propranolol (1, 2, and 4 μg/rat) were injected into the BLA. Open- arms time percentage (%OAT), open- arms entry percentage (%OAE), and locomotor activity were determined by this behavioral test. Retention was tested 24 hours later. Intraperitoneal injection of morphine (6 mg/kg) had an anxiolytic-like effect and improvement of memory. The highest dose of salbutamol decreased the anxiety parameters in test session and improved the memory in retest session. Coadministration of salbutamol and ineffective dose of morphine presenting anxiolytic response. In this case, the memory was improved. Intra-BLA administration of propranolol (4 μg/rat) decreased %OAT in the test session, while had no effect on memory formation. Coadministration of propranolol and morphine (6 mg/kg) showed an increase in %OAT. There was not any significant change in the above- mentioned parameter in the retest session. Coadministration of morphine and propranolol with the effective dose of salbutamol showed that propranolol could reverse anxiolytic-like effect. We found that opioidergic and β-adrenergic systems have the same effects on anxiety and memory in the BLA; but these effects are independent of each other.

Pig Feeding under the Potato-green Forage Base System with or without Addition of Herbs versus a Concentrate Based System: Effect on Post-slaughter Performance and Pork Characteristics

PubMed Central

Turyk, Zofia; Osek, Maria; Olkowski, Bogusław; Janocha, Alina

2014-01-01

This study examined carcass and meat quality parameters in growing/finishing pigs fed unconventionally versus the concentrate-based system. Ninety-six, 12 wk old pigs (34±SD 0.3 kg) were randomly divided into three groups, assigned to one of the three dietary treatments: standard complete concentrate mixture, conventional (C diet); unconventional, steamed potato-green forage-concentrate based diet (U diet), and unconventional basal diet+herbage mix (UH diet). Pigs fed U diet showed lower dressing percentage, meatiness, loin eye area, and weight of pork neck (p≤0.05), but their carcasses were significantly (p≤0.05) longer and had increased backfat depth (p≤0.05). There was no impact of the diet on the meat content of dry matter, crude ash, acidity, and colour parameters of m. longissimus. Unconventional feeding significantly (p≤0.05) elevated water the holding capacity of m. longissimus and slightly improved the sensory attributes analysis of meat. The addition of herbs resulted in increased loin eye area (p≤0.05), decreased fat content (p≤0.05) in m. longissimus, and tended to improve some sensory attributes of meat. There were significant gender differences in response to all diets. There were significant diet×sex interactions for some measured variables, but there were no clearly identifiable trends with regard to any specific carcass or meat parameters. Feeding unconventional diet to pigs may offer better culinary attributes of the meat, and improve some technologically important characteristics of pig carcass, but may negatively affect some carcass or meat parameters. PMID:25050003

Review of 3D image data calibration for heterogeneity correction in proton therapy treatment planning.

PubMed

Zhu, Jiahua; Penfold, Scott N

2016-06-01

Correct modelling of the interaction parameters of patient tissues is of vital importance in proton therapy treatment planning because of the large dose gradients associated with the Bragg peak. Different 3D imaging techniques yield different information regarding these interaction parameters. Given the rapidly expanding interest in proton therapy, this review is written to make readers aware of the current challenges in accounting for tissue heterogeneities and the imaging systems that are proposed to tackle these challenges. A summary of the interaction parameters of interest in proton therapy and the current and developmental 3D imaging techniques used in proton therapy treatment planning is given. The different methods to translate the imaging data to the interaction parameters of interest are reviewed and a summary of the implementations in several commercial treatment planning systems is presented.

Vibrational Relaxation and Collision-Induced Dissociation of Xenon Fluoride by Neon

DTIC Science & Technology

1989-03-01

potential energy surface, which consists of a Morse function for the XeF interaction and Lennard - Jones functions for the NeXe and NeF interactions. Rate...interaction and a Lennard - Jones function for the NeXe and the NeF interactions. The values of the Morse potential parameters for XeF are taken from...interactions are calculated using the theoretical data provided by Svehla.59 The parameters for the Morse potential and the Lennard - Jones potentials are listed

D¯0D0* (D0D¯0*) system in QCD-improved many body potential

NASA Astrophysics Data System (ADS)

Jamil, M. Imran; Masud, Bilal; Akram, Faisal; Sohail Gilani, S. M.

2017-01-01

For a system of current interest (composed of charm, anticharm and a pair of light quarks), we show trends in phenomenological implications of QCD-based improvements to a simple quark model treatment. We employ a resonating group method to render this difficult four-body problem manageable. We use a quadratic confinement so as to be able to improve beyond the Born approximation. We report the position of the pole corresponding to the D¯0D0* molecule for the best fit of a model parameter to the relevant QCD simulations. We point out the interesting possibility that the pole can be shifted to 3872 MeV by introducing another parameter I 0 that changes the strength of the interaction in this one component of X(3872). The revised value of this second parameter can guide future trends in modeling of the full exotic meson X(3872). We also report the changes with I 0 in the S-wave spin averaged cross sections for D¯0D0* ⟶ ωJ/ψ and D¯0D0* ⟶ ρJ/ψ. These cross sections are important regarding the study of QGP (quark gluon plasma). BM and FA acknowledge the support of PU research (D/605/Est.I Sr. 20 Project 2014-15, D/34/Est.1 Sr. 109 Project 2013-14), SG is thankful to the Higher Education Commission (HEC) of Pakistan for its financial support through (17-5-4(Ps3-128) HEC/Sch/2006)

Description of the Hexadecapole Deformation Parameter in the sdg Interacting Boson Model

NASA Astrophysics Data System (ADS)

Liu, Yu-xin; Sun, Di; Wang, Jia-jun; Han, Qi-zhi

1998-04-01

The hexadecapole deformation parameter β4 of the rare-earth and actinide nuclei is investigated in the framework of the sdg interacing boson model. An explicit relation between the geometric hexadecapole deformation parameter β4 and the intrinsic deformation parameters epsilon4, epsilon2 are obtained. The deformation parameters β4 of the rare-earths and actinides are determined without any free parameter. The calculated results agree with experimental data well. It also shows that the SU(5) limit of the sdg interacting boson model can describe the β4 systematics as well as the SU(3) limit.

Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization

PubMed Central

Miller, Mark S.; Lay, Wesley K.

2016-01-01

Recent molecular dynamics (MD) simulations of proteins have suggested that common force fields overestimate the strength of amino acid interactions in aqueous solution. In an attempt to determine the causes of these effects, we have measured the osmotic coefficients of a number of amino acids using the AMBER ff99SB-ILDN force field with two popular water models, and compared the results with available experimental data. With TIP4P-Ew water, interactions between aliphatic residues agree well with experiment, but interactions of the polar residues serine and threonine are found to be excessively attractive. For all tested amino acids, the osmotic coefficients are lower when the TIP3P water model is used. Additional simulations performed on charged amino acids indicate that the osmotic coefficients are strongly dependent on the parameters assigned to the salt ions, with a reparameterization of the sodium:carboxylate interaction reported by the Aksimentiev group significantly improving description of the osmotic coefficient for glutamate. For five neutral amino acids, we also demonstrate a decrease in solute-solute attractions using the recently reported TIP4P-D water model and using the KBFF force field. Finally, we show that for four two-residue peptides improved agreement with experiment can be achieved by re-deriving the partial charges for each peptide. PMID:27052117

Associations between feelings of social anxiety and emotion perception.

PubMed

Lynn, Spencer K; Bui, Eric; Hoeppner, Susanne S; O'Day, Emily B; Palitz, Sophie A; Barrett, Lisa Feldman; Simon, Naomi M

2018-06-01

Abnormally biased perceptual judgment is a feature of many psychiatric disorders. Thus, individuals with social anxiety disorder are biased to recall or interpret social events negatively. Cognitive behavioral therapy addresses such bias by teaching patients, via verbal instruction, to become aware of and change pathological misjudgment. The present study examined whether targeting verbal instruction to specific decision parameters that influence perceptual judgment may affect changes in anger perception. We used a signal detection framework to decompose anger perception into three decision parameters (base rate of encountering anger vs. no-anger, payoff for correct vs. incorrect categorization of face stimuli, and perceptual similarity of angry vs. not-angry facial expressions). We created brief verbal instructions that emphasized each parameter separately. Participants with social anxiety disorder, generalized anxiety disorder, and healthy controls, were assigned to one of the three instruction conditions. We compared anger perception pre-vs. post-instruction. Base rate and payoff instructions affected response bias over and above practice effects, across the three groups. There was no interaction with diagnosis. The ability to target specific decision parameters that underlie perceptual judgment suggests that cognitive behavioral therapy might be improved by tailoring it to patients' individual parameter "estimation" deficits. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evaluating Force-Field London Dispersion Coefficients Using the Exchange-Hole Dipole Moment Model.

PubMed

Mohebifar, Mohamad; Johnson, Erin R; Rowley, Christopher N

2017-12-12

London dispersion interactions play an integral role in materials science and biophysics. Force fields for atomistic molecular simulations typically represent dispersion interactions by the 12-6 Lennard-Jones potential using empirically determined parameters. These parameters are generally underdetermined, and there is no straightforward way to test if they are physically realistic. Alternatively, the exchange-hole dipole moment (XDM) model from density-functional theory predicts atomic and molecular London dispersion coefficients from first principles, providing an innovative strategy to validate the dispersion terms of molecular-mechanical force fields. In this work, the XDM model was used to obtain the London dispersion coefficients of 88 organic molecules relevant to biochemistry and pharmaceutical chemistry and the values compared with those derived from the Lennard-Jones parameters of the CGenFF, GAFF, OPLS, and Drude polarizable force fields. The molecular dispersion coefficients for the CGenFF, GAFF, and OPLS models are systematically higher than the XDM-calculated values by a factor of roughly 1.5, likely due to neglect of higher order dispersion terms and premature truncation of the dispersion-energy summation. The XDM dispersion coefficients span a large range for some molecular-mechanical atom types, suggesting an unrecognized source of error in force-field models, which assume that atoms of the same type have the same dispersion interactions. Agreement with the XDM dispersion coefficients is even poorer for the Drude polarizable force field. Popular water models were also examined, and TIP3P was found to have dispersion coefficients similar to the experimental and XDM references, although other models employ anomalously high values. Finally, XDM-derived dispersion coefficients were used to parametrize molecular-mechanical force fields for five liquids-benzene, toluene, cyclohexane, n-pentane, and n-hexane-which resulted in improved accuracy in the computed enthalpies of vaporization despite only having to evaluate a much smaller section of the parameter space.

A Two-Stage Method to Determine Optimal Product Sampling considering Dynamic Potential Market

PubMed Central

Hu, Zhineng; Lu, Wei; Han, Bing

2015-01-01

This paper develops an optimization model for the diffusion effects of free samples under dynamic changes in potential market based on the characteristics of independent product and presents a two-stage method to figure out the sampling level. The impact analysis of the key factors on the sampling level shows that the increase of the external coefficient or internal coefficient has a negative influence on the sampling level. And the changing rate of the potential market has no significant influence on the sampling level whereas the repeat purchase has a positive one. Using logistic analysis and regression analysis, the global sensitivity analysis gives a whole analysis of the interaction of all parameters, which provides a two-stage method to estimate the impact of the relevant parameters in the case of inaccuracy of the parameters and to be able to construct a 95% confidence interval for the predicted sampling level. Finally, the paper provides the operational steps to improve the accuracy of the parameter estimation and an innovational way to estimate the sampling level. PMID:25821847

Reconstituting protein interaction networks using parameter-dependent domain-domain interactions

PubMed Central

2013-01-01

Background We can describe protein-protein interactions (PPIs) as sets of distinct domain-domain interactions (DDIs) that mediate the physical interactions between proteins. Experimental data confirm that DDIs are more consistent than their corresponding PPIs, lending support to the notion that analyses of DDIs may improve our understanding of PPIs and lead to further insights into cellular function, disease, and evolution. However, currently available experimental DDI data cover only a small fraction of all existing PPIs and, in the absence of structural data, determining which particular DDI mediates any given PPI is a challenge. Results We present two contributions to the field of domain interaction analysis. First, we introduce a novel computational strategy to merge domain annotation data from multiple databases. We show that when we merged yeast domain annotations from six annotation databases we increased the average number of domains per protein from 1.05 to 2.44, bringing it closer to the estimated average value of 3. Second, we introduce a novel computational method, parameter-dependent DDI selection (PADDS), which, given a set of PPIs, extracts a small set of domain pairs that can reconstruct the original set of protein interactions, while attempting to minimize false positives. Based on a set of PPIs from multiple organisms, our method extracted 27% more experimentally detected DDIs than existing computational approaches. Conclusions We have provided a method to merge domain annotation data from multiple sources, ensuring large and consistent domain annotation for any given organism. Moreover, we provided a method to extract a small set of DDIs from the underlying set of PPIs and we showed that, in contrast to existing approaches, our method was not biased towards DDIs with low or high occurrence counts. Finally, we used these two methods to highlight the influence of the underlying annotation density on the characteristics of extracted DDIs. Although increased annotations greatly expanded the possible DDIs, the lack of knowledge of the true biological false positive interactions still prevents an unambiguous assignment of domain interactions responsible for all protein network interactions. Executable files and examples are given at: http://www.bhsai.org/downloads/padds/ PMID:23651452

A comparison of random draw and locally neutral models for the avifauna of an English woodland.

PubMed

Dolman, Andrew M; Blackburn, Tim M

2004-06-03

Explanations for patterns observed in the structure of local assemblages are frequently sought with reference to interactions between species, and between species and their local environment. However, analyses of null models, where non-interactive local communities are assembled from regional species pools, have demonstrated that much of the structure of local assemblages remains in simulated assemblages where local interactions have been excluded. Here we compare the ability of two null models to reproduce the breeding bird community of Eastern Wood, a 16-hectare woodland in England, UK. A random draw model, in which there is complete annual replacement of the community by immigrants from the regional pool, is compared to a locally neutral community model, in which there are two additional parameters describing the proportion of the community replaced annually (per capita death rate) and the proportion of individuals recruited locally rather than as immigrants from the regional pool. Both the random draw and locally neutral model are capable of reproducing with significant accuracy several features of the observed structure of the annual Eastern Wood breeding bird community, including species relative abundances, species richness and species composition. The two additional parameters present in the neutral model result in a qualitatively more realistic representation of the Eastern Wood breeding bird community, particularly of its dynamics through time. The fact that these parameters can be varied, allows for a close quantitative fit between model and observed communities to be achieved, particularly with respect to annual species richness and species accumulation through time. The presence of additional free parameters does not detract from the qualitative improvement in the model and the neutral model remains a model of local community structure that is null with respect to species differences at the local scale. The ability of this locally neutral model to describe a larger number of woodland bird communities with either little variation in its parameters or with variation explained by features local to the woods themselves (such as the area and isolation of a wood) will be a key subsequent test of its relevance.

Precision measurements with LPCTrap at GANIL

NASA Astrophysics Data System (ADS)

Liénard, E.; Ban, G.; Couratin, C.; Delahaye, P.; Durand, D.; Fabian, X.; Fabre, B.; Fléchard, X.; Finlay, P.; Mauger, F.; Méry, A.; Naviliat-Cuncic, O.; Pons, B.; Porobic, T.; Quéméner, G.; Severijns, N.; Thomas, J. C.; Velten, Ph.

2015-11-01

The experimental achievements and the results obtained so far with the LPCTrap device installed at GANIL are presented. The apparatus is dedicated to the study of the weak interaction at low energy by means of precise measurements of the β - ν angular correlation parameter in nuclear β decays. So far, the data collected with three isotopes have enabled to determine, for the first time, the charge state distributions of the recoiling ions, induced by shakeoff process. The analysis is presently refined to deduce the correlation parameters, with the potential of improving both the constraint deduced at low energy on exotic tensor currents (6He1+) and the precision on the V u d element of the quark-mixing matrix (35Ar1+ and 19Ne1+) deduced from the mirror transitions dataset.

Machine learning action parameters in lattice quantum chromodynamics

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

Shanahan, Phiala; Trewartha, Daneil; Detmold, William

Numerical lattice quantum chromodynamics studies of the strong interaction underpin theoretical understanding of many aspects of particle and nuclear physics. Such studies require significant computing resources to undertake. A number of proposed methods promise improved efficiency of lattice calculations, and access to regions of parameter space that are currently computationally intractable, via multi-scale action-matching approaches that necessitate parametric regression of generated lattice datasets. The applicability of machine learning to this regression task is investigated, with deep neural networks found to provide an efficient solution even in cases where approaches such as principal component analysis fail. Finally, the high information contentmore » and complex symmetries inherent in lattice QCD datasets require custom neural network layers to be introduced and present opportunities for further development.« less

Assessment of Reinforced Concrete Surface Breaking Crack Using Rayleigh Wave Measurement.

PubMed

Lee, Foo Wei; Chai, Hwa Kian; Lim, Kok Sing

2016-03-05

An improved single sided Rayleigh wave (R-wave) measurement was suggested to characterize surface breaking crack in steel reinforced concrete structures. Numerical simulations were performed to clarify the behavior of R-waves interacting with surface breaking crack with different depths and degrees of inclinations. Through analysis of simulation results, correlations between R-wave parameters of interest and crack characteristics (depth and degree of inclination) were obtained, which were then validated by experimental measurement of concrete specimens instigated with vertical and inclined artificial cracks of different depths. Wave parameters including velocity and amplitude attenuation for each case were studied. The correlations allowed us to estimate the depth and inclination of cracks measured experimentally with acceptable discrepancies, particularly for cracks which are relatively shallow and when the crack depth is smaller than the wavelength.

Machine learning action parameters in lattice quantum chromodynamics

DOE PAGES

Shanahan, Phiala; Trewartha, Daneil; Detmold, William

2018-05-16

Numerical lattice quantum chromodynamics studies of the strong interaction underpin theoretical understanding of many aspects of particle and nuclear physics. Such studies require significant computing resources to undertake. A number of proposed methods promise improved efficiency of lattice calculations, and access to regions of parameter space that are currently computationally intractable, via multi-scale action-matching approaches that necessitate parametric regression of generated lattice datasets. The applicability of machine learning to this regression task is investigated, with deep neural networks found to provide an efficient solution even in cases where approaches such as principal component analysis fail. Finally, the high information contentmore » and complex symmetries inherent in lattice QCD datasets require custom neural network layers to be introduced and present opportunities for further development.« less

Distinguishing boson stars from black holes and neutron stars from tidal interactions in inspiraling binary systems

NASA Astrophysics Data System (ADS)

Sennett, Noah; Hinderer, Tanja; Steinhoff, Jan; Buonanno, Alessandra; Ossokine, Serguei

2017-07-01

Binary systems containing boson stars—self-gravitating configurations of a complex scalar field—can potentially mimic black holes or neutron stars as gravitational-wave sources. We investigate the extent to which tidal effects in the gravitational-wave signal can be used to discriminate between these standard sources and boson stars. We consider spherically symmetric boson stars within two classes of scalar self-interactions: an effective-field-theoretically motivated quartic potential and a solitonic potential constructed to produce very compact stars. We compute the tidal deformability parameter characterizing the dominant tidal imprint in the gravitational-wave signals for a large span of the parameter space of each boson star model, covering the entire space in the quartic case, and an extensive portion of interest in the solitonic case. We find that the tidal deformability for boson stars with a quartic self-interaction is bounded below by Λmin≈280 and for those with a solitonic interaction by Λmin≈1.3 . We summarize our results as ready-to-use fits for practical applications. Employing a Fisher matrix analysis, we estimate the precision with which Advanced LIGO and third-generation detectors can measure these tidal parameters using the inspiral portion of the signal. We discuss a novel strategy to improve the distinguishability between black holes/neutrons stars and boson stars by combining tidal deformability measurements of each compact object in a binary system, thereby eliminating the scaling ambiguities in each boson star model. Our analysis shows that current-generation detectors can potentially distinguish boson stars with quartic potentials from black holes, as well as from neutron-star binaries if they have either a large total mass or a large (asymmetric) mass ratio. Discriminating solitonic boson stars from black holes using only tidal effects during the inspiral will be difficult with Advanced LIGO, but third-generation detectors should be able to distinguish between binary black holes and these binary boson stars.

Family relations and eating disorders. The effectiveness of an integrated approach in the treatment of anorexia and bulimia in teenagers: results of a case-control systemic research.

PubMed

Onnis, L; Barbara, E; Bernardini, M; Caggese, A; Di Giacomo, S; Giambartolomei, A; Leonelli, A; Mule', A M; Nicoletti, P G; Vietri, A

2012-03-01

This article presents the results of a broader clinical research into the effectiveness of integrated treatments in teenage eating disorders, carried out at the Complex Operative Unit of Psychotherapy (Unità Operativa Complessa or U.O.C.) of the Department of Psychiatric Sciences and Psychological Medicine in collaboration with the Department of Neuropsychiatric Science for Child Development (Dipartimento di Scienze Neuropsichiatriche dell'Età Evolutiva), both at the "La Sapienza" University of Rome. The hypothesis of this research project is that in diagnosticable situations such as anorexia or bulimia, an integrated and multidisciplinary treatment, which combines medical-nutritional interventions and family psychotherapy, allows better results than a single kind of treatment, which is the usual medical- nutritional intervention supported by psychiatric counselling. Twenty-eight cases (16 of bulimia and 12 of anorexia) were selected and then subdivided, with a randomized distribution, into two (experimental and control) homogeneous groups of 14 patients. The grouping variables were the diagnosis, the disorder's seriousness and duration, BMI, gender, age, family composition and social status. The variables which have been examined in this article are the clinical parameters, which were valuated in accordance with the DSM IV-TR criteria, and relational parameters which were explored through the use of the W.F.T. Test (Wiltwyck Family Tasks). These parameters were tested at beginning as well as at the end of the therapies, in both the experimental group and the control group. Statistical analysis has shown that the experimental group, which was followed with the integrated treatment, experienced a significant improvement of the parameters as related to dysfunctional family interaction modalities, and that this improvement was correlated to the positive evolution of the clinical parameters. This improvement was not present or not of the same degree in the control group. The results, moreover, demonstrate the effectiveness of an integrated systemic treatment based on a complex approach compared to a reductionist approach.

Analysis of the influence of passenger vehicles front-end design on pedestrian lower extremity injuries by means of the LLMS model.

PubMed

Scattina, Alessandro; Mo, Fuhao; Masson, Catherine; Avalle, Massimiliano; Arnoux, Pierre Jean

2018-01-30

This work aims at investigating the influence of some front-end design parameters of a passenger vehicle on the behavior and damage occurring in the human lower limbs when impacted in an accident. The analysis is carried out by means of finite element analysis using a generic car model for the vehicle and the lower limbs model for safety (LLMS) for the purpose of pedestrian safety. Considering the pedestrian standardized impact procedure (as in the 2003/12/EC Directive), a parametric analysis, through a design of experiments plan, was performed. Various material properties, bumper thickness, position of the higher and lower bumper beams, and position of pedestrian, were made variable in order to identify how they influence the injury occurrence. The injury prediction was evaluated from the knee lateral flexion, ligament elongation, and state of stress in the bone structure. The results highlighted that the offset between the higher and lower bumper beams is the most influential parameter affecting the knee ligament response. The influence is smaller or absent considering the other responses and the other considered parameters. The stiffness characteristics of the bumper are, instead, more notable on the tibia. Even if an optimal value of the variables could not be identified trends were detected, with the potential of indicating strategies for improvement. The behavior of a vehicle front end in the impact against a pedestrian can be improved optimizing its design. The work indicates potential strategies for improvement. In this work, each parameter was changed independently one at a time; in future works, the interaction between the design parameters could be also investigated. Moreover, a similar parametric analysis can be carried out using a standard mechanical legform model in order to understand potential diversities or correlations between standard tools and human models.

A new methodology to determine kinetic parameters for one- and two-step chemical models

NASA Technical Reports Server (NTRS)

Mantel, T.; Egolfopoulos, F. N.; Bowman, C. T.

1996-01-01

In this paper, a new methodology to determine kinetic parameters for simple chemical models and simple transport properties classically used in DNS of premixed combustion is presented. First, a one-dimensional code is utilized to performed steady unstrained laminar methane-air flame in order to verify intrinsic features of laminar flames such as burning velocity and temperature and concentration profiles. Second, the flame response to steady and unsteady strain in the opposed jet configuration is numerically investigated. It appears that for a well determined set of parameters, one- and two-step mechanisms reproduce the extinction limit of a laminar flame submitted to a steady strain. Computations with the GRI-mech mechanism (177 reactions, 39 species) and multicomponent transport properties are used to validate these simplified models. A sensitivity analysis of the preferential diffusion of heat and reactants when the Lewis number is close to unity indicates that the response of the flame to an oscillating strain is very sensitive to this number. As an application of this methodology, the interaction between a two-dimensional vortex pair and a premixed laminar flame is performed by Direct Numerical Simulation (DNS) using the one- and two-step mechanisms. Comparison with the experimental results of Samaniego et al. (1994) shows a significant improvement in the description of the interaction when the two-step model is used.

Criticality triggers the emergence of collective intelligence in groups.

PubMed

De Vincenzo, Ilario; Giannoccaro, Ilaria; Carbone, Giuseppe; Grigolini, Paolo

2017-08-01

A spinlike model mimicking human behavior in groups is employed to investigate the dynamics of the decision-making process. Within the model, the temporal evolution of the state of systems is governed by a time-continuous Markov chain. The transition rates of the resulting master equation are defined in terms of the change of interaction energy between the neighboring agents (change of the level of conflict) and the change of a locally defined agent fitness. Three control parameters can be identified: (i) the social interaction strength βJ measured in units of social temperature, (ii) the level of confidence β^{'} that each individual has on his own expertise, and (iii) the level of knowledge p that identifies the expertise of each member. Based on these three parameters, the phase diagrams of the system show that a critical transition front exists where a sharp and concurrent change in fitness and consensus takes place. We show that at the critical front, the information leakage from the fitness landscape to the agents is maximized. This event triggers the emergence of the collective intelligence of the group, and in the end it leads to a dramatic improvement in the decision-making performance of the group. The effect of size M of the system is also investigated, showing that, depending on the value of the control parameters, increasing M may be either beneficial or detrimental.

Criticality triggers the emergence of collective intelligence in groups

NASA Astrophysics Data System (ADS)

De Vincenzo, Ilario; Giannoccaro, Ilaria; Carbone, Giuseppe; Grigolini, Paolo

2017-08-01

A spinlike model mimicking human behavior in groups is employed to investigate the dynamics of the decision-making process. Within the model, the temporal evolution of the state of systems is governed by a time-continuous Markov chain. The transition rates of the resulting master equation are defined in terms of the change of interaction energy between the neighboring agents (change of the level of conflict) and the change of a locally defined agent fitness. Three control parameters can be identified: (i) the social interaction strength β J measured in units of social temperature, (ii) the level of confidence β' that each individual has on his own expertise, and (iii) the level of knowledge p that identifies the expertise of each member. Based on these three parameters, the phase diagrams of the system show that a critical transition front exists where a sharp and concurrent change in fitness and consensus takes place. We show that at the critical front, the information leakage from the fitness landscape to the agents is maximized. This event triggers the emergence of the collective intelligence of the group, and in the end it leads to a dramatic improvement in the decision-making performance of the group. The effect of size M of the system is also investigated, showing that, depending on the value of the control parameters, increasing M may be either beneficial or detrimental.

Adaptive control based on an on-line parameter estimation of an upper limb exoskeleton.

PubMed

Riani, Akram; Madani, Tarek; Hadri, Abdelhafid El; Benallegue, Abdelaziz

2017-07-01

This paper presents an adaptive control strategy for an upper-limb exoskeleton based on an on-line dynamic parameter estimator. The objective is to improve the control performance of this system that plays a critical role in assisting patients for shoulder, elbow and wrist joint movements. In general, the dynamic parameters of the human limb are unknown and differ from a person to another, which degrade the performances of the exoskeleton-human control system. For this reason, the proposed control scheme contains a supplementary loop based on a new efficient on-line estimator of the dynamic parameters. Indeed, the latter is acting upon the parameter adaptation of the controller to ensure the performances of the system in the presence of parameter uncertainties and perturbations. The exoskeleton used in this work is presented and a physical model of the exoskeleton interacting with a 7 Degree of Freedom (DoF) upper limb model is generated using the SimMechanics library of MatLab/Simulink. To illustrate the effectiveness of the proposed approach, an example of passive rehabilitation movements is performed using multi-body dynamic simulation. The aims is to maneuver the exoskeleton that drive the upper limb to track desired trajectories in the case of the passive arm movements.

Interrogating selectivity in catalysis using molecular vibrations

NASA Astrophysics Data System (ADS)

Milo, Anat; Bess, Elizabeth N.; Sigman, Matthew S.

2014-03-01

The delineation of molecular properties that underlie reactivity and selectivity is at the core of physical organic chemistry, and this knowledge can be used to inform the design of improved synthetic methods or identify new chemical transformations. For this reason, the mathematical representation of properties affecting reactivity and selectivity trends, that is, molecular parameters, is paramount. Correlations produced by equating these molecular parameters with experimental outcomes are often defined as free-energy relationships and can be used to evaluate the origin of selectivity and to generate new, experimentally testable hypotheses. The premise behind successful correlations of this type is that a systematically perturbed molecular property affects a transition-state interaction between the catalyst, substrate and any reaction components involved in the determination of selectivity. Classic physical organic molecular descriptors, such as Hammett, Taft or Charton parameters, seek to independently probe isolated electronic or steric effects. However, these parameters cannot address simultaneous, non-additive variations to more than one molecular property, which limits their utility. Here we report a parameter system based on the vibrational response of a molecule to infrared radiation that can be used to mathematically model and predict selectivity trends for reactions with interlinked steric and electronic effects at positions of interest. The disclosed parameter system is mechanistically derived and should find broad use in the study of chemical and biological systems.

Density functional theory based study of molecular interactions, recognition, engineering, and quantum transport in π molecular systems.

PubMed

Cho, Yeonchoo; Cho, Woo Jong; Youn, Il Seung; Lee, Geunsik; Singh, N Jiten; Kim, Kwang S

2014-11-18

CONSPECTUS: In chemical and biological systems, various interactions that govern the chemical and physical properties of molecules, assembling phenomena, and electronic transport properties compete and control the microscopic structure of materials. The well-controlled manipulation of each component can allow researchers to design receptors or sensors, new molecular architectures, structures with novel morphology, and functional molecules or devices. In this Account, we describe the structures and electronic and spintronic properties of π-molecular systems that are important for controlling the architecture of a variety of carbon-based systems. Although DFT is an important tool for describing molecular interactions, the inability of DFT to accurately represent dispersion interactions has made it difficult to properly describe π-interactions. However, the recently developed dispersion corrections for DFT have allowed us to include these dispersion interactions cost-effectively. We have investigated noncovalent interactions of various π-systems including aromatic-π, aliphatic-π, and non-π systems based on dispersion-corrected DFT (DFT-D). In addition, we have addressed the validity of DFT-D compared with the complete basis set (CBS) limit values of coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)] and Møller-Plesset second order perturbation theory (MP2). The DFT-D methods are still unable to predict the correct ordering in binding energies within the benzene dimer and the cyclohexane dimer. Nevertheless, the overall DFT-D predicted binding energies are in reasonable agreement with the CCSD(T) results. In most cases, results using the B97-D3 method closely reproduce the CCSD(T) results with the optimized energy-fitting parameters. On the other hand, vdW-DF2 and PBE0-TS methods estimate the dispersion energies from the calculated electron density. In these approximations, the interaction energies around the equilibrium point are reasonably close to the CCSD(T) results but sometimes slightly deviate from them because interaction energies were not particularly optimized with parameters. Nevertheless, because the electron cloud deforms when neighboring atoms/ions induce an electric field, both vdW-DF2 and PBE0-TS seem to properly reproduce the resulting change of dispersion interaction. Thus, improvements are needed in both vdW-DF2 and PBE0-TS to better describe the interaction energies, while the B97-D3 method could benefit from the incorporation of polarization-driven energy changes that show highly anisotropic behavior. Although the current DFT-D methods need further improvement, DFT-D is very useful for computer-aided molecular design. We have used these newly developed DFT-D methods to calculate the interactions between graphene and DNA nucleobases. Using DFT-D, we describe the design of molecular receptors of π-systems, graphene based electronic devices, metalloporphyrin half-metal based spintronic devices as graphene nanoribbon (GNR) analogs, and graphene based molecular electronic devices for DNA sequencing. DFT-D has also helped us understand quantum phenomena in materials and devices of π-systems including graphene.

Post-Planck constraints on interacting vacuum energy

NASA Astrophysics Data System (ADS)

Wang, Yuting; Wands, David; Zhao, Gong-Bo; Xu, Lixin

2014-07-01

We present improved constraints on an interacting vacuum model using updated astronomical observations including the first data release from Planck. We consider a model with one dimensionless parameter, α, describing the interaction between dark matter and vacuum energy (with fixed equation of state w=-1). The background dynamics correspond to a generalized Chaplygin gas cosmology, but the perturbations have a zero sound speed. The tension between the value of the Hubble constant, H0, determined by Planck data plus WMAP polarization (Planck +WP) and that determined by the Hubble Space Telescope (HST) can be alleviated by energy transfer from dark matter to vacuum (α>0). A positive α increases the allowed values of H0 due to parameter degeneracy within the model using only cosmic microwave background data. Combining with additional data sets of including supernova type Ia (SN Ia) and baryon acoustic oscillation (BAO), we can significantly tighten the bounds on α. Redshift-space distortions (RSD), which constrain the linear growth of structure, provide the tightest constraints on vacuum interaction when combined with Planck+WP, and prefer energy transfer from vacuum to dark matter (α<0) which suppresses the growth of structure. Using the combined data sets of Planck +WP+Union2.1+BAO+RSD, we obtain the constraint on α to be -0.083<α<-0.006 (95% C.L.), allowing low H0 consistent with the measurement from 6dF Galaxy survey. This interacting vacuum model can alleviate the tension between RSD and Planck +WP in the ΛCDM model for α <0, or between HST measurements of H0 and Planck+WP for α>0, but not both at the same time.

Dark soliton dynamics and interactions in continuous-wave-induced lattices.

PubMed

Tsopelas, Ilias; Kominis, Yannis; Hizanidis, Kyriakos

2007-10-01

The dynamics of dark spatial soliton beams and their interaction under the presence of a continuous wave (CW), which dynamically induces a photonic lattice, are investigated. It is shown that appropriate selection of the characteristic parameters of the CW result in controllable steering of a single soliton as well as controllable interaction between two solitons. Depending on the CW parameters, the soliton angle of propagation can be changed drastically, while two-soliton interaction can be either enhanced or reduced, suggesting a reconfigurable soliton control mechanism. Our analytical approach, based on the variational perturbation method, provides a dynamical system for the dark soliton evolution parameters. Analytical results are shown in good agreement with direct numerical simulations.

Sensitivity Analysis of an ENteric Immunity SImulator (ENISI)-Based Model of Immune Responses to Helicobacter pylori Infection

PubMed Central

Alam, Maksudul; Deng, Xinwei; Philipson, Casandra; Bassaganya-Riera, Josep; Bisset, Keith; Carbo, Adria; Eubank, Stephen; Hontecillas, Raquel; Hoops, Stefan; Mei, Yongguo; Abedi, Vida; Marathe, Madhav

2015-01-01

Agent-based models (ABM) are widely used to study immune systems, providing a procedural and interactive view of the underlying system. The interaction of components and the behavior of individual objects is described procedurally as a function of the internal states and the local interactions, which are often stochastic in nature. Such models typically have complex structures and consist of a large number of modeling parameters. Determining the key modeling parameters which govern the outcomes of the system is very challenging. Sensitivity analysis plays a vital role in quantifying the impact of modeling parameters in massively interacting systems, including large complex ABM. The high computational cost of executing simulations impedes running experiments with exhaustive parameter settings. Existing techniques of analyzing such a complex system typically focus on local sensitivity analysis, i.e. one parameter at a time, or a close “neighborhood” of particular parameter settings. However, such methods are not adequate to measure the uncertainty and sensitivity of parameters accurately because they overlook the global impacts of parameters on the system. In this article, we develop novel experimental design and analysis techniques to perform both global and local sensitivity analysis of large-scale ABMs. The proposed method can efficiently identify the most significant parameters and quantify their contributions to outcomes of the system. We demonstrate the proposed methodology for ENteric Immune SImulator (ENISI), a large-scale ABM environment, using a computational model of immune responses to Helicobacter pylori colonization of the gastric mucosa. PMID:26327290

Assessment of the Thermodynamic Properties of DL-p-Mentha-1,8-diene, 4-Isopropyl-1-Methylcyclohexene (DL-limonene) by Inverse Gas Chromatography (IGC).

PubMed

Farshchi, Negin; Abbasian, Ali; Larijani, Kambiz

2018-05-10

Limonene is a colorless liquid hydrocarbon and had been investigated as a plasticizer for many plastics. Prediction of solubility between different materials is an advantage in many ways, one of the most convenient ways to know the compatibility of materials is to determine the degree of solubility of them in each other. The concept of "solubility parameter" can help practitioners in this way.In this study, inverse gas chromatography (IGC) method at infinite dilution was used for determination of the thermodynamic properties of DL-p-mentha-1,8-diene, 4-Isopropyl-1-methylcyclohexene (DL-limonene). The interaction between DL-limonene and 13 solvents were examined in the temperature range of 63-123°C through the assessment of the thermodynamic sorption parameters, the parameters of mixing at infinite dilution, the weight fraction activity coefficient and the Flory-Huggins interaction parameters. Additionally, the solubility parameter for DL-limonene and the temperature dependence of these parameters was investigated as well.Results show that there is a temperature dependence in solubility parameter, which increases by decreasing temperature. However, there were no specific dependence between interaction parameters and temperature, but chemical structure appeared to have a significant effect on them as well as on the type and strength of intermolecular interactions between DL-limonene and investigated solvents. The solubility parameter δ2 of DL-limonene determined to be 19.20 (J/cm3)0.5 at 25°C.

Sensitivity Analysis of an ENteric Immunity SImulator (ENISI)-Based Model of Immune Responses to Helicobacter pylori Infection.

PubMed

Alam, Maksudul; Deng, Xinwei; Philipson, Casandra; Bassaganya-Riera, Josep; Bisset, Keith; Carbo, Adria; Eubank, Stephen; Hontecillas, Raquel; Hoops, Stefan; Mei, Yongguo; Abedi, Vida; Marathe, Madhav

2015-01-01

Agent-based models (ABM) are widely used to study immune systems, providing a procedural and interactive view of the underlying system. The interaction of components and the behavior of individual objects is described procedurally as a function of the internal states and the local interactions, which are often stochastic in nature. Such models typically have complex structures and consist of a large number of modeling parameters. Determining the key modeling parameters which govern the outcomes of the system is very challenging. Sensitivity analysis plays a vital role in quantifying the impact of modeling parameters in massively interacting systems, including large complex ABM. The high computational cost of executing simulations impedes running experiments with exhaustive parameter settings. Existing techniques of analyzing such a complex system typically focus on local sensitivity analysis, i.e. one parameter at a time, or a close "neighborhood" of particular parameter settings. However, such methods are not adequate to measure the uncertainty and sensitivity of parameters accurately because they overlook the global impacts of parameters on the system. In this article, we develop novel experimental design and analysis techniques to perform both global and local sensitivity analysis of large-scale ABMs. The proposed method can efficiently identify the most significant parameters and quantify their contributions to outcomes of the system. We demonstrate the proposed methodology for ENteric Immune SImulator (ENISI), a large-scale ABM environment, using a computational model of immune responses to Helicobacter pylori colonization of the gastric mucosa.

Interactive vs. Non-Interactive Ensembles for Weather Prediction and Climate Projection

NASA Astrophysics Data System (ADS)

Duane, Gregory

2013-04-01

If the members of an ensemble of different models are allowed to interact with one another in run time, predictive skill can be improved as compared to that of any individual model or any average of indvidual model outputs. Inter-model connections in such an interactive ensemble can be trained, using historical data, so that the resulting ``supermodel" synchronizes with reality when used in weather-prediction mode, where the individual models perform data assimilation from each other (with trainable inter-model "observation error") as well as from real observations. In climate-projection mode, parameters of the individual models are changed, as might occur from an increase in GHG levels, and one obtains relevant statistical properties of the new supermodel attractor. In simple cases, it has been shown that training of the inter-model connections with the old parameter values gives a supermodel that is still predictive when the parameter values are changed. Here we inquire as to the circumstances under which supermodel performance can be expected to exceed that of the customary weighted average of model outputs. We consider a supermodel formed from quasigeostrophic channel models with different forcing coefficients, and introduce an effective training scheme for the inter-model connections. We show that the blocked-zonal index cycle is reproduced better by the supermodel than by any non-interactive ensemble in the extreme case where the forcing coefficients of the different models are very large or very small. With realistic differences in forcing coefficients, as would be representative of actual differences among IPCC-class models, the usual linearity assumption is justified and a weighted average of model outputs is adequate. It is therefore hypothesized that supermodeling is likely to be useful in situations where there are qualitative model differences, as arising from sub-gridscale parameterizations, that affect overall model behavior. Otherwise the usual ex post facto averaging will probably suffice. Previous results from an ENSO-prediction supermodel [Kirtman et al.] are re-examined in light of the hypothesis about the importance of qualitative inter-model differences.

The zero-multipole summation method for estimating electrostatic interactions in molecular dynamics: analysis of the accuracy and application to liquid systems.

PubMed

Fukuda, Ikuo; Kamiya, Narutoshi; Nakamura, Haruki

2014-05-21

In the preceding paper [I. Fukuda, J. Chem. Phys. 139, 174107 (2013)], the zero-multipole (ZM) summation method was proposed for efficiently evaluating the electrostatic Coulombic interactions of a classical point charge system. The summation takes a simple pairwise form, but prevents the electrically non-neutral multipole states that may artificially be generated by a simple cutoff truncation, which often causes large energetic noises and significant artifacts. The purpose of this paper is to judge the ability of the ZM method by investigating the accuracy, parameter dependencies, and stability in applications to liquid systems. To conduct this, first, the energy-functional error was divided into three terms and each term was analyzed by a theoretical error-bound estimation. This estimation gave us a clear basis of the discussions on the numerical investigations. It also gave a new viewpoint between the excess energy error and the damping effect by the damping parameter. Second, with the aid of these analyses, the ZM method was evaluated based on molecular dynamics (MD) simulations of two fundamental liquid systems, a molten sodium-chlorine ion system and a pure water molecule system. In the ion system, the energy accuracy, compared with the Ewald summation, was better for a larger value of multipole moment l currently induced until l ≲ 3 on average. This accuracy improvement with increasing l is due to the enhancement of the excess-energy accuracy. However, this improvement is wholly effective in the total accuracy if the theoretical moment l is smaller than or equal to a system intrinsic moment L. The simulation results thus indicate L ∼ 3 in this system, and we observed less accuracy in l = 4. We demonstrated the origins of parameter dependencies appearing in the crossing behavior and the oscillations of the energy error curves. With raising the moment l we observed, smaller values of the damping parameter provided more accurate results and smoother behaviors with respect to cutoff length were obtained. These features can be explained, on the basis of the theoretical error analyses, such that the excess energy accuracy is improved with increasing l and that the total accuracy improvement within l ⩽ L is facilitated by a small damping parameter. Although the accuracy was fundamentally similar to the ion system, the bulk water system exhibited distinguishable quantitative behaviors. A smaller damping parameter was effective in all the practical cutoff distance, and this fact can be interpreted by the reduction of the excess subset. A lower moment was advantageous in the energy accuracy, where l = 1 was slightly superior to l = 2 in this system. However, the method with l = 2 (viz., the zero-quadrupole sum) gave accurate results for the radial distribution function. We confirmed the stability in the numerical integration for MD simulations employing the ZM scheme. This result is supported by the sufficient smoothness of the energy function. Along with the smoothness, the pairwise feature and the allowance of the atom-based cutoff mode on the energy formula lead to the exact zero total-force, ensuring the total-momentum conservations for typical MD equations of motion.

The zero-multipole summation method for estimating electrostatic interactions in molecular dynamics: Analysis of the accuracy and application to liquid systems

NASA Astrophysics Data System (ADS)

Fukuda, Ikuo; Kamiya, Narutoshi; Nakamura, Haruki

2014-05-01

In the preceding paper [I. Fukuda, J. Chem. Phys. 139, 174107 (2013)], the zero-multipole (ZM) summation method was proposed for efficiently evaluating the electrostatic Coulombic interactions of a classical point charge system. The summation takes a simple pairwise form, but prevents the electrically non-neutral multipole states that may artificially be generated by a simple cutoff truncation, which often causes large energetic noises and significant artifacts. The purpose of this paper is to judge the ability of the ZM method by investigating the accuracy, parameter dependencies, and stability in applications to liquid systems. To conduct this, first, the energy-functional error was divided into three terms and each term was analyzed by a theoretical error-bound estimation. This estimation gave us a clear basis of the discussions on the numerical investigations. It also gave a new viewpoint between the excess energy error and the damping effect by the damping parameter. Second, with the aid of these analyses, the ZM method was evaluated based on molecular dynamics (MD) simulations of two fundamental liquid systems, a molten sodium-chlorine ion system and a pure water molecule system. In the ion system, the energy accuracy, compared with the Ewald summation, was better for a larger value of multipole moment l currently induced until l ≲ 3 on average. This accuracy improvement with increasing l is due to the enhancement of the excess-energy accuracy. However, this improvement is wholly effective in the total accuracy if the theoretical moment l is smaller than or equal to a system intrinsic moment L. The simulation results thus indicate L ˜ 3 in this system, and we observed less accuracy in l = 4. We demonstrated the origins of parameter dependencies appearing in the crossing behavior and the oscillations of the energy error curves. With raising the moment l we observed, smaller values of the damping parameter provided more accurate results and smoother behaviors with respect to cutoff length were obtained. These features can be explained, on the basis of the theoretical error analyses, such that the excess energy accuracy is improved with increasing l and that the total accuracy improvement within l ⩽ L is facilitated by a small damping parameter. Although the accuracy was fundamentally similar to the ion system, the bulk water system exhibited distinguishable quantitative behaviors. A smaller damping parameter was effective in all the practical cutoff distance, and this fact can be interpreted by the reduction of the excess subset. A lower moment was advantageous in the energy accuracy, where l = 1 was slightly superior to l = 2 in this system. However, the method with l = 2 (viz., the zero-quadrupole sum) gave accurate results for the radial distribution function. We confirmed the stability in the numerical integration for MD simulations employing the ZM scheme. This result is supported by the sufficient smoothness of the energy function. Along with the smoothness, the pairwise feature and the allowance of the atom-based cutoff mode on the energy formula lead to the exact zero total-force, ensuring the total-momentum conservations for typical MD equations of motion.

Interactions of donor sources and media influence the histo-morphological quality of full-thickness skin models.

PubMed

Lange, Julia; Weil, Frederik; Riegler, Christoph; Groeber, Florian; Rebhan, Silke; Kurdyn, Szymon; Alb, Miriam; Kneitz, Hermann; Gelbrich, Götz; Walles, Heike; Mielke, Stephan

2016-10-01

Human artificial skin models are increasingly employed as non-animal test platforms for research and medical purposes. However, the overall histopathological quality of such models may vary significantly. Therefore, the effects of manufacturing protocols and donor sources on the quality of skin models built-up from fibroblasts and keratinocytes derived from juvenile foreskins is studied. Histo-morphological parameters such as epidermal thickness, number of epidermal cell layers, dermal thickness, dermo-epidermal adhesion and absence of cellular nuclei in the corneal layer are obtained and scored accordingly. In total, 144 full-thickness skin models derived from 16 different donors, built-up in triplicates using three different culture conditions were successfully generated. In univariate analysis both media and donor age affected the quality of skin models significantly. Both parameters remained statistically significant in multivariate analyses. Performing general linear model analyses we could show that individual medium-donor-interactions influence the quality. These observations suggest that the optimal choice of media may differ from donor to donor and coincides with findings where significant inter-individual variations of growth rates in keratinocytes and fibroblasts have been described. Thus, the consideration of individual medium-donor-interactions may improve the overall quality of human organ models thereby forming a reproducible test platform for sophisticated clinical research. Copyright © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bead-bead interaction parameters in dissipative particle dynamics: Relation to bead-size, solubility parameter, and surface tension

NASA Astrophysics Data System (ADS)

Maiti, Amitesh; McGrother, Simon

2004-01-01

Dissipative particle dynamics (DPD) is a mesoscale modeling method for simulating equilibrium and dynamical properties of polymers in solution. The basic idea has been around for several decades in the form of bead-spring models. A few years ago, Groot and Warren [J. Chem. Phys. 107, 4423 (1997)] established an important link between DPD and the Flory-Huggins χ-parameter theory for polymer solutions. We revisit the Groot-Warren theory and investigate the DPD interaction parameters as a function of bead size. In particular, we show a consistent scheme of computing the interfacial tension in a segregated binary mixture. Results for three systems chosen for illustration are in excellent agreement with experimental results. This opens the door for determining DPD interactions using interfacial tension as a fitting parameter.

Reconstruction of interaction rate in holographic dark energy

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

Mukherjee, Ankan, E-mail: ankan_ju@iiserkol.ac.in

2016-11-01

The present work is based on the holographic dark energy model with Hubble horizon as the infrared cut-off. The interaction rate between dark energy and dark matter has been reconstructed for three different parameterizations of the deceleration parameter. Observational constraints on the model parameters have been obtained by maximum likelihood analysis using the observational Hubble parameter data (OHD), type Ia supernovab data (SNe), baryon acoustic oscillation data (BAO) and the distance prior of cosmic microwave background (CMB) namely the CMB shift parameter data (CMBShift). The interaction rate obtained in the present work remains always positive and increases with expansion. Itmore » is very similar to the result obtained by Sen and Pavon [1] where the interaction rate has been reconstructed for a parametrization of the dark energy equation of state. Tighter constraints on the interaction rate have been obtained in the present work as it is based on larger data sets. The nature of the dark energy equation of state parameter has also been studied for the present models. Though the reconstruction is done from different parametrizations, the overall nature of the interaction rate is very similar in all the cases. Different information criteria and the Bayesian evidence, which have been invoked in the context of model selection, show that the these models are at close proximity of each other.« less

Building alternate protein structures using the elastic network model.

PubMed

Yang, Qingyi; Sharp, Kim A

2009-02-15

We describe a method for efficiently generating ensembles of alternate, all-atom protein structures that (a) differ significantly from the starting structure, (b) have good stereochemistry (bonded geometry), and (c) have good steric properties (absence of atomic overlap). The method uses reconstruction from a series of backbone framework structures that are obtained from a modified elastic network model (ENM) by perturbation along low-frequency normal modes. To ensure good quality backbone frameworks, the single force parameter ENM is modified by introducing two more force parameters to characterize the interaction between the consecutive carbon alphas and those within the same secondary structure domain. The relative stiffness of the three parameters is parameterized to reproduce B-factors, while maintaining good bonded geometry. After parameterization, violations of experimental Calpha-Calpha distances and Calpha-Calpha-Calpha pseudo angles along the backbone are reduced to less than 1%. Simultaneously, the average B-factor correlation coefficient improves to R = 0.77. Two applications illustrate the potential of the approach. (1) 102,051 protein backbones spanning a conformational space of 15 A root mean square deviation were generated from 148 nonredundant proteins in the PDB database, and all-atom models with minimal bonded and nonbonded violations were produced from this ensemble of backbone structures using the SCWRL side chain building program. (2) Improved backbone templates for homology modeling. Fifteen query sequences were each modeled on two targets. For each of the 30 target frameworks, dozens of improved templates could be produced In all cases, improved full atom homology models resulted, of which 50% could be identified blind using the D-Fire statistical potential. (c) 2008 Wiley-Liss, Inc.

Progressive Learning of Topic Modeling Parameters: A Visual Analytics Framework.

PubMed

El-Assady, Mennatallah; Sevastjanova, Rita; Sperrle, Fabian; Keim, Daniel; Collins, Christopher

2018-01-01

Topic modeling algorithms are widely used to analyze the thematic composition of text corpora but remain difficult to interpret and adjust. Addressing these limitations, we present a modular visual analytics framework, tackling the understandability and adaptability of topic models through a user-driven reinforcement learning process which does not require a deep understanding of the underlying topic modeling algorithms. Given a document corpus, our approach initializes two algorithm configurations based on a parameter space analysis that enhances document separability. We abstract the model complexity in an interactive visual workspace for exploring the automatic matching results of two models, investigating topic summaries, analyzing parameter distributions, and reviewing documents. The main contribution of our work is an iterative decision-making technique in which users provide a document-based relevance feedback that allows the framework to converge to a user-endorsed topic distribution. We also report feedback from a two-stage study which shows that our technique results in topic model quality improvements on two independent measures.

Phenomenological Study of Interaction between Solar Acoustic Waves and Sunspots from Measured Scattered Wavefunctions

NASA Astrophysics Data System (ADS)

Yang, Ming-Hsu; Chou, Dean-Yi; Zhao, Hui; Liang, Zhi-Chao

2012-08-01

The solar acoustic waves around a sunspot are modified because of the interaction with the sunspot. The interaction can be viewed as that the sunspot, excited by the incident wave, generates the scattered wave, and the scattered wave is added to the incident wave to form the total wave around the sunspot. We define an interaction parameter, which could be complex, describing the interaction between the acoustic waves and the sunspot. The scattered wavefunction on the surface can be expressed as a two-dimensional integral of the product of the Green's function, the wavefunction, and the two-dimensional interaction parameter over the sunspot area for the Born approximation of different orders. We assume a simple model for the two-dimensional interaction parameter distribution: its absolute value is axisymmetric with a Gaussian distribution and its phase is a constant. The measured scattered wavefunctions of various modes for NOAAs 11084 and 11092 are fitted to the theoretical scattered wavefunctions to determine the three model parameters, magnitude, Gaussian radius, and phase, for the Born approximation of different orders. The three model parameters converge to some values at high-order Born approximations. The result of the first-order Born approximation is significantly different from the convergent value in some cases. The rate of convergence depends on the sunspot size and wavelength. It converges more rapidly for the smaller sunspot and longer wavelength. The magnitude increases with mode frequency and degree for each radial order. The Gaussian radius is insensitive to frequency and degree. The spatial range of the interaction parameter is greater than that of the continuum intensity deficit, but smaller than that of the acoustic power deficit of the sunspot. The phase versus phase speed falls into a small range. This suggests that the phase could be a function phase speed. NOAAs 11084 and 11092 have a similar magnitude and phase, although the ratio of their sizes is 0.75.

The DIII-D Plasma Control System as a Scientific Research Tool

NASA Astrophysics Data System (ADS)

Hyatt, A. W.; Ferron, J. R.; Humphreys, D. A.; Leuer, J. A.; Walker, M. L.; Welander, A. S.

2006-10-01

The digital plasma control system (PCS) is an essential element of the DIII-D tokamak as a scientific research instrument, providing experimenters with real-time measurement and control of the plasma equilibrium, heating, current drive, transport, stability, and plasma-wall interactions. A wide range of sensors and actuators allow feedback control not only of global quantities such as discharge shape, plasma energy, and toroidal rotation, but also of non-axisymmetric magnetic fields and features of the internal profiles of temperature and current density. These diverse capabilities of the PCS improve the effectiveness of tokamak operation and enable unique physics experiments. We will present an overview of the PCS and the systems it controls and interacts with, and show examples of various plasma parameters controlled by the PCS and its actuators.

On the stiffness analysis of a cable driven leg exoskeleton.

PubMed

Sanjeevi, N S S; Vashista, Vineet

2017-07-01

Robotic systems are being used for gait rehabilitation of patients with neurological disorder. These devices are externally powered to apply external forces on human limbs to assist the leg motion. Patients while walking with these devices adapt their walking pattern in response to the applied forces. The efficacy of a rehabilitation paradigm thus depends on the human-robot interaction. A cable driven leg exoskeleton (CDLE) use actuated cables to apply external joint torques on human leg. Cables are lightweight and flexible but can only be pulled, thus a CDLE requires redundant cables. Redundancy in CDLE can be utilized to appropriately tune a robot's performance. In this work, we present the stiffness analysis of CDLE. Different stiffness performance indices are established to study the role of system parameters in improving the human-robot interaction.

Lamp reliability studies for improved satellite rubidium frequency standard

NASA Technical Reports Server (NTRS)

Frueholz, R. P.; Wun-Fogle, M.; Eckert, H. U.; Volk, C. H.; Jones, P. F.

1982-01-01

In response to the premature failure of Rb lamps used in Rb atomic clocks onboard NAVSTAR GPS satellites experimental and theoretical investigations into their failure mechanism were initiated. The primary goal of these studies is the development of an accelerated life test for future GPS lamps. The primary failure mechanism was identified as consumption of the lamp's Rb charge via direct interaction between Rb and the lamp's glass surface. The most effective parameters to accelerate the interaction between the Rb and the glass are felt to be RF excitation power and lamp temperature. Differential scanning calorimetry is used to monitor the consumption of Rb within a lamp as a function of operation time. This technique yielded base line Rb consumption data for GPS lamps operating under normal conditions.

Dependence of the multiplicities of secondary particles on the impact parameter in collisions of high-energy neon and iron nuclei with photoemulsion nuclei

NASA Technical Reports Server (NTRS)

Dudkin, V. E.; Kovalev, E. E.; Nefedov, N. A.; Antonchik, V. A.; Bogdanov, S. D.; Kosmach, V. F.; Likhachev, A. YU.; Benton, E. V.; Crawford, H. J.

1995-01-01

A method is proposed for finding the dependence of mean multiplicities of secondaries on the nucleus-collision impact parameter from the data on the total interaction ensemble. The impact parameter has been shown to completely define the mean characteristics of an individual interaction event. A difference has been found between experimental results and the data calculated in terms of the cascade-evaporation model at impact-parameter values below 3 fm.

Hospital level analysis to improve patient flow.

PubMed

Khanna, Sankalp; Boyle, Justin; Good, Norm; Bugden, Simon; Scott, Mark

2013-01-01

The complexity of hospital operations ensures that one-size-fits-all solutions seldom work. As hospitals turn to evidence based strategies to redesign flow, it is critical that they tailor the strategies to suit their individual service. This paper analyses the effect of hospital occupancy on inpatient and emergency department patient flow parameters at the Caboolture hospital in Queensland, Australia, and identifies critical levels, or choke points, that result in performance decline. The effect of weekdays and weekends on patient flow is also investigated. We compare these findings to a previous study that has analysed patient flow across Queensland hospitals grouped by size, and discover several differences in the interaction between rising occupancy and patient flow parameters including rates of patient flow, length of stay, and access block. We also identify significantly higher choke points for Caboolture hospital as compared to other similarly sized Queensland hospitals, which suggest that patient flow here can be redesigned to operate at higher levels of occupancy without degrading flow performance. The findings support arguments for hospitals to analyse patient flow at a service level to deliver optimum service improvement.

Optimization of Aqueous Ammonia Soaking of manure fibers by Response Surface Methodology for unlocking the methane potential of swine manure.

PubMed

Lymperatou, Anna; Gavala, Hariklia N; Skiadas, Ioannis V

2017-11-01

Swine manure mono-digestion often results to economically non-feasible processes, due to the high dilution and ammonia concentration together with the low degradation rates it presents. The effects of different parameters of Aqueous Ammonia Soaking (AAS) as a pretreatment for improving the digestion of manure fibers when coupled to an ammonia removal step were investigated in this study. Response Surface Methodology was followed and the influence and interactions of the following AAS parameters were studied: NH 3 concentration, duration and solid-to-liquid ratio. The mild conditions found to be optimal (7%w/w NH 3 , 96h, and 0.16kg/L) in combination to a significant increase of the short term CH 4 yield (244% in 17days), make this pretreatment a promising solution for improving swine manure mono-digestion. Furthermore, compositional analysis of the manure fibers revealed significant solubilization of hemicellulose, while no lignin removal or loss of cellulose occurred under optimal conditions. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

An algorithm-based topographical biomaterials library to instruct cell fate

PubMed Central

Unadkat, Hemant V.; Hulsman, Marc; Cornelissen, Kamiel; Papenburg, Bernke J.; Truckenmüller, Roman K.; Carpenter, Anne E.; Wessling, Matthias; Post, Gerhard F.; Uetz, Marc; Reinders, Marcel J. T.; Stamatialis, Dimitrios; van Blitterswijk, Clemens A.; de Boer, Jan

2011-01-01

It is increasingly recognized that material surface topography is able to evoke specific cellular responses, endowing materials with instructive properties that were formerly reserved for growth factors. This opens the window to improve upon, in a cost-effective manner, biological performance of any surface used in the human body. Unfortunately, the interplay between surface topographies and cell behavior is complex and still incompletely understood. Rational approaches to search for bioactive surfaces will therefore omit previously unperceived interactions. Hence, in the present study, we use mathematical algorithms to design nonbiased, random surface features and produce chips of poly(lactic acid) with 2,176 different topographies. With human mesenchymal stromal cells (hMSCs) grown on the chips and using high-content imaging, we reveal unique, formerly unknown, surface topographies that are able to induce MSC proliferation or osteogenic differentiation. Moreover, we correlate parameters of the mathematical algorithms to cellular responses, which yield novel design criteria for these particular parameters. In conclusion, we demonstrate that randomized libraries of surface topographies can be broadly applied to unravel the interplay between cells and surface topography and to find improved material surfaces. PMID:21949368

Constraints on the dark matter and dark energy interactions from weak lensing bispectrum tomography

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

An, Rui; Feng, Chang; Wang, Bin, E-mail: an_rui@sjtu.edu.cn, E-mail: chang.feng@uci.edu, E-mail: wang_b@sjtu.edu.cn

We estimate uncertainties of cosmological parameters for phenomenological interacting dark energy models using weak lensing convergence power spectrum and bispectrum. We focus on the bispectrum tomography and examine how well the weak lensing bispectrum with tomography can constrain the interactions between dark sectors, as well as other cosmological parameters. Employing the Fisher matrix analysis, we forecast parameter uncertainties derived from weak lensing bispectra with a two-bin tomography and place upper bounds on strength of the interactions between the dark sectors. The cosmic shear will be measured from upcoming weak lensing surveys with high sensitivity, thus it enables us to usemore » the higher order correlation functions of weak lensing to constrain the interaction between dark sectors and will potentially provide more stringent results with other observations combined.« less

Vertical Eddy Diffusivity as a Control Parameter in the Tropical Pacific Ocean

NASA Astrophysics Data System (ADS)

Martinez Avellaneda, N.; Cornuelle, B.; Mazloff, M. R.; Stammer, D.

2012-12-01

Ocean models suffer from errors in the treatment of turbulent sub-grid scale motions causing mixing and energy dissipation. Unrealistic small-scale features in models can have large-scale consequences, such as biases in the upper ocean temperature, a symptom of poorly-simulated upwelling, currents and air-sea interactions. This is of special importance in the tropical Pacific Ocean, which is home to energetic air-sea interactions that affect global climate. It has been shown in a number of studies that the simulated ENSO variability is highly dependent on the state of the ocean (e.g.: background mixing). Moreover, the magnitude of the vertical numerical diffusion is of primary importance in properly reproducing the Pacific equatorial thermocline. Yet, it is a common practice to use spatially uniform mixing parameters in ocean simulations. This work is part of a NASA-funded project to estimate the space-varying ocean mixing coefficients in an eddy-permitting model of the tropical Pacific. The usefulness of assimilation techniques in estimating mixing parameters has been previously explored (e.g.: Stammer, 2005, Ferreira et al., 2005). The authors also demonstrated that the spatial structure of the Equatorial Undercurrent (EUC) could be improved by adjusting wind-stress and surface buoyancy flux within their error bounds. In our work, we address the important question of whether adjusting mixing parameterizations can bring about similar improvements. To that end, an eddy-permitting state estimate for the tropical Pacific is developed using the MIT general circulation model and its adjoint where the vertical diffusivity is set as a control parameter. Complementary adjoint-based sensitivity results show strong sensitivities of the Tropical Pacific thermocline (thickness and location) and the EUC transport to the vertical diffusivity in the tropics. Argo, CTD, XBT and mooring in-situ data, as well as TMI SST and altimetry observations are assimilated in order to reduce the misfit between the model simulations and the ocean observations. Model domain topography of 1/3dgr of spatial resolution interpolated from ETOPO 2. The first and the last color levels represent regions shallower than 100m and deeper than 5000m, respectively

Design analysis and simulation study of an efficiency enhanced L-band MILO

NASA Astrophysics Data System (ADS)

Dixit, Gargi; Kumar, Arjun; Jain, P. K.

2017-01-01

In this article, an experimental L-band compact magnetically insulated transmission line oscillator (MILO) has been simulated using the 3D PIC simulation code "Particle Studio," and an improvement in the device efficiency has been obtained. The detailed interaction and operating mechanism describing the role of sub-assemblies have been explained. The performance of the device was found to be the function of the distance between the end-surface of the cathode and the beam-dump disk. During simulation, a high power microwave of the TM01 mode is generated with the peak RF-power of 6 GW and the power conversion efficiency of 19.2%, at the operating voltage of ˜600 kV and at the current of 52 kA. For better impedance matching or maximum power transfer, four stubs have been placed at the λg/4 distance from the extractor cavity, which results in the stable RF power output. In this work, an improved L-band MILO along with a new type beam-dump disk is selected for performance improvement with typical design parameters and beam parameters. The total peak power of improved MILO is 7 GW, and the maximum power conversion efficiency is 22.4%. This improvement is achieved due to the formation of the virtual cathode at the load side, which helps in modulating the energy of electrons owing to maximum reflection of electrons from the mesh or foil.

Novel design of interactive multimodal biofeedback system for neurorehabilitation.

PubMed

Huang, He; Chen, Y; Xu, W; Sundaram, H; Olson, L; Ingalls, T; Rikakis, T; He, Jiping

2006-01-01

A previous design of a biofeedback system for Neurorehabilitation in an interactive multimodal environment has demonstrated the potential of engaging stroke patients in task-oriented neuromotor rehabilitation. This report explores the new concept and alternative designs of multimedia based biofeedback systems. In this system, the new interactive multimodal environment was constructed with abstract presentation of movement parameters. Scenery images or pictures and their clarity and orientation are used to reflect the arm movement and relative position to the target instead of the animated arm. The multiple biofeedback parameters were classified into different hierarchical levels w.r.t. importance of each movement parameter to performance. A new quantified measurement for these parameters were developed to assess the patient's performance both real-time and offline. These parameters were represented by combined visual and auditory presentations with various distinct music instruments. Overall, the objective of newly designed system is to explore what information and how to feedback information in interactive virtual environment could enhance the sensorimotor integration that may facilitate the efficient design and application of virtual environment based therapeutic intervention.

Parametrization of free ion levels of four isoelectronic 4f2 systems: Insights into configuration interaction parameters

NASA Astrophysics Data System (ADS)

Yeung, Yau Yuen; Tanner, Peter A.

2013-12-01

The experimental free ion 4f2 energy level data sets comprising 12 or 13 J-multiplets of La+, Ce2+, Pr3+ and Nd4+ have been fitted by a semiempirical atomic Hamiltonian comprising 8, 10, or 12 freely-varying parameters. The root mean square errors were 16.1, 1.3, 0.3 and 0.3 cm-1, respectively for fits with 10 parameters. The fitted inter-electronic repulsion and magnetic parameters vary linearly with ionic charge, i, but better linear fits are obtained with (4-i)2, although the reason is unclear at present. The two-body configuration interaction parameters α and β exhibit a linear relation with [ΔE(bc)]-1, where ΔE(bc) is the energy difference between the 4f2 barycentre and that of the interacting configuration, namely 4f6p for La+, Ce2+, and Pr3+, and 5p54f3 for Nd4+. The linear fit provides the rationale for the negative value of α for the case of La+, where the interacting configuration is located below 4f2.

Spray-drying nanocapsules in presence of colloidal silica as drying auxiliary agent: formulation and process variables optimization using experimental designs.

PubMed

Tewa-Tagne, Patrice; Degobert, Ghania; Briançon, Stéphanie; Bordes, Claire; Gauvrit, Jean-Yves; Lanteri, Pierre; Fessi, Hatem

2007-04-01

Spray-drying process was used for the development of dried polymeric nanocapsules. The purpose of this research was to investigate the effects of formulation and process variables on the resulting powder characteristics in order to optimize them. Experimental designs were used in order to estimate the influence of formulation parameters (nanocapsules and silica concentrations) and process variables (inlet temperature, spray-flow air, feed flow rate and drying air flow rate) on spray-dried nanocapsules when using silica as drying auxiliary agent. The interactions among the formulation parameters and process variables were also studied. Responses analyzed for computing these effects and interactions were outlet temperature, moisture content, operation yield, particles size, and particulate density. Additional qualitative responses (particles morphology, powder behavior) were also considered. Nanocapsules and silica concentrations were the main factors influencing the yield, particulate density and particle size. In addition, they were concerned for the only significant interactions occurring among two different variables. None of the studied variables had major effect on the moisture content while the interaction between nanocapsules and silica in the feed was of first interest and determinant for both the qualitative and quantitative responses. The particles morphology depended on the feed formulation but was unaffected by the process conditions. This study demonstrated that drying nanocapsules using silica as auxiliary agent by spray drying process enables the obtaining of dried micronic particle size. The optimization of the process and the formulation variables resulted in a considerable improvement of product yield while minimizing the moisture content.

The Euler’s Graphical User Interface Spreadsheet Calculator for Solving Ordinary Differential Equations by Visual Basic for Application Programming

NASA Astrophysics Data System (ADS)

Gaik Tay, Kim; Cheong, Tau Han; Foong Lee, Ming; Kek, Sie Long; Abdul-Kahar, Rosmila

2017-08-01

In the previous work on Euler’s spreadsheet calculator for solving an ordinary differential equation, the Visual Basic for Application (VBA) programming was used, however, a graphical user interface was not developed to capture users input. This weakness may make users confuse on the input and output since those input and output are displayed in the same worksheet. Besides, the existing Euler’s spreadsheet calculator is not interactive as there is no prompt message if there is a mistake in inputting the parameters. On top of that, there are no users’ instructions to guide users to input the derivative function. Hence, in this paper, we improved previous limitations by developing a user-friendly and interactive graphical user interface. This improvement is aimed to capture users’ input with users’ instructions and interactive prompt error messages by using VBA programming. This Euler’s graphical user interface spreadsheet calculator is not acted as a black box as users can click on any cells in the worksheet to see the formula used to implement the numerical scheme. In this way, it could enhance self-learning and life-long learning in implementing the numerical scheme in a spreadsheet and later in any programming language.

Improved Limits on Axionlike-Particle-Mediated P , T -Violating Interactions between Electrons and Nucleons from Electric Dipole Moments of Atoms and Molecules

NASA Astrophysics Data System (ADS)

Stadnik, Y. V.; Dzuba, V. A.; Flambaum, V. V.

2018-01-01

In the presence of P , T -violating interactions, the exchange of axionlike particles between electrons and nucleons in atoms and molecules induces electric dipole moments (EDMs) of atoms and molecules. We perform calculations of such axion-exchange-induced atomic EDMs using the relativistic Hartree-Fock-Dirac method including electron core polarization corrections. We present analytical estimates to explain the dependence of these induced atomic EDMs on the axion mass and atomic parameters. From the experimental bounds on the EDMs of atoms and molecules, including Cs 133 , Tl 205 , Xe 129 , Hg 199 , Yb 171 F 19 , Hf 180 F+ 19 , and Th 232 O 16 , we constrain the P , T -violating scalar-pseudoscalar nucleon-electron and electron-electron interactions mediated by a generic axionlike particle of arbitrary mass. Our limits improve on existing laboratory bounds from other experiments by many orders of magnitude for ma≳10-2 eV . We also place constraints on C P violation in certain types of relaxion models.

Effects of 12-week concurrent high-intensity interval strength and endurance training programme on physical performance in healthy older people.

PubMed

García-Pinillos, Felipe; Laredo-Aguilera, José A; Muñoz-Jiménez, Marcos; Latorre-Román, Pedro A

2017-03-13

This study aimed to analyse the effect of 12-week low-volume HIIT-based concurrent training programme on body composition, upper- and lower-body muscle strength, mobility and balance in older adults, as well as to compare it with a low- moderate-intensity continuous training. 90 active older adults were randomly assigned to experimental (EG, n=47), and control (CG, n=43) groups. Body composition and physical functioning were assessed before (pre-test) and after (post-test) a 12-week intervention. A 2-way repeated measures ANOVA was used to test for an interaction between training programme and groups. The time x group interaction revealed no significant between-group differences at pre-test (p≥0.05). The group x time interaction showed significant improvements for the EG in body composition parameters (p<0.05) and physical functioning (muscle strength: p<0.001; mobility: p<0.001; and balance: p<0.05); while the CG remained unchanged (p≥0.05). This HIIT-based concurrent training programme led to greater improvements in body composition, muscle strength, mobility and balance in healthy older people than a regular low- moderate-intensity continuous training, despite the reduction in overall training volume.

Neutrino oscillations and Non-Standard Interactions

NASA Astrophysics Data System (ADS)

Farzan, Yasaman; Tórtola, Mariam

2018-02-01

Current neutrino experiments are measuring the neutrino mixing parameters with an unprecedented accuracy. The upcoming generation of neutrino experiments will be sensitive to subdominant oscillation effects that can give information on the yet-unknown neutrino parameters: the Dirac CP-violating phase, the mass ordering and the octant of θ_{23}. Determining the exact values of neutrino mass and mixing parameters is crucial to test neutrino models and flavor symmetries designed to predict these neutrino parameters. In the first part of this review, we summarize the current status of the neutrino oscillation parameter determination. We consider the most recent data from all solar experiments and the atmospheric data from Super-Kamiokande, IceCube and ANTARES. We also implement the data from the reactor neutrino experiments KamLAND, Daya Bay, RENO and Double Chooz as well as the long baseline neutrino data from MINOS, T2K and NOvA. If in addition to the standard interactions, neutrinos have subdominant yet-unknown Non-Standard Interactions (NSI) with matter fields, extracting the values of these parameters will suffer from new degeneracies and ambiguities. We review such effects and formulate the conditions on the NSI parameters under which the precision measurement of neutrino oscillation parameters can be distorted. Like standard weak interactions, the non-standard interaction can be categorized into two groups: Charged Current (CC) NSI and Neutral Current (NC) NSI. Our focus will be mainly on neutral current NSI because it is possible to build a class of models that give rise to sizeable NC NSI with discernible effects on neutrino oscillation. These models are based on new U(1) gauge symmetry with a gauge boson of mass ≲ 10 MeV. The UV complete model should be of course electroweak invariant which in general implies that along with neutrinos, charged fermions also acquire new interactions on which there are strong bounds. We enumerate the bounds that already exist on the electroweak symmetric models and demonstrate that it is possible to build viable models avoiding all these bounds. In the end, we review methods to test these models and suggest approaches to break the degeneracies in deriving neutrino mass parameters caused by NSI.

Structural and interaction parameters of thermosensitive native α-elastin biohybrid microgel

NASA Astrophysics Data System (ADS)

Balaceanu, Andreea; Singh, Smriti; Demco, Dan E.; Möller, Martin

2014-09-01

The structural and water interaction parameters for native, α-elastin biohybrid microgel crosslinked with hydrophilic and hydrophobic crosslinkers are obtained from the volume phase transition temperature behaviour, 1H high-resolution magic-angle sample spinning transverse magnetization relaxation NMR, and modified Flory-Rehner swelling theory. Firstly, considering a homogeneous morphology the number of subchains in the biohybrid microgel, the residual water in deswollen state as a function of crosslink density and the temperature dependence of the Flory biopolymer-water interaction parameters are reported for the biohybrid microgels prepared with hydrophilic (PEG-DGE) and hydrophobic (BS3) crosslinkers. The Flory-Rehner classical approach is subsequently modified taking into account the heterogeneities observed by NMR transverse relaxation measurements. Two differently mobile regions are determined, a hydrophobic domain and a crosslinking domain with relative reduced mobility. For the first time, the influence of chain mobility on the Flory interaction parameter is investigated through a modified Flory state equation. The contributions of amino-acids located in the hydrophobic and crosslinking domains in the polypeptide sequence are separated while analyzing the biopolymer-water interaction.

Cryogenic wind tunnels: Unique capabilities for the aerodynamicist

NASA Technical Reports Server (NTRS)

Hall, R. M.

1976-01-01

The cryogenic wind-tunnel concept as a practical means for improving ground simulation of transonic flight conditions. The Langley 1/3-meter transonic cryogenic tunnel is operational, and the design of a cryogenic National Transonic Facility is undertaken. A review of some of the unique capabilities of cryogenic wind tunnels is presented. In particular, the advantages of having independent control of tunnel Mach number, total pressure, and total temperature are highlighted. This separate control over the three tunnel parameters will open new frontiers in Mach number, Reynolds number, aeroelastic, and model-tunnel interaction studies.

Near-field thermal radiation of deep- subwavelength slits in the near infrared range.

PubMed

Guo, Yan; Li, Kuanbiao; Xu, Ying; Wei, Kaihua

2017-09-18

We numerically investigate the thermal radiation of one-dimensional deep subwavelength slits in the near infrared range. Using numerical calculations of single-slit and multi-slit structures, we find that high-level radiation efficiency can be achieved for a wide spectrum when ultra-thin intermediate layers are used, and it is less affected by structure parameters. The underlying mechanisms involve Surface Plasmon Polaritons resonance and Fabry-Perot interference at each slit and the interaction between adjacent slits. This structure helps understand and improve the design of thermal radiation control devices.

Space proton transport in one dimension

NASA Technical Reports Server (NTRS)

Lamkin, S. L.; Khandelwal, G. S.; Shinn, J. L.; Wilson, J. W.

1994-01-01

An approximate evaluation procedure is derived for a second-order theory of coupled nucleon transport in one dimension. An analytical solution with a simplified interaction model is used to determine quadrature parameters to minimize truncation error. Effects of the improved method on transport solutions with the BRYNTRN data base are evaluated. Comparisons with Monte Carlo benchmarks are given. Using different shield materials, the computational procedure is used to study the physics of space protons. A transition effect occurs in tissue near the shield interface and is most important in shields of high atomic number.

Heat flux estimates of power balance on Proto-MPEX with IR imaging

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

Showers, M., E-mail: mshower1@vols.utk.edu; Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831; Biewer, T. M.

The Prototype Material Plasma Exposure eXperiment (Proto-MPEX) at Oak Ridge National Laboratory (ORNL) is a precursor linear plasma device to the Material Plasma Exposure eXperiment (MPEX), which will study plasma material interactions (PMIs) for future fusion reactors. This paper will discuss the initial steps performed towards completing a power balance on Proto-MPEX to quantify where energy is lost from the plasma, including the relevant diagnostic package implemented. Machine operating parameters that will improve Proto-MPEX’s performance may be identified, increasing its PMI research capabilities.

Scaling of plasma-body interactions in low Earth orbit

NASA Astrophysics Data System (ADS)

Capon, C. J.; Brown, M.; Boyce, R. R.

2017-04-01

This paper derives the generalised set of dimensionless parameters that scale the interaction of an unmagnetised multi-species plasma with an arbitrarily charged object - the application in this work being to the interaction of the ionosphere with Low Earth Orbiting (LEO) objects. We find that a plasma with K ion species can be described by 1 + 4 K independent dimensionless parameters. These parameters govern the deflection and coupling of ion species k , the relative electrical shielding of the body, electron energy, and scaling of temporal effects. The general shielding length λ ϕ is introduced, which reduces to the Debye length in the high-temperature (weakly coupled) limit. The ability of the scaling parameters to predict the self-similar transformations of single and multi-species plasma interactions is demonstrated numerically using pdFOAM, an electrostatic Particle-in-Cell—Direct Simulation Monte Carlo code. The presented scaling relationships represent a significant generalisation of past work, linking low and high voltage plasma phenomena. Further, the presented parameters capture the scaling of multi-species plasmas with multiply charged ions, demonstrating previously unreported scaling relationship transformations. The implications of this work are not limited to LEO plasma-body interactions but apply to processes governed by the Vlasov-Maxwell equations and represent a framework upon which to incorporate the scaling of additional phenomena, e.g., magnetism and charging.

Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA

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

Talukder, Srijeeta; Sen, Shrabani; Chaudhury, Pinaki, E-mail: pinakc@rediffmail.com

We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters is estimated for this purpose for three different DNA sequences. The analysis leads us to a better understanding of the sequence dependent nature of the breathing dynamics of hetero-polymeric DNA. Out of the 14 model parameters for DNA stability in the statistical Poland-Scheraga approach, the hydrogen bond interaction ε{sub hb}(AT) for an AT base pair and the ring factor ξ turn out to be the most sensitive parameters. In addition, the stackingmore » interaction ε{sub st}(TA-TA) for an TA-TA nearest neighbor pair of base-pairs is found to be the most sensitive one among all stacking interactions. Moreover, we also establish that the nature of stacking interaction has a deciding effect on the DNA breathing dynamics, not the number of times a particular stacking interaction appears in a sequence. We show that the sensitivity analysis can be used as an effective measure to guide a stochastic optimization technique to find the kinetic rate constants related to the dynamics as opposed to the case where the rate constants are measured using the conventional unbiased way of optimization.« less

Molybdenum disulfide and water interaction parameters

NASA Astrophysics Data System (ADS)

Heiranian, Mohammad; Wu, Yanbin; Aluru, Narayana R.

2017-09-01

Understanding the interaction between water and molybdenum disulfide (MoS2) is of crucial importance to investigate the physics of various applications involving MoS2 and water interfaces. An accurate force field is required to describe water and MoS2 interactions. In this work, water-MoS2 force field parameters are derived using the high-accuracy random phase approximation (RPA) method and validated by comparing to experiments. The parameters obtained from the RPA method result in water-MoS2 interface properties (solid-liquid work of adhesion) in good comparison to the experimental measurements. An accurate description of MoS2-water interaction will facilitate the study of MoS2 in applications such as DNA sequencing, sea water desalination, and power generation.

Update of KDBI: Kinetic Data of Bio-molecular Interaction database

PubMed Central

Kumar, Pankaj; Han, B. C.; Shi, Z.; Jia, J.; Wang, Y. P.; Zhang, Y. T.; Liang, L.; Liu, Q. F.; Ji, Z. L.; Chen, Y. Z.

2009-01-01

Knowledge of the kinetics of biomolecular interactions is important for facilitating the study of cellular processes and underlying molecular events, and is essential for quantitative study and simulation of biological systems. Kinetic Data of Bio-molecular Interaction database (KDBI) has been developed to provide information about experimentally determined kinetic data of protein–protein, protein–nucleic acid, protein–ligand, nucleic acid–ligand binding or reaction events described in the literature. To accommodate increasing demand for studying and simulating biological systems, numerous improvements and updates have been made to KDBI, including new ways to access data by pathway and molecule names, data file in System Biology Markup Language format, more efficient search engine, access to published parameter sets of simulation models of 63 pathways, and 2.3-fold increase of data (19 263 entries of 10 532 distinctive biomolecular binding and 11 954 interaction events, involving 2635 proteins/protein complexes, 847 nucleic acids, 1603 small molecules and 45 multi-step processes). KDBI is publically available at http://bidd.nus.edu.sg/group/kdbi/kdbi.asp. PMID:18971255

Compliance control based on PSO algorithm to improve the feeling during physical human-robot interaction.

PubMed

Jiang, Zhongliang; Sun, Yu; Gao, Peng; Hu, Ying; Zhang, Jianwei

2016-01-01

Robots play more important roles in daily life and bring us a lot of convenience. But when people work with robots, there remain some significant differences in human-human interactions and human-robot interaction. It is our goal to make robots look even more human-like. We design a controller which can sense the force acting on any point of a robot and ensure the robot can move according to the force. First, a spring-mass-dashpot system was used to describe the physical model, and the second-order system is the kernel of the controller. Then, we can establish the state space equations of the system. In addition, the particle swarm optimization algorithm had been used to obtain the system parameters. In order to test the stability of system, the root-locus diagram had been shown in the paper. Ultimately, some experiments had been carried out on the robotic spinal surgery system, which is developed by our team, and the result shows that the new controller performs better during human-robot interaction.

Superheavy dark matter through Higgs portal operators

NASA Astrophysics Data System (ADS)

Kolb, Edward W.; Long, Andrew J.

2017-11-01

The WIMPzilla hypothesis is that the dark matter is a super-weakly-interacting and superheavy particle. Conventionally, the WIMPzilla abundance is set by gravitational particle production during or at the end of inflation. In this study we allow the WIMPzilla to interact directly with Standard Model fields through the Higgs portal, and we calculate the thermal production (freeze-in) of WIMPzilla dark matter from the annihilation of Higgs boson pairs in the plasma. The two particle-physics model parameters are the WIMPzilla mass and the Higgs-WIMPzilla coupling. The two cosmological parameters are the reheating temperature and the expansion rate of the universe at the end of inflation. We delineate the regions of parameter space where either gravitational or thermal production is dominant, and within those regions we identify the parameters that predict the observed dark matter relic abundance. Allowing for thermal production opens up the parameter space, even for Planck-suppressed Higgs-WIMPzilla interactions.

Reproducible research in palaeomagnetism

NASA Astrophysics Data System (ADS)

Lurcock, Pontus; Florindo, Fabio

2015-04-01

The reproducibility of research findings is attracting increasing attention across all scientific disciplines. In palaeomagnetism as elsewhere, computer-based analysis techniques are becoming more commonplace, complex, and diverse. Analyses can often be difficult to reproduce from scratch, both for the original researchers and for others seeking to build on the work. We present a palaeomagnetic plotting and analysis program designed to make reproducibility easier. Part of the problem is the divide between interactive and scripted (batch) analysis programs. An interactive desktop program with a graphical interface is a powerful tool for exploring data and iteratively refining analyses, but usually cannot operate without human interaction. This makes it impossible to re-run an analysis automatically, or to integrate it into a larger automated scientific workflow - for example, a script to generate figures and tables for a paper. In some cases the parameters of the analysis process itself are not saved explicitly, making it hard to repeat or improve the analysis even with human interaction. Conversely, non-interactive batch tools can be controlled by pre-written scripts and configuration files, allowing an analysis to be 'replayed' automatically from the raw data. However, this advantage comes at the expense of exploratory capability: iteratively improving an analysis entails a time-consuming cycle of editing scripts, running them, and viewing the output. Batch tools also tend to require more computer expertise from their users. PuffinPlot is a palaeomagnetic plotting and analysis program which aims to bridge this gap. First released in 2012, it offers both an interactive, user-friendly desktop interface and a batch scripting interface, both making use of the same core library of palaeomagnetic functions. We present new improvements to the program that help to integrate the interactive and batch approaches, allowing an analysis to be interactively explored and refined, then saved as a self-contained configuration which can be re-run without human interaction. PuffinPlot can thus be used as a component of a larger scientific workflow, integrated with workflow management tools such as Kepler, without compromising its capabilities as an exploratory tool. Since both PuffinPlot and the platform it runs on (Java) are Free/Open Source software, even the most fundamental components of an analysis can be verified and reproduced.

Indications of a late-time interaction in the dark sector.

PubMed

Salvatelli, Valentina; Said, Najla; Bruni, Marco; Melchiorri, Alessandro; Wands, David

2014-10-31

We show that a general late-time interaction between cold dark matter and vacuum energy is favored by current cosmological data sets. We characterize the strength of the coupling by a dimensionless parameter q(V) that is free to take different values in four redshift bins from the primordial epoch up to today. This interacting scenario is in agreement with measurements of cosmic microwave background temperature anisotropies from the Planck satellite, supernovae Ia from Union 2.1 and redshift space distortions from a number of surveys, as well as with combinations of these different data sets. Our analysis of the 4-bin interaction shows that a nonzero interaction is likely at late times. We then focus on the case q(V)≠0 in a single low-redshift bin, obtaining a nested one parameter extension of the standard ΛCDM model. We study the Bayesian evidence, with respect to ΛCDM, of this late-time interaction model, finding moderate evidence for an interaction starting at z=0.9, dependent upon the prior range chosen for the interaction strength parameter q(V). For this case the null interaction (q(V)=0, i.e., ΛCDM) is excluded at 99% C.L.

Probing transverse momentum broadening via jet-related angular correlations in relativistic nuclear collisions

NASA Astrophysics Data System (ADS)

Chen, Lin; Qin, Guang-You; Wei, Shu-Yi; Xiao, Bo-Wen; Zhang, Han-Zhong

2017-11-01

Jet-related correlations have been regarded as important tools for studying jet-medium interaction and jet quenching in relativistic heavy-ion collisions at RHIC and the LHC. Here we present our recent work [L. Chen, G.-Y. Qin, S.-Y. Wei, B.-W. Xiao, H.-Z. Zhang, Probing Transverse Momentum Broadening via Dihadron and Hadron-jet Angular Correlations in Relativistic Heavy-ion Collisions, arxiv:arXiv:1607.01932] and show that the back-to-back angular correlations in dijet, dihadron and hadron-jet measurements can be utilized as a quantitative tool to probe the medium-induced transverse momentum broadening and to extract jet quenching parameter q̂. By comparing with the dihadron and hadron-jet angular correlation data at RHIC, we obtain the medium-induced transverse momentum broadening, averaged over different jet paths, 〈 p⊥2 〉 ∼ 13 GeV2 for a quark jet in most central Au-Au collisions at 200A GeV. Future experiments with statistically improved data on jet-related (angular) correlations will allow us to obtain more precise knowledge of jet quenching parameter and parton-medium interaction in high-energy nuclear collisions.

Effect of pH and interaction between egg white protein and hydroxypropymethylcellulose in bulk aqueous medium on foaming properties.

PubMed

Sadahira, Mitie S; Lopes, Fernanda C Rezende; Rodrigues, Maria I; Yamada, Aureo T; Cunha, Rosiane L; Netto, Flavia M

2015-07-10

Egg white protein (EW) is used as surface-active ingredient in aerated food and hydroxypropylmethylcellulose (HPMC) is a polysaccharide that behaves as a surfactant. This study aimed at investigating the effects of process parameters biopolymer concentration (2.0-5.0%, w/w), EW:HPMC ratio (2:1-18:1), pH (3.0-6.0), and the influence of biopolymers' behavior in aqueous solution at different pH on the foaming properties (overrun, drainage, and bubble growth rate). Process parameters had effect on foaming properties. The pH was the major factor influencing the type of EW/HPMC interaction and affected the foaming properties of biopolymer mixture. At pH 3.0, EW and HPMC showed thermodynamic compatibility leading to better foaming properties, higher foaming capacity, and stability than without HPMC addition whereas at pH 4.5 and 6.0, EW and HPMC are incompatible that causes lower stability concerning the disproportionation comparing to foam without HPMC. At pH between 3.0 and 4.5, HPMC improves foaming properties of aerated products. Copyright © 2015 Elsevier Ltd. All rights reserved.

Computational model to investigate the relative contributions of different neuromuscular properties of tibialis anterior on force generated during ankle dorsiflexion.

PubMed

Siddiqi, Ariba; Poosapadi Arjunan, Sridhar; Kumar, Dinesh Kant

2018-01-16

This study describes a new model of the force generated by tibialis anterior muscle with three new features: single-fiber action potential, twitch force, and pennation angle. This model was used to investigate the relative effects and interaction of ten age-associated neuromuscular parameters. Regression analysis (significance level of 0.05) between the neuromuscular properties and corresponding simulated force produced at the footplate was performed. Standardized slope coefficients were computed to rank the effect of the parameters. The results show that reduction in the average firing rate is the reason for the sharp decline in the force and other factors, such as number of muscle fibers, specific force, pennation angle, and innervation ratio. The fast fiber ratio affects the simulated force through two significant interactions. This study has ranked the individual contributions of the neuromuscular factors to muscle strength decline of the TA and identified firing rate decline as the biggest cause followed by decrease in muscle fiber number and specific force. The strategy for strength preservation for the elderly should focus on improving firing rate. Graphical abstract Neuromuscular properties of Tibialis Anterior on force generated during ankle dorsiflexion.

Astrobiology as a framework for investigating antibiotic susceptibility: a study of Halomonas hydrothermalis

PubMed Central

Cockell, Charles S.

2017-01-01

Physical and chemical boundaries for microbial multiplication on Earth are strongly influenced by interactions between environmental extremes. However, little is known about how interactions between multiple stress parameters affect the sensitivity of microorganisms to antibiotics. Here, we assessed how 12 distinct permutations of salinity, availability of an essential nutrient (iron) and atmospheric composition (aerobic or microaerobic) affect the susceptibility of a polyextremotolerant bacterium, Halomonas hydrothermalis, to ampicillin, kanamycin and ofloxacin. While salinity had a significant impact on sensitivity to all three antibiotics (as shown by turbidimetric analyses), the nature of this impact was modified by iron availability and the ambient gas composition, with differing effects observed for each compound. These two parameters were found to be of particular importance when considered in combination and, in the case of ampicillin, had a stronger combined influence on antibiotic tolerance than salinity. Our data show how investigating microbial responses to multiple extremes, which are more representative of natural habitats than single extremes, can improve our understanding of the effects of antimicrobial compounds and suggest how studies of habitability, motivated by the desire to map the limits of life, can be used to systematically assess the effectiveness of antibiotics. PMID:28123098

Astrobiology as a framework for investigating antibiotic susceptibility: a study of Halomonas hydrothermalis.

PubMed

Harrison, Jesse P; Angel, Roey; Cockell, Charles S

2017-01-01

Physical and chemical boundaries for microbial multiplication on Earth are strongly influenced by interactions between environmental extremes. However, little is known about how interactions between multiple stress parameters affect the sensitivity of microorganisms to antibiotics. Here, we assessed how 12 distinct permutations of salinity, availability of an essential nutrient (iron) and atmospheric composition (aerobic or microaerobic) affect the susceptibility of a polyextremotolerant bacterium, Halomonas hydrothermalis, to ampicillin, kanamycin and ofloxacin. While salinity had a significant impact on sensitivity to all three antibiotics (as shown by turbidimetric analyses), the nature of this impact was modified by iron availability and the ambient gas composition, with differing effects observed for each compound. These two parameters were found to be of particular importance when considered in combination and, in the case of ampicillin, had a stronger combined influence on antibiotic tolerance than salinity. Our data show how investigating microbial responses to multiple extremes, which are more representative of natural habitats than single extremes, can improve our understanding of the effects of antimicrobial compounds and suggest how studies of habitability, motivated by the desire to map the limits of life, can be used to systematically assess the effectiveness of antibiotics. © 2017 The Author(s).

Interactive K-Means Clustering Method Based on User Behavior for Different Analysis Target in Medicine.

PubMed

Lei, Yang; Yu, Dai; Bin, Zhang; Yang, Yang

2017-01-01

Clustering algorithm as a basis of data analysis is widely used in analysis systems. However, as for the high dimensions of the data, the clustering algorithm may overlook the business relation between these dimensions especially in the medical fields. As a result, usually the clustering result may not meet the business goals of the users. Then, in the clustering process, if it can combine the knowledge of the users, that is, the doctor's knowledge or the analysis intent, the clustering result can be more satisfied. In this paper, we propose an interactive K -means clustering method to improve the user's satisfactions towards the result. The core of this method is to get the user's feedback of the clustering result, to optimize the clustering result. Then, a particle swarm optimization algorithm is used in the method to optimize the parameters, especially the weight settings in the clustering algorithm to make it reflect the user's business preference as possible. After that, based on the parameter optimization and adjustment, the clustering result can be closer to the user's requirement. Finally, we take an example in the breast cancer, to testify our method. The experiments show the better performance of our algorithm.

Improved InGaN LED System Efficacy and Cost via Droop Reduction

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

Wildeson, Isaac

Efficiency droop is a non-thermal process intrinsic to indium gallium nitride light emitting diodes (LEDs) in which the external quantum efficiency (EQE) decreases with increasing drive current density. Mitigating droop would allow one to reduce the size of LEDs driven at a given current or to drive LEDs of given size at higher current while maintaining high efficiencies. In other words, droop mitigation can lead to significant gains in light output per dollar and/or light output per watt of input power. This project set an EQE improvement goal at high drive current density which was to be attained by improvingmore » the LED active region design and growth process following a droop mitigation strategy. The interactions between LED active region design parameters and efficiency droop were studied by modeling and experiments. The crystal defects that tend to form in more complex LED designs intended to mitigate droop were studied with advanced characterization methods that provided insight into the structural and electronic properties of the material. This insight was applied to improve the epitaxy process both in terms of active region design and optimization of growth parameters. The final project goals were achieved on schedule and an epitaxy process leading to LEDs with EQE exceeding the project target was demonstrated.« less

Optimized Design and Analysis of Sparse-Sampling fMRI Experiments

PubMed Central

Perrachione, Tyler K.; Ghosh, Satrajit S.

2013-01-01

Sparse-sampling is an important methodological advance in functional magnetic resonance imaging (fMRI), in which silent delays are introduced between MR volume acquisitions, allowing for the presentation of auditory stimuli without contamination by acoustic scanner noise and for overt vocal responses without motion-induced artifacts in the functional time series. As such, the sparse-sampling technique has become a mainstay of principled fMRI research into the cognitive and systems neuroscience of speech, language, hearing, and music. Despite being in use for over a decade, there has been little systematic investigation of the acquisition parameters, experimental design considerations, and statistical analysis approaches that bear on the results and interpretation of sparse-sampling fMRI experiments. In this report, we examined how design and analysis choices related to the duration of repetition time (TR) delay (an acquisition parameter), stimulation rate (an experimental design parameter), and model basis function (an analysis parameter) act independently and interactively to affect the neural activation profiles observed in fMRI. First, we conducted a series of computational simulations to explore the parameter space of sparse design and analysis with respect to these variables; second, we validated the results of these simulations in a series of sparse-sampling fMRI experiments. Overall, these experiments suggest the employment of three methodological approaches that can, in many situations, substantially improve the detection of neurophysiological response in sparse fMRI: (1) Sparse analyses should utilize a physiologically informed model that incorporates hemodynamic response convolution to reduce model error. (2) The design of sparse fMRI experiments should maintain a high rate of stimulus presentation to maximize effect size. (3) TR delays of short to intermediate length can be used between acquisitions of sparse-sampled functional image volumes to increase the number of samples and improve statistical power. PMID:23616742

Optimized design and analysis of sparse-sampling FMRI experiments.

PubMed

Perrachione, Tyler K; Ghosh, Satrajit S

2013-01-01

Sparse-sampling is an important methodological advance in functional magnetic resonance imaging (fMRI), in which silent delays are introduced between MR volume acquisitions, allowing for the presentation of auditory stimuli without contamination by acoustic scanner noise and for overt vocal responses without motion-induced artifacts in the functional time series. As such, the sparse-sampling technique has become a mainstay of principled fMRI research into the cognitive and systems neuroscience of speech, language, hearing, and music. Despite being in use for over a decade, there has been little systematic investigation of the acquisition parameters, experimental design considerations, and statistical analysis approaches that bear on the results and interpretation of sparse-sampling fMRI experiments. In this report, we examined how design and analysis choices related to the duration of repetition time (TR) delay (an acquisition parameter), stimulation rate (an experimental design parameter), and model basis function (an analysis parameter) act independently and interactively to affect the neural activation profiles observed in fMRI. First, we conducted a series of computational simulations to explore the parameter space of sparse design and analysis with respect to these variables; second, we validated the results of these simulations in a series of sparse-sampling fMRI experiments. Overall, these experiments suggest the employment of three methodological approaches that can, in many situations, substantially improve the detection of neurophysiological response in sparse fMRI: (1) Sparse analyses should utilize a physiologically informed model that incorporates hemodynamic response convolution to reduce model error. (2) The design of sparse fMRI experiments should maintain a high rate of stimulus presentation to maximize effect size. (3) TR delays of short to intermediate length can be used between acquisitions of sparse-sampled functional image volumes to increase the number of samples and improve statistical power.

Auditory display as feedback for a novel eye-tracking system for sterile operating room interaction.

PubMed

Black, David; Unger, Michael; Fischer, Nele; Kikinis, Ron; Hahn, Horst; Neumuth, Thomas; Glaser, Bernhard

2018-01-01

The growing number of technical systems in the operating room has increased attention on developing touchless interaction methods for sterile conditions. However, touchless interaction paradigms lack the tactile feedback found in common input devices such as mice and keyboards. We propose a novel touchless eye-tracking interaction system with auditory display as a feedback method for completing typical operating room tasks. Auditory display provides feedback concerning the selected input into the eye-tracking system as well as a confirmation of the system response. An eye-tracking system with a novel auditory display using both earcons and parameter-mapping sonification was developed to allow touchless interaction for six typical scrub nurse tasks. An evaluation with novice participants compared auditory display with visual display with respect to reaction time and a series of subjective measures. When using auditory display to substitute for the lost tactile feedback during eye-tracking interaction, participants exhibit reduced reaction time compared to using visual-only display. In addition, the auditory feedback led to lower subjective workload and higher usefulness and system acceptance ratings. Due to the absence of tactile feedback for eye-tracking and other touchless interaction methods, auditory display is shown to be a useful and necessary addition to new interaction concepts for the sterile operating room, reducing reaction times while improving subjective measures, including usefulness, user satisfaction, and cognitive workload.

Quality improvement of a rice-substituted fried noodle by utilizing the protein-polyphenol interaction between a pea protein isolate and green tea (Camellia sinensis) extract.

PubMed

Song, Youngwoon; Yoo, Sang-Ho

2017-11-15

The quality of rice-substituted fried noodles was improved by applying interaction between pea protein isolate (PPI) and green tea extract (GTE). Radical-scavenging activities of GTE were stably maintained when exposed to acidic pH, UV light, and fluorescent light, but decreased by approximately 65% when exposed to 80°C for 168h. The RVA profiles of noodle dough showed that peak viscosity and breakdown increased significantly but that setback and final viscosity remained unchanged with 20% rice flour replacement. PPI significantly decreased the viscosity parameters of rice-supplemented dough, and the addition of GTE recovered these values significantly. The cooking loss and viscoelasticity (R max ) of cooked rice-supplemented noodles were fully restored by combined treatment of PPI and GTE. GTE decreased the peroxide value of fried noodles by 14% after storage at 63°C for 16days. Therefore, PPI+GTE treatment has great potential for use in fried noodles owing to the reinforced network and antioxidant activity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Decoupling Polymer Properties to Elucidate Mechanisms Governing Cell Behavior

PubMed Central

Wang, Xintong; Boire, Timothy C.; Bronikowski, Christine; Zachman, Angela L.; Crowder, Spencer W.

2012-01-01

Determining how a biomaterial interacts with cells (“structure-function relationship”) reflects its eventual clinical applicability. Therefore, a fundamental understanding of how individual material properties modulate cell-biomaterial interactions is pivotal to improving the efficacy and safety of clinically translatable biomaterial systems. However, due to the coupled nature of material properties, their individual effects on cellular responses are difficult to understand. Structure-function relationships can be more clearly understood by the effective decoupling of each individual parameter. In this article, we discuss three basic decoupling strategies: (1) surface modification, (2) cross-linking, and (3) combinatorial approaches (i.e., copolymerization and polymer blending). Relevant examples of coupled material properties are briefly reviewed in each section to highlight the need for improved decoupling methods. This follows with examples of more effective decoupling techniques, mainly from the perspective of three primary classes of synthetic materials: polyesters, polyethylene glycol, and polyacrylamide. Recent strides in decoupling methodologies, especially surface-patterning and combinatorial techniques, offer much promise in further understanding the structure-function relationships that largely govern the success of future advancements in biomaterials, tissue engineering, and drug delivery. PMID:22536977

Identifying differentially expressed genes in cancer patients using a non-parameter Ising model.

PubMed

Li, Xumeng; Feltus, Frank A; Sun, Xiaoqian; Wang, James Z; Luo, Feng

2011-10-01

Identification of genes and pathways involved in diseases and physiological conditions is a major task in systems biology. In this study, we developed a novel non-parameter Ising model to integrate protein-protein interaction network and microarray data for identifying differentially expressed (DE) genes. We also proposed a simulated annealing algorithm to find the optimal configuration of the Ising model. The Ising model was applied to two breast cancer microarray data sets. The results showed that more cancer-related DE sub-networks and genes were identified by the Ising model than those by the Markov random field model. Furthermore, cross-validation experiments showed that DE genes identified by Ising model can improve classification performance compared with DE genes identified by Markov random field model. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interactive spectral analyzer and comparator (ISAAC)

NASA Astrophysics Data System (ADS)

Latković, O.; Cséki, A.; Vince, I.

2003-10-01

We are developing an application for graphical comparison of observed and synthetic spectra (ISAAC). Synthetic spectrum calculation is performed by SPECTRUM, Stellar Spectral Synthesis Program by Richard O. Gray that we use with his kind permission. This program computes line profiles under LTE conditions in the given wavelength interval using a stellar (solar) atmosphere model, a spectral line data list (wavelength, energy levels, oscillator strengths, and damping constants), a file containing data for atoms and molecules, as well as a data file for hydrogen line profiles calculation. ISAAC offers a simple interface for viewing and changing any atomic parameter SPECTRUM uses for line profile calculation, enabling quick comparison of the new synthetic line profile with the observed one. In this way parameters like relative abundances, oscillator strengths and van der Waals damping constants can be improved, achieving a better agreement with the observed spectrum.

Effects of photosynthetic photon flux density, frequency, duty ratio, and their interactions on net photosynthetic rate of cos lettuce leaves under pulsed light: explanation based on photosynthetic-intermediate pool dynamics.

PubMed

Jishi, Tomohiro; Matsuda, Ryo; Fujiwara, Kazuhiro

2018-06-01

Square-wave pulsed light is characterized by three parameters, namely average photosynthetic photon flux density (PPFD), pulsed-light frequency, and duty ratio (the ratio of light-period duration to that of the light-dark cycle). In addition, the light-period PPFD is determined by the averaged PPFD and duty ratio. We investigated the effects of these parameters and their interactions on net photosynthetic rate (P n ) of cos lettuce leaves for every combination of parameters. Averaged PPFD values were 0-500 µmol m -2  s -1 . Frequency values were 0.1-1000 Hz. White LED arrays were used as the light source. Every parameter affected P n and interactions between parameters were observed for all combinations. The P n under pulsed light was lower than that measured under continuous light of the same averaged PPFD, and this difference was enhanced with decreasing frequency and increasing light-period PPFD. A mechanistic model was constructed to estimate the amount of stored photosynthetic intermediates over time under pulsed light. The results indicated that all effects of parameters and their interactions on P n were explainable by consideration of the dynamics of accumulation and consumption of photosynthetic intermediates.

PRIMO: An Interactive Homology Modeling Pipeline.

PubMed

Hatherley, Rowan; Brown, David K; Glenister, Michael; Tastan Bishop, Özlem

2016-01-01

The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduces the workload required by the user, while still allowing engagement from the user during every step. Default parameters are given for each step, which can either be modified or supplemented with additional external input. PRIMO has been designed for users of varying levels of experience with homology modeling. The pipeline incorporates a user-friendly interface that makes it easy to alter parameters used during modeling. During each stage of the modeling process, the site provides suggestions for novice users to improve the quality of their models. PRIMO provides functionality that allows users to also model ligands and ions in complex with their protein targets. Herein, we assess the accuracy of the fully automated capabilities of the server, including a comparative analysis of the available alignment programs, as well as of the refinement levels used during modeling. The tests presented here demonstrate the reliability of the PRIMO server when producing a large number of protein models. While PRIMO does focus on user involvement in the homology modeling process, the results indicate that in the presence of suitable templates, good quality models can be produced even without user intervention. This gives an idea of the base level accuracy of PRIMO, which users can improve upon by adjusting parameters in their modeling runs. The accuracy of PRIMO's automated scripts is being continuously evaluated by the CAMEO (Continuous Automated Model EvaluatiOn) project. The PRIMO site is free for non-commercial use and can be accessed at https://primo.rubi.ru.ac.za/.

Graphical user interface to optimize image contrast parameters used in object segmentation - biomed 2009.

PubMed

Anderson, Jeffrey R; Barrett, Steven F

2009-01-01

Image segmentation is the process of isolating distinct objects within an image. Computer algorithms have been developed to aid in the process of object segmentation, but a completely autonomous segmentation algorithm has yet to be developed [1]. This is because computers do not have the capability to understand images and recognize complex objects within the image. However, computer segmentation methods [2], requiring user input, have been developed to quickly segment objects in serial sectioned images, such as magnetic resonance images (MRI) and confocal laser scanning microscope (CLSM) images. In these cases, the segmentation process becomes a powerful tool in visualizing the 3D nature of an object. The user input is an important part of improving the performance of many segmentation methods. A double threshold segmentation method has been investigated [3] to separate objects in gray scaled images, where the gray level of the object is among the gray levels of the background. In order to best determine the threshold values for this segmentation method the image must be manipulated for optimal contrast. The same is true of other segmentation and edge detection methods as well. Typically, the better the image contrast, the better the segmentation results. This paper describes a graphical user interface (GUI) that allows the user to easily change image contrast parameters that will optimize the performance of subsequent object segmentation. This approach makes use of the fact that the human brain is extremely effective in object recognition and understanding. The GUI provides the user with the ability to define the gray scale range of the object of interest. These lower and upper bounds of this range are used in a histogram stretching process to improve image contrast. Also, the user can interactively modify the gamma correction factor that provides a non-linear distribution of gray scale values, while observing the corresponding changes to the image. This interactive approach gives the user the power to make optimal choices in the contrast enhancement parameters.

PRIMO: An Interactive Homology Modeling Pipeline

PubMed Central

Glenister, Michael

2016-01-01

The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduces the workload required by the user, while still allowing engagement from the user during every step. Default parameters are given for each step, which can either be modified or supplemented with additional external input. PRIMO has been designed for users of varying levels of experience with homology modeling. The pipeline incorporates a user-friendly interface that makes it easy to alter parameters used during modeling. During each stage of the modeling process, the site provides suggestions for novice users to improve the quality of their models. PRIMO provides functionality that allows users to also model ligands and ions in complex with their protein targets. Herein, we assess the accuracy of the fully automated capabilities of the server, including a comparative analysis of the available alignment programs, as well as of the refinement levels used during modeling. The tests presented here demonstrate the reliability of the PRIMO server when producing a large number of protein models. While PRIMO does focus on user involvement in the homology modeling process, the results indicate that in the presence of suitable templates, good quality models can be produced even without user intervention. This gives an idea of the base level accuracy of PRIMO, which users can improve upon by adjusting parameters in their modeling runs. The accuracy of PRIMO’s automated scripts is being continuously evaluated by the CAMEO (Continuous Automated Model EvaluatiOn) project. The PRIMO site is free for non-commercial use and can be accessed at https://primo.rubi.ru.ac.za/. PMID:27855192

Combining techniques for screening and evaluating interaction terms on high-dimensional time-to-event data.

PubMed

Sariyar, Murat; Hoffmann, Isabell; Binder, Harald

2014-02-26

Molecular data, e.g. arising from microarray technology, is often used for predicting survival probabilities of patients. For multivariate risk prediction models on such high-dimensional data, there are established techniques that combine parameter estimation and variable selection. One big challenge is to incorporate interactions into such prediction models. In this feasibility study, we present building blocks for evaluating and incorporating interactions terms in high-dimensional time-to-event settings, especially for settings in which it is computationally too expensive to check all possible interactions. We use a boosting technique for estimation of effects and the following building blocks for pre-selecting interactions: (1) resampling, (2) random forests and (3) orthogonalization as a data pre-processing step. In a simulation study, the strategy that uses all building blocks is able to detect true main effects and interactions with high sensitivity in different kinds of scenarios. The main challenge are interactions composed of variables that do not represent main effects, but our findings are also promising in this regard. Results on real world data illustrate that effect sizes of interactions frequently may not be large enough to improve prediction performance, even though the interactions are potentially of biological relevance. Screening interactions through random forests is feasible and useful, when one is interested in finding relevant two-way interactions. The other building blocks also contribute considerably to an enhanced pre-selection of interactions. We determined the limits of interaction detection in terms of necessary effect sizes. Our study emphasizes the importance of making full use of existing methods in addition to establishing new ones.

The prospects of selection for social genetic effects to improve welfare and productivity in livestock

PubMed Central

Ellen, Esther D.; Rodenburg, T. Bas; Albers, Gerard A. A.; Bolhuis, J. Elizabeth; Camerlink, Irene; Duijvesteijn, Naomi; Knol, Egbert F.; Muir, William M.; Peeters, Katrijn; Reimert, Inonge; Sell-Kubiak, Ewa; van Arendonk, Johan A. M.; Visscher, Jeroen; Bijma, Piter

2014-01-01

Social interactions between individuals living in a group can have both positive and negative effects on welfare, productivity, and health of these individuals. Negative effects of social interactions in livestock are easier to observe than positive effects. For example, laying hens may develop feather pecking, which can cause mortality due to cannibalism, and pigs may develop tail biting or excessive aggression. Several studies have shown that social interactions affect the genetic variation in a trait. Genetic improvement of socially-affected traits, however, has proven to be difficult until relatively recently. The use of classical selection methods, like individual selection, may result in selection responses opposite to expected, because these methods neglect the effect of an individual on its group mates (social genetic effects). It has become clear that improvement of socially-affected traits requires selection methods that take into account not only the direct effect of an individual on its own phenotype but also the social genetic effects, also known as indirect genetic effects, of an individual on the phenotypes of its group mates. Here, we review the theoretical and empirical work on social genetic effects, with a focus on livestock. First, we present the theory of social genetic effects. Subsequently, we evaluate the evidence for social genetic effects in livestock and other species, by reviewing estimates of genetic parameters for direct and social genetic effects. Then we describe the results of different selection experiments. Finally, we discuss issues concerning the implementation of social genetic effects in livestock breeding programs. This review demonstrates that selection for socially-affected traits, using methods that target both the direct and social genetic effects, is a promising, but sometimes difficult to use in practice, tool to simultaneously improve production and welfare in livestock. PMID:25426136

The prospects of selection for social genetic effects to improve welfare and productivity in livestock.

PubMed

Ellen, Esther D; Rodenburg, T Bas; Albers, Gerard A A; Bolhuis, J Elizabeth; Camerlink, Irene; Duijvesteijn, Naomi; Knol, Egbert F; Muir, William M; Peeters, Katrijn; Reimert, Inonge; Sell-Kubiak, Ewa; van Arendonk, Johan A M; Visscher, Jeroen; Bijma, Piter

2014-01-01

Social interactions between individuals living in a group can have both positive and negative effects on welfare, productivity, and health of these individuals. Negative effects of social interactions in livestock are easier to observe than positive effects. For example, laying hens may develop feather pecking, which can cause mortality due to cannibalism, and pigs may develop tail biting or excessive aggression. Several studies have shown that social interactions affect the genetic variation in a trait. Genetic improvement of socially-affected traits, however, has proven to be difficult until relatively recently. The use of classical selection methods, like individual selection, may result in selection responses opposite to expected, because these methods neglect the effect of an individual on its group mates (social genetic effects). It has become clear that improvement of socially-affected traits requires selection methods that take into account not only the direct effect of an individual on its own phenotype but also the social genetic effects, also known as indirect genetic effects, of an individual on the phenotypes of its group mates. Here, we review the theoretical and empirical work on social genetic effects, with a focus on livestock. First, we present the theory of social genetic effects. Subsequently, we evaluate the evidence for social genetic effects in livestock and other species, by reviewing estimates of genetic parameters for direct and social genetic effects. Then we describe the results of different selection experiments. Finally, we discuss issues concerning the implementation of social genetic effects in livestock breeding programs. This review demonstrates that selection for socially-affected traits, using methods that target both the direct and social genetic effects, is a promising, but sometimes difficult to use in practice, tool to simultaneously improve production and welfare in livestock.

Efficient creation of dipolar coupled nitrogen-vacancy spin qubits in diamond

NASA Astrophysics Data System (ADS)

Jakobi, I.; Momenzadeh, S. A.; Fávaro de Oliveira, F.; Michl, J.; Ziem, F.; Schreck, M.; Neumann, P.; Denisenko, A.; Wrachtrup, J.

2016-09-01

Coherently coupled pairs or multimers of nitrogen-vacancy defect electron spins in diamond have many promising applications especially in quantum information processing (QIP) but also in nanoscale sensing applications. Scalable registers of spin qubits are essential to the progress of QIP. Ion implantation is the only known technique able to produce defect pairs close enough to allow spin coupling via dipolar interaction. Although several competing methods have been proposed to increase the resulting resolution of ion implantation, the reliable creation of working registers is still to be demonstrated. The current limitation are residual radiation-induced defects, resulting in degraded qubit performance as trade-off for positioning accuracy. Here we present an optimized estimation of nanomask implantation parameters that are most likely to produce interacting qubits under standard conditions. We apply our findings to a well-established technique, namely masks written in electron-beam lithography, to create coupled defect pairs with a reasonable probability. Furthermore, we investigate the scaling behavior and necessary improvements to efficiently engineer interacting spin architectures.

ICAP - An Interactive Cluster Analysis Procedure for analyzing remotely sensed data

NASA Technical Reports Server (NTRS)

Wharton, S. W.; Turner, B. J.

1981-01-01

An Interactive Cluster Analysis Procedure (ICAP) was developed to derive classifier training statistics from remotely sensed data. ICAP differs from conventional clustering algorithms by allowing the analyst to optimize the cluster configuration by inspection, rather than by manipulating process parameters. Control of the clustering process alternates between the algorithm, which creates new centroids and forms clusters, and the analyst, who can evaluate and elect to modify the cluster structure. Clusters can be deleted, or lumped together pairwise, or new centroids can be added. A summary of the cluster statistics can be requested to facilitate cluster manipulation. The principal advantage of this approach is that it allows prior information (when available) to be used directly in the analysis, since the analyst interacts with ICAP in a straightforward manner, using basic terms with which he is more likely to be familiar. Results from testing ICAP showed that an informed use of ICAP can improve classification, as compared to an existing cluster analysis procedure.

A network-based training environment: a medical image processing paradigm.

PubMed

Costaridou, L; Panayiotakis, G; Sakellaropoulos, P; Cavouras, D; Dimopoulos, J

1998-01-01

The capability of interactive multimedia and Internet technologies is investigated with respect to the implementation of a distance learning environment. The system is built according to a client-server architecture, based on the Internet infrastructure, composed of server nodes conceptually modelled as WWW sites. Sites are implemented by customization of available components. The environment integrates network-delivered interactive multimedia courses, network-based tutoring, SIG support, information databases of professional interest, as well as course and tutoring management. This capability has been demonstrated by means of an implemented system, validated with digital image processing content, specifically image enhancement. Image enhancement methods are theoretically described and applied to mammograms. Emphasis is given to the interactive presentation of the effects of algorithm parameters on images. The system end-user access depends on available bandwidth, so high-speed access can be achieved via LAN or local ISDN connections. Network based training offers new means of improved access and sharing of learning resources and expertise, as promising supplements in training.

Quantum mechanical electronic structure calculation reveals orientation dependence of hydrogen bond energy in proteins.

PubMed

Mondal, Abhisek; Datta, Saumen

2017-06-01

Hydrogen bond plays a unique role in governing macromolecular interactions with exquisite specificity. These interactions govern the fundamental biological processes like protein folding, enzymatic catalysis, molecular recognition. Despite extensive research work, till date there is no proper report available about the hydrogen bond's energy surface with respect to its geometric parameters, directly derived from proteins. Herein, we have deciphered the potential energy landscape of hydrogen bond directly from the macromolecular coordinates obtained from Protein Data Bank using quantum mechanical electronic structure calculations. The findings unravel the hydrogen bonding energies of proteins in parametric space. These data can be used to understand the energies of such directional interactions involved in biological molecules. Quantitative characterization has also been performed using Shannon entropic calculations for atoms participating in hydrogen bond. Collectively, our results constitute an improved way of understanding hydrogen bond energies in case of proteins and complement the knowledge-based potential. Proteins 2017; 85:1046-1055. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

First and Higher Order Effects on Zero Order Radiative Transfer Model

NASA Astrophysics Data System (ADS)

Neelam, M.; Mohanty, B.

2014-12-01

Microwave radiative transfer model are valuable tool in understanding the complex land surface interactions. Past literature has largely focused on local sensitivity analysis for factor priotization and ignoring the interactions between the variables and uncertainties around them. Since land surface interactions are largely nonlinear, there always exist uncertainties, heterogeneities and interactions thus it is important to quantify them to draw accurate conclusions. In this effort, we used global sensitivity analysis to address the issues of variable uncertainty, higher order interactions, factor priotization and factor fixing for zero-order radiative transfer (ZRT) model. With the to-be-launched Soil Moisture Active Passive (SMAP) mission of NASA, it is very important to have a complete understanding of ZRT for soil moisture retrieval to direct future research and cal/val field campaigns. This is a first attempt to use GSA technique to quantify first order and higher order effects on brightness temperature from ZRT model. Our analyses reflect conditions observed during the growing agricultural season for corn and soybeans in two different regions in - Iowa, U.S.A and Winnipeg, Canada. We found that for corn fields in Iowa, there exist significant second order interactions between soil moisture, surface roughness parameters (RMS height and correlation length) and vegetation parameters (vegetation water content, structure and scattering albedo), whereas in Winnipeg, second order interactions are mainly due to soil moisture and vegetation parameters. But for soybean fields in both Iowa and Winnipeg, we found significant interactions only to exist between soil moisture and surface roughness parameters.

Topology and dynamics of the interaction between 5-nitroimidazole radiosensitizers and duplex DNA studied by a combination of docking, molecular dynamic simulations and NMR spectroscopy

NASA Astrophysics Data System (ADS)

Ramalho, Teodorico C.; França, Tanos C. C.; Cortopassi, Wilian A.; Gonçalves, Arlan S.; da Silva, Alan W. S.; da Cunha, Elaine F. F.

2011-04-01

In spite of recent progress, cancer is still one of the most serious health problems of mankind. Recently, it has been discovered that tumor hypoxia can be exploited for selective anticancer treatment using radiosensitizers that are activated only under hypoxic conditions. The most commonly used radiosensitizers are the 5-nitroimidazole derivatives. The toxicity of bioreductive anticancer drugs, such as radiosensitizers is associated to their interaction with DNA. In this work, we have investigated the interaction between the model radiosensitizers metronizole, nimorazole and secnidazole with salmon DNA in order to get insights on the drug-macromolecule interactions. To this end, we have employed NMR techniques (PFG NMR spectra and spin-lattice relaxation rates) in combination with theoretical tools, such as docking calculations and MD simulations. Initially, results show that the δ values are not the most appropriated NMR parameters to map the interaction topology of drug-macromolecule complexes. Furthermore our data indicate that radiosensitizers, in the inactive form, interact considerably with DNA, significantly increasing its toxicity. In fact, we obtained a good agreement between that technique and docking and MD simulations. This suggests that improvements in the structures of these molecules in order to achieve new and more selective bioreductive anticancer drugs are still necessary.

Establishment of a protein frequency library and its application in the reliable identification of specific protein interaction partners.

PubMed

Boulon, Séverine; Ahmad, Yasmeen; Trinkle-Mulcahy, Laura; Verheggen, Céline; Cobley, Andy; Gregor, Peter; Bertrand, Edouard; Whitehorn, Mark; Lamond, Angus I

2010-05-01

The reliable identification of protein interaction partners and how such interactions change in response to physiological or pathological perturbations is a key goal in most areas of cell biology. Stable isotope labeling with amino acids in cell culture (SILAC)-based mass spectrometry has been shown to provide a powerful strategy for characterizing protein complexes and identifying specific interactions. Here, we show how SILAC can be combined with computational methods drawn from the business intelligence field for multidimensional data analysis to improve the discrimination between specific and nonspecific protein associations and to analyze dynamic protein complexes. A strategy is shown for developing a protein frequency library (PFL) that improves on previous use of static "bead proteomes." The PFL annotates the frequency of detection in co-immunoprecipitation and pulldown experiments for all proteins in the human proteome. It can provide a flexible and objective filter for discriminating between contaminants and specifically bound proteins and can be used to normalize data values and facilitate comparisons between data obtained in separate experiments. The PFL is a dynamic tool that can be filtered for specific experimental parameters to generate a customized library. It will be continuously updated as data from each new experiment are added to the library, thereby progressively enhancing its utility. The application of the PFL to pulldown experiments is especially helpful in identifying either lower abundance or less tightly bound specific components of protein complexes that are otherwise lost among the large, nonspecific background.

Electronic structure, dielectric response, and surface charge distribution of RGD (1FUV) peptide.

PubMed

Adhikari, Puja; Wen, Amy M; French, Roger H; Parsegian, V Adrian; Steinmetz, Nicole F; Podgornik, Rudolf; Ching, Wai-Yim

2014-07-08

Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor.

The Influence of Interactions and Minor Mergers on the Structure of Galactic Disks

NASA Astrophysics Data System (ADS)

Schwarzkopf, U.

1999-07-01

A detailed statistical study is presented focused on the effects of minor mergers and tidal interactions on the radial and vertical structure of galactic disks. The fundamental disk parameters of 112 highly-inclined/edge-on galaxies are studied in optical and in near-infrared passbands. This sample consists of two subsamples of 65 non-interacting and 47 interacting/merging galaxies. Additionally, 41 of these galaxies were observed in the near-infrared. A 3-dimensional disk modelling and -fitting procedure was applied in order to analyze and to compare characteristic disk parameters of all sample galaxies. Furthermore, n-body simulations were performed in order to study the influence of minor mergers in the mass range Msat/Mdisk 0.1 on the vertical structure of disks in spiral galaxies. In particular, the dependence of vertical, tidally-triggered disk thickening on initial disk parameters is investigated. The quantitative results of both simulation and observation are compared in order to find similarities in the distribution of characteristic disk parameters.

Measuring The Neutron Lifetime to One Second Using in Beam Techniques

NASA Astrophysics Data System (ADS)

Mulholland, Jonathan; NIST In Beam Lifetime Collaboration

2013-10-01

The decay of the free neutron is the simplest nuclear beta decay and is the prototype for charged current semi-leptonic weak interactions. A precise value for the neutron lifetime is required for consistency tests of the Standard Model and is an essential parameter in the theory of Big Bang Nucleosynthesis. A new measurement of the neutron lifetime using the in-beam method is planned at the National Institute of Standards and Technology Center for Neutron Research. The systematic effects associated with the in-beam method are markedly different than those found in storage experiments utilizing ultracold neutrons. Experimental improvements, specifically recent advances in the determination of absolute neutron fluence, should permit an overall uncertainty of 1 second on the neutron lifetime. The technical improvements in the in-beam technique, and the path toward improving the precision of the new measurement will be discussed.

Flavor-dependent eigenvolume interactions in a hadron resonance gas

NASA Astrophysics Data System (ADS)

Alba, P.; Vovchenko, V.; Gorenstein, M. I.; Stoecker, H.

2018-06-01

Eigenvolume effects in the hadron resonance gas (HRG) model are studied for experimental hadronic yields in nucleus-nucleus collisions. If particle eigenvolumes are different for different hadron species, the excluded volume HRG (EV-HRG) improves fits to multiplicity data. In particular, using different mass-volume relations for strange and non-strange hadrons we observe a remarkable improvement in the quality of the fits. This effect appears to be rather insensitive to other details in the schemes employed in the EV-HRG. We show that the parameters found from fitting the data of the ALICE Collaboration in central Pb+Pb collisions at the collision energy √{sNN } = 2.76 TeV entail the same improvement for all centralities at the same collision energy, and for the RHIC and SPS data at lower collision energies. Our findings are put in the context of recent fits of lattice QCD results.

Relationship of goat milk flow emission variables with milking routine, milking parameters, milking machine characteristics and goat physiology.

PubMed

Romero, G; Panzalis, R; Ruegg, P

2017-11-01

The aim of this paper was to study the relationship between milk flow emission variables recorded during milking of dairy goats with variables related to milking routine, goat physiology, milking parameters and milking machine characteristics, to determine the variables affecting milking performance and help the goat industry pinpoint farm and milking practices that improve milking performance. In total, 19 farms were visited once during the evening milking. Milking parameters (vacuum level (VL), pulsation ratio and pulsation rate, vacuum drop), milk emission flow variables (milking time, milk yield, maximum milk flow (MMF), average milk flow (AVMF), time until 500 g/min milk flow is established (TS500)), doe characteristics of 8 to 10 goats/farm (breed, days in milk and parity), milking practices (overmilking, overstripping, pre-lag time) and milking machine characteristics (line height, presence of claw) were recorded on every farm. The relationships between recorded variables and farm were analysed by a one-way ANOVA analysis. The relationships of milk yield, MMF, milking time and TS500 with goat physiology, milking routine, milking parameters and milking machine design were analysed using a linear mixed model, considering the farm as the random effect. Farm was significant (P<0.05) in all the studied variables. Milk emission flow variables were similar to those recommended in scientific studies. Milking parameters were adequate in most of the farms, being similar to those recommended in scientific studies. Few milking parameters and milking machine characteristics affected the tested variables: average vacuum level only showed tendency on MMF, and milk pipeline height on TS500. Milk yield (MY) was mainly affected by parity, as the interaction of days in milk with parity was also significant. Milking time was mainly affected by milk yield and breed. Also significant were parity, the interaction of days in milk with parity and overstripping, whereas overmilking showed a slight tendency. We concluded that most of the studied variables were mainly related to goat physiology characteristics, as the effects of milking parameters and milking machine characteristics were scarce.

Experiments on Adaptive Self-Tuning of Seismic Signal Detector Parameters

NASA Astrophysics Data System (ADS)

Knox, H. A.; Draelos, T.; Young, C. J.; Chael, E. P.; Peterson, M. G.; Lawry, B.; Phillips-Alonge, K. E.; Balch, R. S.; Ziegler, A.

2016-12-01

Scientific applications, including underground nuclear test monitoring and microseismic monitoring can benefit enormously from data-driven dynamic algorithms for tuning seismic and infrasound signal detection parameters since continuous streams are producing waveform archives on the order of 1TB per month. Tuning is a challenge because there are a large number of data processing parameters that interact in complex ways, and because the underlying populating of true signal detections is generally unknown. The largely manual process of identifying effective parameters, often performed only over a subset of stations over a short time period, is painstaking and does not guarantee that the resulting controls are the optimal configuration settings. We present improvements to an Adaptive Self-Tuning algorithm for continuously adjusting detection parameters based on consistency with neighboring sensors. Results are shown for 1) data from a very dense network ( 120 stations, 10 km radius) deployed during 2008 on Erebus Volcano, Antarctica, and 2) data from a continuous downhole seismic array in the Farnsworth Field, an oil field in Northern Texas that hosts an ongoing carbon capture, utilization, and storage project. Performance is assessed in terms of missed detections and false detections relative to human analyst detections, simulated waveforms where ground-truth detections exist and visual inspection.

Behaviour of conductivity improvers in jet fuel

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

Dacre, B.; Hetherington, J.I.

1995-05-01

Dangerous accumulation of electrostatic charge can occur due to high speed pumping and microfiltration of fuel. This can be avoided by increasing the electrical conductivity of the fuel using conductivity improver additives. However, marked variations occur in the conductivity response of different fuels when doped to the same level with conductivity improver. This has been attributed to interactions of the conductivity improver with other fuel additives or fuel contaminants. The present work concentrates on the effects of fuel contaminants, in particular polar compounds, on the performance of the conductivity improver. Conductivity is the fuel property of prime interest. The conductivitymore » response of model systems of the conductivity improver STADIS 450 in dodecane has been measured and the effect on this conductivity of additions of model polar contaminants sodium naphthenate, sodium dodecyl benzene sulphonate, and sodium phenate have been measured. The sodium salts have been found to have a complex effect on the performance of STADIS 450, reducing the conductivity at low concentrations to a minimum value and then increasing the conductivity at high concentrations of sodium salts. This work has focused on characterising this minimum in the conductivity values and on understanding the reason for its occurrence. The effects on the minimum conductivity value of the following parameters are investigated: (a) time, (b) STADIS 450 concentration, (c) sodium salt concentration, (d) mixed sodium salts, (e) experimental method, (f) a phenol, (g) individual components of STADIS 450. The complex conductivity response of the STADIS 450 to sodium salt impurities is discussed in terms of possible inter-molecular interactions.« less

Investigation of intermolecular interaction of binary mixture of acrylonitrile with bromobenzene

NASA Astrophysics Data System (ADS)

Deshmukh, S. D.; Pattebahadur, K. L.; Mohod, A. G.; Patil, S. S.; Khirade, P. W.

2018-04-01

In this paper, study of binary mixture of Acrylonitrile (ACN)with Bromobenzene(BB) has been carried out at eleven concentrations at room temperature. The determined density(ρ) and refractive index (nD) values of binary mixture are used to calculate the excess properties of mixture over the entire composition range. The aforesaid parameters are used to calculate excess parameters and fitted to the Redlich-Kister equation to determine the bj coefficients. From the above parameters, intermolecular interaction and dynamics of molecules of binary mixture at molecular level are discussed. The Conformational analysis of the intermolecular interaction between Acrylonitrile and Bromobenzene is supported by the FTIR spectra.

Parameter optimization and stretch enhancement of AISI 316 sheet using rapid prototyping technique

NASA Astrophysics Data System (ADS)

Moayedfar, M.; Rani, A. M.; Hanaei, H.; Ahmad, A.; Tale, A.

2017-10-01

Incremental sheet forming is a flexible manufacturing process which uses the indenter point-to-point force to shape the sheet metal workpiece into manufactured parts in batch production series. However, the problem sometimes arising from this process is the low plastic point in the stress-strain diagram of the material which leads the low stretching amount before ultra-tensile strain point. Hence, a set of experiments is designed to find the optimum forming parameters in this process for optimum sheet thickness distribution while both sides of the sheet are considered for the surface quality improvement. A five-axis high-speed CNC milling machine is employed to deliver the proper motion based on the programming system while the clamping system for holding the sheet metal was a blank mould. Finally, an electron microscope and roughness machine are utilized to evaluate the surface structure of final parts, illustrate any defect may cause during the forming process and examine the roughness of the final part surface accordingly. The best interaction between parameters is obtained with the optimum values which lead the maximum sheet thickness distribution of 4.211e-01 logarithmic elongation when the depth was 24mm with respect to the design. This study demonstrates that this rapid forming method offers an alternative solution for surface quality improvement of 65% avoiding the low probability of cracks and low probability of crystal structure changes.

Immersive Virtual Reality to Improve Walking Abilities in Cerebral Palsy: A Pilot Study.

PubMed

Gagliardi, Chiara; Turconi, Anna Carla; Biffi, Emilia; Maghini, Cristina; Marelli, Alessia; Cesareo, Ambra; Diella, Eleonora; Panzeri, Daniele

2018-04-27

Immersive virtual reality (IVR) offers new possibilities to perform treatments in an ecological and interactive environment with multimodal online feedbacks. Sixteen school-aged children (mean age 11 ± 2.4 years) with Bilateral CP-diplegia, attending mainstream schools were recruited for a pilot study in a pre-post treatment experimental design. The intervention was focused on walking competences and endurance and performed by the Gait Real-time Analysis Interactive Lab (GRAIL), an innovative treadmill platform based on IVR. The participants underwent eighteen therapy sessions in 4 weeks. Functional evaluations, instrumental measures including GAIT analysis and parental questionnaire were utilized to assess the treatment effects. Walking pattern (stride length left and right side, respectively p = 0.001 and 0.003; walking speed p = 0.001), endurance (6MWT, p = 0.026), gross motor abilities (GMFM-88, p = 0.041) and most kinematic and kinetic parameters significantly improved after the intervention. The changes were mainly predicted by age and cognitive abilities. The effect could have been due to the possibility of IVR to foster integration of motor/perceptual competences beyond the training of the walking ability, giving a chance of improvement also to older and already treated children.

Anharmonic Normal Mode Analysis of Elastic Network Model Improves the Modeling of Atomic Fluctuations in Protein Crystal Structures

PubMed Central

Zheng, Wenjun

2010-01-01

Abstract Protein conformational dynamics, despite its significant anharmonicity, has been widely explored by normal mode analysis (NMA) based on atomic or coarse-grained potential functions. To account for the anharmonic aspects of protein dynamics, this study proposes, and has performed, an anharmonic NMA (ANMA) based on the Cα-only elastic network models, which assume elastic interactions between pairs of residues whose Cα atoms or heavy atoms are within a cutoff distance. The key step of ANMA is to sample an anharmonic potential function along the directions of eigenvectors of the lowest normal modes to determine the mean-squared fluctuations along these directions. ANMA was evaluated based on the modeling of anisotropic displacement parameters (ADPs) from a list of 83 high-resolution protein crystal structures. Significant improvement was found in the modeling of ADPs by ANMA compared with standard NMA. Further improvement in the modeling of ADPs is attained if the interactions between a protein and its crystalline environment are taken into account. In addition, this study has determined the optimal cutoff distances for ADP modeling based on elastic network models, and these agree well with the peaks of the statistical distributions of distances between Cα atoms or heavy atoms derived from a large set of protein crystal structures. PMID:20550915

Discriminative Relational Topic Models.

PubMed

Chen, Ning; Zhu, Jun; Xia, Fei; Zhang, Bo

2015-05-01

Relational topic models (RTMs) provide a probabilistic generative process to describe both the link structure and document contents for document networks, and they have shown promise on predicting network structures and discovering latent topic representations. However, existing RTMs have limitations in both the restricted model expressiveness and incapability of dealing with imbalanced network data. To expand the scope and improve the inference accuracy of RTMs, this paper presents three extensions: 1) unlike the common link likelihood with a diagonal weight matrix that allows the-same-topic interactions only, we generalize it to use a full weight matrix that captures all pairwise topic interactions and is applicable to asymmetric networks; 2) instead of doing standard Bayesian inference, we perform regularized Bayesian inference (RegBayes) with a regularization parameter to deal with the imbalanced link structure issue in real networks and improve the discriminative ability of learned latent representations; and 3) instead of doing variational approximation with strict mean-field assumptions, we present collapsed Gibbs sampling algorithms for the generalized relational topic models by exploring data augmentation without making restricting assumptions. Under the generic RegBayes framework, we carefully investigate two popular discriminative loss functions, namely, the logistic log-loss and the max-margin hinge loss. Experimental results on several real network datasets demonstrate the significance of these extensions on improving prediction performance.

Complex molecular assemblies at hand via interactive simulations.

PubMed

Delalande, Olivier; Férey, Nicolas; Grasseau, Gilles; Baaden, Marc

2009-11-30

Studying complex molecular assemblies interactively is becoming an increasingly appealing approach to molecular modeling. Here we focus on interactive molecular dynamics (IMD) as a textbook example for interactive simulation methods. Such simulations can be useful in exploring and generating hypotheses about the structural and mechanical aspects of biomolecular interactions. For the first time, we carry out low-resolution coarse-grain IMD simulations. Such simplified modeling methods currently appear to be more suitable for interactive experiments and represent a well-balanced compromise between an important gain in computational speed versus a moderate loss in modeling accuracy compared to higher resolution all-atom simulations. This is particularly useful for initial exploration and hypothesis development for rare molecular interaction events. We evaluate which applications are currently feasible using molecular assemblies from 1900 to over 300,000 particles. Three biochemical systems are discussed: the guanylate kinase (GK) enzyme, the outer membrane protease T and the soluble N-ethylmaleimide-sensitive factor attachment protein receptors complex involved in membrane fusion. We induce large conformational changes, carry out interactive docking experiments, probe lipid-protein interactions and are able to sense the mechanical properties of a molecular model. Furthermore, such interactive simulations facilitate exploration of modeling parameters for method improvement. For the purpose of these simulations, we have developed a freely available software library called MDDriver. It uses the IMD protocol from NAMD and facilitates the implementation and application of interactive simulations. With MDDriver it becomes very easy to render any particle-based molecular simulation engine interactive. Here we use its implementation in the Gromacs software as an example. Copyright 2009 Wiley Periodicals, Inc.

A Toolkit to Study Sensitivity of the Geant4 Predictions to the Variations of the Physics Model Parameters

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

Fields, Laura; Genser, Krzysztof; Hatcher, Robert

Geant4 is the leading detector simulation toolkit used in high energy physics to design detectors and to optimize calibration and reconstruction software. It employs a set of carefully validated physics models to simulate interactions of particles with matter across a wide range of interaction energies. These models, especially the hadronic ones, rely largely on directly measured cross-sections and phenomenological predictions with physically motivated parameters estimated by theoretical calculation or measurement. Because these models are tuned to cover a very wide range of possible simulation tasks, they may not always be optimized for a given process or a given material. Thismore » raises several critical questions, e.g. how sensitive Geant4 predictions are to the variations of the model parameters, or what uncertainties are associated with a particular tune of a Geant4 physics model, or a group of models, or how to consistently derive guidance for Geant4 model development and improvement from a wide range of available experimental data. We have designed and implemented a comprehensive, modular, user-friendly software toolkit to study and address such questions. It allows one to easily modify parameters of one or several Geant4 physics models involved in the simulation, and to perform collective analysis of multiple variants of the resulting physics observables of interest and comparison against a variety of corresponding experimental data. Based on modern event-processing infrastructure software, the toolkit offers a variety of attractive features, e.g. flexible run-time configurable workflow, comprehensive bookkeeping, easy to expand collection of analytical components. Design, implementation technology, and key functionalities of the toolkit are presented and illustrated with results obtained with Geant4 key hadronic models.« less

Experimentally fitted biodynamic models for pedestrian-structure interaction in walking situations

NASA Astrophysics Data System (ADS)

Toso, Marcelo André; Gomes, Herbert Martins; da Silva, Felipe Tavares; Pimentel, Roberto Leal

2016-05-01

The interaction between moving humans and structures usually occurs in slender structures in which the level of vibration is potentially high. Furthermore, there is the addition of mass to the structural system due to the presence of people and an increase in damping due to the human body´s ability to absorb vibrational energy. In this paper, a test campaign is presented to obtain parameters for a single degree of freedom (SDOF) biodynamic model that represents the action of a walking pedestrian in the vertical direction. The parameters of this model are the mass (m), damping (c) and stiffness (k). The measurements were performed on a force platform, and the inputs were the spectral acceleration amplitudes of the first three harmonics at the waist level of the test subjects and the corresponding amplitudes of the first three harmonics of the vertical ground reaction force. This leads to a system of nonlinear equations that is solved using a gradient-based optimization algorithm. A set of individuals took part in the tests to ensure inter-subject variability, and, regression expressions and an artificial neural network (ANN) were used to relate the biodynamic parameters to the pacing rate and the body mass of the pedestrians. The results showed some scatter in damping and stiffness that could not be precisely correlated with the masses and pacing rates of the subjects. The use of the ANN resulted in significant improvements in the parameter expressions with a low uncertainty. Finally, the measured vertical accelerations on a prototype footbridge show the adequacy of the numerical model for the representation of the effects of walking pedestrians on a structure. The results are consistent for many crowd densities.

Optimal properties for coated titanium implants with the hydroxyapatite layer formed by the pulsed laser deposition technique

NASA Astrophysics Data System (ADS)

Himmlova, Lucia; Dostalova, Tatjana; Jelinek, Miroslav; Bartova, Jirina; Pesakova, V.; Adam, M.

1999-02-01

Pulsed laser deposition technique allow to 'tailor' bioceramic coat for metal implants by the change of deposition conditions. Each attribute is influenced by the several deposition parameters and each parameter change several various properties. Problem caused that many parameters has an opposite function and improvement of one property is followed by deterioration of other attribute. This study monitor influence of each single deposition parameter and evaluate its importance form the point of view of coat properties. For deposition KrF excimer laser in stainless-steel deposition chamber was used. Deposition conditions (ambient composition and pressures, metallic substrate temperature, energy density and target-substrate distance) were changed according to the film properties. A non-coated titanium implant was used as a control. Films with promising mechanical quality underwent an in vitro biological tests -- measurement of proliferation activity, observing cell interactions with macrophages, fibroblasts, testing toxicity of percolates, observing a solubility of hydroxyapatite (HA) coat. Deposition conditions corresponding with the optimal mechanical and biochemical properties are: metal temperature 490 degrees Celsius, ambient-mixture of argon and water vapor, energy density 3 Jcm-2, target-substrate distance 7.5 cm.

Atomistic modeling of metallic thin films by modified embedded atom method

NASA Astrophysics Data System (ADS)

Hao, Huali; Lau, Denvid

2017-11-01

Molecular dynamics simulation is applied to investigate the deposition process of metallic thin films. Eight metals, titanium, vanadium, iron, cobalt, nickel, copper, tungsten, and gold, are chosen to be deposited on the aluminum substrate. The second nearest-neighbor modified embedded atom method potential is adopted to predict their thermal and mechanical properties. When quantifying the screening parameters of the potential, the error for Young's modulus and coefficient of thermal expansion between the simulated results and the experimental measurements is less than 15%, demonstrating the reliability of the potential to predict metallic behaviors related to thermal and mechanical properties. A set of potential parameters which governs the interactions between aluminum and other metals in a binary system is also generated from ab initio calculation. The details of interfacial structures between the chosen films and substrate are successfully simulated with the help of these parameters. Our results indicate that the preferred orientation of film growth depends on the film crystal structure, and the inter-diffusion at the interface is correlated the cohesive energy parameter of potential for the binary system. Such finding provides an important basis to further understand the interfacial science, which contributes to the improvement of the mechanical properties, reliability and durability of films.

Theory of the Interfacial Dzyaloshinskii-Moriya Interaction in Rashba Antiferromagnets

NASA Astrophysics Data System (ADS)

Qaiumzadeh, Alireza; Ado, Ivan A.; Duine, Rembert A.; Titov, Mikhail; Brataas, Arne

2018-05-01

In antiferromagnetic (AFM) thin films, broken inversion symmetry or coupling to adjacent heavy metals can induce Dzyaloshinskii-Moriya (DM) interactions. Knowledge of the DM parameters is essential for understanding and designing exotic spin structures, such as hedgehog Skyrmions and chiral Néel walls, which are attractive for use in novel information storage technologies. We introduce a framework for computing the DM interaction in two-dimensional Rashba antiferromagnets. Unlike in Rashba ferromagnets, the DM interaction is not suppressed even at low temperatures. The material parameters control both the strength and the sign of the interfacial DM interaction. Our results suggest a route toward controlling the DM interaction in AFM materials by means of doping and electric fields.

Two-dimensional melting of colloids with long-range attractive interactions.

PubMed

Du, Di; Doxastakis, Manolis; Hilou, Elaa; Biswal, Sibani Lisa

2017-02-22

The solid-liquid melting transition in a two-dimensional (2-D) attractive colloidal system is visualized using superparamagnetic colloids that interact through a long-range isotropic attractive interaction potential, which is induced using a high-frequency rotating magnetic field. Various experiments, supported by Monte Carlo simulations, are carried out over a range of interaction potentials and densities to determine structure factors, Lindermann parameters, and translational and orientational order parameters. The system shows a first-order solid-liquid melting transition. Simulations and experiments suggest that dislocations and disclinations simultaneously unbind during melting. This is in direct contrast with reports of 2-D melting of paramagnetic particles that interact with a repulsive interaction potential.

A Computational Model of Active Vision for Visual Search in Human-Computer Interaction

DTIC Science & Technology

2010-08-01

processors that interact with the production rules to produce behavior, and (c) parameters that constrain the behavior of the model (e.g., the...velocity of a saccadic eye movement). While the parameters can be task-specific, the majority of the parameters are usually fixed across a wide variety...previously estimated durations. Hooge and Erkelens (1996) review these four explanations of fixation duration control. A variety of research

Controlling measurement-induced nonlocality in the Heisenberg XX model by three-spin interactions

NASA Astrophysics Data System (ADS)

Xie, Yu-Xia; Sun, Yu-Hang; Li, Zhao

2018-01-01

We investigate the well-defined measures of measurement-induced nonlocality (MIN) for thermal states of the transverse field XX model, with the addition of three-spin interaction terms being introduced. The results showed that the MINs are very sensitive to system parameters of the chain. The three-spin interactions can serve as flexible parameters for enhancing MINs of the boundary spins, and the maximum enhancement achievable by varying strengths of the three-spin interactions are different for the chain with different number of spins.

A global sensitivity analysis approach for morphogenesis models.

PubMed

Boas, Sonja E M; Navarro Jimenez, Maria I; Merks, Roeland M H; Blom, Joke G

2015-11-21

Morphogenesis is a developmental process in which cells organize into shapes and patterns. Complex, non-linear and multi-factorial models with images as output are commonly used to study morphogenesis. It is difficult to understand the relation between the uncertainty in the input and the output of such 'black-box' models, giving rise to the need for sensitivity analysis tools. In this paper, we introduce a workflow for a global sensitivity analysis approach to study the impact of single parameters and the interactions between them on the output of morphogenesis models. To demonstrate the workflow, we used a published, well-studied model of vascular morphogenesis. The parameters of this cellular Potts model (CPM) represent cell properties and behaviors that drive the mechanisms of angiogenic sprouting. The global sensitivity analysis correctly identified the dominant parameters in the model, consistent with previous studies. Additionally, the analysis provided information on the relative impact of single parameters and of interactions between them. This is very relevant because interactions of parameters impede the experimental verification of the predicted effect of single parameters. The parameter interactions, although of low impact, provided also new insights in the mechanisms of in silico sprouting. Finally, the analysis indicated that the model could be reduced by one parameter. We propose global sensitivity analysis as an alternative approach to study the mechanisms of morphogenesis. Comparison of the ranking of the impact of the model parameters to knowledge derived from experimental data and from manipulation experiments can help to falsify models and to find the operand mechanisms in morphogenesis. The workflow is applicable to all 'black-box' models, including high-throughput in vitro models in which output measures are affected by a set of experimental perturbations.

Thermodynamic Approach to Boron Nitride Nanotube Solubility and Dispersion

NASA Technical Reports Server (NTRS)

Tiano, A. L.; Gibbons, L.; Tsui, M.; Applin, S. I.; Silva, R.; Park, C.; Fay, C. C.

2016-01-01

Inadequate dispersion of nanomaterials is a critical issue that significantly limits the potential properties of nanocomposites and when overcome, will enable further enhancement of material properties. The most common methods used to improve dispersion include surface functionalization, surfactants, polymer wrapping, and sonication. Although these approaches have proven effective, they often achieve dispersion by altering the surface or structure of the nanomaterial and ultimately, their intrinsic properties. Co-solvents are commonly utilized in the polymer, paint, and art conservation industries to selectively dissolve materials. These co-solvents are utilized based on thermodynamic interaction parameters and are chosen so that the original materials are not affected. The same concept was applied to enhance the dispersion of boron nitride nanotubes (BNNTs) to facilitate the fabrication of BNNT nanocomposites. Of the solvents tested, dimethylacetamide (DMAc) exhibited the most stable, uniform dispersion of BNNTs, followed by N,N-dimethylformamide (DMF), acetone, and N-methyl-2-pyrrolidone (NMP). Utilizing the known Hansen solubility parameters of these solvents in comparison to the BNNT dispersion state, a region of good solubility was proposed. This solubility region was used to identify co-solvent systems that led to improved BNNT dispersion in poor solvents such as toluene, hexane, and ethanol. Incorporating the data from the co-solvent studies further refined the proposed solubility region. From this region, the Hansen solubility parameters for BNNTs are thought to lie at the midpoint of the solubility sphere: 16.8, 10.7, and 9.0 MPa(exp 1/2) for delta d, delta p, and delta h, respectively, with a calculated Hildebrand parameter of 21.8 MPa)exp 1/2).

A Bayesian approach to model structural error and input variability in groundwater modeling

NASA Astrophysics Data System (ADS)

Xu, T.; Valocchi, A. J.; Lin, Y. F. F.; Liang, F.

2015-12-01

Effective water resource management typically relies on numerical models to analyze groundwater flow and solute transport processes. Model structural error (due to simplification and/or misrepresentation of the "true" environmental system) and input forcing variability (which commonly arises since some inputs are uncontrolled or estimated with high uncertainty) are ubiquitous in groundwater models. Calibration that overlooks errors in model structure and input data can lead to biased parameter estimates and compromised predictions. We present a fully Bayesian approach for a complete assessment of uncertainty for spatially distributed groundwater models. The approach explicitly recognizes stochastic input and uses data-driven error models based on nonparametric kernel methods to account for model structural error. We employ exploratory data analysis to assist in specifying informative prior for error models to improve identifiability. The inference is facilitated by an efficient sampling algorithm based on DREAM-ZS and a parameter subspace multiple-try strategy to reduce the required number of forward simulations of the groundwater model. We demonstrate the Bayesian approach through a synthetic case study of surface-ground water interaction under changing pumping conditions. It is found that explicit treatment of errors in model structure and input data (groundwater pumping rate) has substantial impact on the posterior distribution of groundwater model parameters. Using error models reduces predictive bias caused by parameter compensation. In addition, input variability increases parametric and predictive uncertainty. The Bayesian approach allows for a comparison among the contributions from various error sources, which could inform future model improvement and data collection efforts on how to best direct resources towards reducing predictive uncertainty.

Thermodynamic approach to boron nitride nanotube solubility and dispersion.

PubMed

Tiano, A L; Gibbons, L; Tsui, M; Applin, S I; Silva, R; Park, C; Fay, C C

2016-02-21

Inadequate dispersion of nanomaterials is a critical issue that significantly limits the potential properties of nanocomposites and when overcome, will enable further enhancement of material properties. The most common methods used to improve dispersion include surface functionalization, surfactants, polymer wrapping, and sonication. Although these approaches have proven effective, they often achieve dispersion by altering the surface or structure of the nanomaterial and ultimately, their intrinsic properties. Co-solvents are commonly utilized in the polymer, paint, and art conservation industries to selectively dissolve materials. These co-solvents are utilized based on thermodynamic interaction parameters and are chosen so that the original materials are not affected. The same concept was applied to enhance the dispersion of boron nitride nanotubes (BNNTs) to facilitate the fabrication of BNNT nanocomposites. Of the solvents tested, dimethylacetamide (DMAc) exhibited the most stable, uniform dispersion of BNNTs, followed by N,N-dimethylformamide (DMF), acetone, and N-methyl-2-pyrrolidone (NMP). Utilizing the known Hansen solubility parameters of these solvents in comparison to the BNNT dispersion state, a region of good solubility was proposed. This solubility region was used to identify co-solvent systems that led to improved BNNT dispersion in poor solvents such as toluene, hexane, and ethanol. Incorporating the data from the co-solvent studies further refined the proposed solubility region. From this region, the Hansen solubility parameters for BNNTs are thought to lie at the midpoint of the solubility sphere: 16.8, 10.7, and 9.0 MPa(1/2) for δd, δp, and δh, respectively, with a calculated Hildebrand parameter of 21.8 MPa(1/2).

Optimization of mass spectrometry acquisition parameters for determination of polycarbonate additives, degradation products, and colorants migrating from food contact materials to chocolate.

PubMed

Bignardi, Chiara; Cavazza, Antonella; Laganà, Carmen; Salvadeo, Paola; Corradini, Claudio

2018-01-01

The interest towards "substances of emerging concerns" referred to objects intended to come into contact with food is recently growing. Such substances can be found in traces in simulants and in food products put in contact with plastic materials. In this context, it is important to set up analytical systems characterized by high sensitivity and to improve detection parameters to enhance signals. This work was aimed at optimizing a method based on UHPLC coupled to high resolution mass spectrometry to quantify the most common plastic additives, and able to detect the presence of polymers degradation products and coloring agents migrating from plastic re-usable containers. The optimization of mass spectrometric parameter settings for quantitative analysis of additives has been achieved by a chemometric approach, using a full factorial and d-optimal experimental designs, allowing to evaluate possible interactions between the investigated parameters. Results showed that the optimized method was characterized by improved features in terms of sensitivity respect to existing methods and was successfully applied to the analysis of a complex model food system such as chocolate put in contact with 14 polycarbonate tableware samples. A new procedure for sample pre-treatment was carried out and validated, showing high reliability. Results reported, for the first time, the presence of several molecules migrating to chocolate, in particular belonging to plastic additives, such Cyasorb UV5411, Tinuvin 234, Uvitex OB, and oligomers, whose amount was found to be correlated to age and degree of damage of the containers. Copyright © 2017 John Wiley & Sons, Ltd.

An Asynchronous Cellular Automata-Based Adaptive Illumination Facility

NASA Astrophysics Data System (ADS)

Bandini, Stefania; Bonomi, Andrea; Vizzari, Giuseppe; Acconci, Vito

The term Ambient Intelligence refers to electronic environments that are sensitive and responsive to the presence of people; in the described scenario the environment itself is endowed with a set of sensors (to perceive humans or other physical entities such as dogs, bicycles, etc.), interacting with a set of actuators (lights) that choose their actions (i.e. state of illumination) in an attempt improve the overall experience of these users. The model for the interaction and action of sensors and actuators is an asynchronous Cellular Automata (CA) with memory, supporting a self-organization of the system as a response to the presence and movements of people inside it. The paper will introduce the model, as well as an ad hoc user interface for the specification of the relevant parameters of the CA transition rule that determines the overall system behaviour.

Polymer Nanocomposites: Insights from Theory and Molecular Simulations

NASA Astrophysics Data System (ADS)

Pani, Rakhee

Advantages of polymer nanocomposites have attracted great industrial attention due to their multifunctionality and innovative technological properties. Addition of small amount of nanoparticle (nanospheres, nanotubes, nanorods, nanoplatelets, or sheets) to polymer matrix cause dramatic improvement in structural and functional properties, which is difficult to attain from those of individual components. The interaction between polymer and nanoparticle create bulk materials dominated by solid state physics at the nanoscale. Furthermore, morphology of nanocomposites depends on structural arrangements of nanoparticles. Thus, for achievement of optimized functionality like electrical, optical, mechanical and thermal properties control over the dispersion of the nanoparticle is essential. However, properties of polymer nanocomposites depend on morphology control and nature of interfacial interactions. In order to control the morphology it is necessary to understand how the processing conditions, shape and size of nanoparticle influence the structure of composite. Molecular simulations can help us to predict the parameters that control the structural changes and we could design polymer nanocomposite entailing their end-use. In this work, we addressed the following research questions: (1) the dependence of nanoparticle ligand corona structure on solvent quality and (2) the role of interfacial energy and interactions on the dispersion of molecules and nanoparticles. Specifically, this research assessed the effect of solvent interactions on the structure of nanoparticles on the example of redox core encapsulating dendrimer and ligand functionalized gold nanoparticles, role of chemical interaction on solubility of glucose in ionic liquids, diffusion of fullerene nanoparticles in polymer matrix and influence of solubility parameters on the compatibility of gold nanoparticles with diblock copolymers. Computational methods allow quantifying the structure and flexibility of the polymer chains, how energetics and surface tension change with chemical composition of the polymer/dendrimer blocks, influence of nanoparticle on structural properties of polymer and factors which may contribute to the phase separation of the polymer from nanoparticle. Interfacial characteristics are not only determined by the size-induced properties, but also the surface chemistry of the particles. Presence of solvent and the resultant interactions with the solvent are known to influence the morphology and prevent or induce aggregation of nanoparticles in polymers. We found that surface chemistry can induce change in the structure of dendrimers encapsulating a redox active core and change the solubility of the nanoparticles. The interactions between nanoparticles and polymers can also influence the morphology. We performed investigation on the role of orientation of fullerene derivatives and surface energy of polymer surface which may induce the aggregation of the fullerene nanoparticles. Furthermore, we used quantitative measurements like cluster analysis to understand the most probable orientation of the fullerene derivative with respect to the polymer chains and the diffusion of the fullerene nanoparticle, which is related to the efficiency of solar cells, can change on presence of regiorandom and regioregular polymer chains. Furthermore, we have also used different solvents based on their Hildebrand solubility parameters to investigate factors governing the morphology of polymer nanocomposite via solvent interactions. We showed that change in solvent interactions affect the compatibility, aggregation/dispersion of the gold nanoparticles, which will directly affect the morphology of polymer matrix and structural aspects which can impact their functionality. Overall, our research indicated that solvent interaction play a role in controlling the morphology of polymer nanocomposite and solubility parameter can help us to predict the resulting morphology.

Density perturbation in the models reconstructed from jerk parameter

NASA Astrophysics Data System (ADS)

Sinha, Srijita; Banerjee, Narayan

2018-06-01

The present work deals with the late time evolution of the linear density contrast in the dark energy models reconstructed from the jerk parameter. It is found that the non-interacting models are favoured compared to the models where an interaction is allowed in the dark sector.

Rhodopsin-lipid interactions studied by NMR.

PubMed

Soubias, Olivier; Gawrisch, Klaus

2013-01-01

The biophysical properties of the lipid matrix are known to influence function of integral membrane proteins. We report on a sample preparation method for reconstitution of membrane proteins which uses porous anodic aluminum oxide (AAO) filters with 200-nm-wide pores of high density. The substrate permits formation of tubular, single membranes that line the inner surface of pores. One square centimeter of filter with a thickness of 60μm yields on the order of 500cm(2) of solid-supported single bilayer surface, sufficient for NMR studies. The tubular bilayers are free of detergent, fully hydrated, and accessible for ligands from one side of the membrane. The use of AAO filters greatly improves reproducibility of the reconstitution process such that the influence of protein on lipid order parameters can be studied with high resolution. As an example, results for the G protein-coupled receptor of class A, bovine rhodopsin, are shown. By (2)H NMR order parameter measurements, it is detected that rhodopsin insertion elastically deforms membranes near the protein. Furthermore, by (1)H saturation-transfer NMR under conditions of magic angle spinning, we demonstrate detection of preferences in interactions of rhodopsin with particular lipid species. It is assumed that function of integral membrane proteins depends on both protein-induced elastic deformations of the lipid matrix and preferences for interaction of the protein with particular lipid species in the first layer of lipids surrounding the protein. Copyright © 2013 Elsevier Inc. All rights reserved.

Investigation, sensitivity analysis, and multi-objective optimization of effective parameters on temperature and force in robotic drilling cortical bone.

PubMed

Tahmasbi, Vahid; Ghoreishi, Majid; Zolfaghari, Mojtaba

2017-11-01

The bone drilling process is very prominent in orthopedic surgeries and in the repair of bone fractures. It is also very common in dentistry and bone sampling operations. Due to the complexity of bone and the sensitivity of the process, bone drilling is one of the most important and sensitive processes in biomedical engineering. Orthopedic surgeries can be improved using robotic systems and mechatronic tools. The most crucial problem during drilling is an unwanted increase in process temperature (higher than 47 °C), which causes thermal osteonecrosis or cell death and local burning of the bone tissue. Moreover, imposing higher forces to the bone may lead to breaking or cracking and consequently cause serious damage. In this study, a mathematical second-order linear regression model as a function of tool drilling speed, feed rate, tool diameter, and their effective interactions is introduced to predict temperature and force during the bone drilling process. This model can determine the maximum speed of surgery that remains within an acceptable temperature range. Moreover, for the first time, using designed experiments, the bone drilling process was modeled, and the drilling speed, feed rate, and tool diameter were optimized. Then, using response surface methodology and applying a multi-objective optimization, drilling force was minimized to sustain an acceptable temperature range without damaging the bone or the surrounding tissue. In addition, for the first time, Sobol statistical sensitivity analysis is used to ascertain the effect of process input parameters on process temperature and force. The results show that among all effective input parameters, tool rotational speed, feed rate, and tool diameter have the highest influence on process temperature and force, respectively. The behavior of each output parameters with variation in each input parameter is further investigated. Finally, a multi-objective optimization has been performed considering all the aforementioned parameters. This optimization yielded a set of data that can considerably improve orthopedic osteosynthesis outcomes.

The influence of the nature of a substituent on the parameters of the intra- and intermolecular interactions in molecules of cross-conjugated ketones

NASA Astrophysics Data System (ADS)

Kompaneets, V. V.; Vasilieva, I. A.

2017-08-01

We have quantitatively analyzed the vibronic parameters of two cross-conjugated δ-dimethylaminoketones. The presence of the -N(CH3)2, C=O, and -NO2 groups in the benzene ring has been shown to affect the manifestation of the vibronic parameters of characteristic bands that describe the state (vibrations, types of deformation upon excitation) of polyene systems with aromatic rings. Data on the influence of the nature of the substituent on the parameters of intra- and intermolecular interactions in the examined compounds have been presented.

Adapting the iSNOBAL model for improved visualization in a GIS environment

NASA Astrophysics Data System (ADS)

Johansen, W. J.; Delparte, D.

2014-12-01

Snowmelt is a primary means of crucial water resources in much of the western United States. Researchers are developing models that estimate snowmelt to aid in water resource management. One such model is the image snowcover energy and mass balance (iSNOBAL) model. It uses input climate grids to simulate the development and melting of snowpack in mountainous regions. This study looks at applying this model to the Reynolds Creek Experimental Watershed in southwestern Idaho, utilizing novel approaches incorporating geographic information systems (GIS). To improve visualization of the iSNOBAL model, we have adapted it to run in a GIS environment. This type of environment is suited to both the input grid creation and the visualization of results. The data used for input grid creation can be stored locally or on a web-server. Kriging interpolation embedded within Python scripts are used to create air temperature, soil temperature, humidity, and precipitation grids, while built-in GIS and existing tools are used to create solar radiation and wind grids. Additional Python scripting is then used to perform model calculations. The final product is a user-friendly and accessible version of the iSNOBAL model, including the ability to easily visualize and interact with model results, all within a web- or desktop-based GIS environment. This environment allows for interactive manipulation of model parameters and visualization of the resulting input grids for the model calculations. Future work is moving towards adapting the model further for use in a 3D gaming engine for improved visualization and interaction.

Ultrasonic studies of intermolecular interactions in binary mixtures of 4-methoxy benzoin with various solvents: Excess molar functions of ultrasonic parameters at different concentrations and in different solvents.

PubMed

Thanuja, B; Nithya, G; Kanagam, Charles C

2012-11-01

Density (ρ), ultrasonic velocity (U), for the binary mixtures of 4-methoxy benzoin (4MB) with ethanol, chloroform, acetonitrile, benzene, and di-oxane were measured at 298K. The solute-solvent interactions and the effect of the polarity of the solvent on the type of intermolecular interactions are discussed here. From the above data, adiabatic compressibility (β), intermolecular free length (L(f)), acoustic impedance (Z), apparent molar volume (Ø), relative association (RA) have been calculated. Other useful parameters such as excess density, excess velocity and excess adiabatic compressibility have also been calculated. These parameters were used to study the nature and extent of intermolecular interactions between component molecules in the binary mixtures. Copyright © 2012 Elsevier B.V. All rights reserved.

An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions

NASA Astrophysics Data System (ADS)

Lin, Yuchun; Baumketner, Andrij; Deng, Shaozhong; Xu, Zhenli; Jacobs, Donald; Cai, Wei

2009-10-01

In this paper, a new solvation model is proposed for simulations of biomolecules in aqueous solutions that combines the strengths of explicit and implicit solvent representations. Solute molecules are placed in a spherical cavity filled with explicit water, thus providing microscopic detail where it is most needed. Solvent outside of the cavity is modeled as a dielectric continuum whose effect on the solute is treated through the reaction field corrections. With this explicit/implicit model, the electrostatic potential represents a solute molecule in an infinite bath of solvent, thus avoiding unphysical interactions between periodic images of the solute commonly used in the lattice-sum explicit solvent simulations. For improved computational efficiency, our model employs an accurate and efficient multiple-image charge method to compute reaction fields together with the fast multipole method for the direct Coulomb interactions. To minimize the surface effects, periodic boundary conditions are employed for nonelectrostatic interactions. The proposed model is applied to study liquid water. The effect of model parameters, which include the size of the cavity, the number of image charges used to compute reaction field, and the thickness of the buffer layer, is investigated in comparison with the particle-mesh Ewald simulations as a reference. An optimal set of parameters is obtained that allows for a faithful representation of many structural, dielectric, and dynamic properties of the simulated water, while maintaining manageable computational cost. With controlled and adjustable accuracy of the multiple-image charge representation of the reaction field, it is concluded that the employed model achieves convergence with only one image charge in the case of pure water. Future applications to pKa calculations, conformational sampling of solvated biomolecules and electrolyte solutions are briefly discussed.

Interacting 3-form dark energy models: Distinguishing interactions and avoiding the Little Sibling of the Big Rip

NASA Astrophysics Data System (ADS)

Morais, João; Bouhmadi-López, Mariam; Kumar, K. Sravan; Marto, João; Tavakoli, Yaser

2017-03-01

In this paper we consider 3-form dark energy (DE) models with interactions in the dark sector. We aim to distinguish the phenomenological interactions that are defined through the dark matter (DM) and the DE energy densities. We do our analysis mainly in two stages. In the first stage, we identify the non-interacting 3-form DE model which generically leads to an abrupt late-time cosmological event which is known as the little sibling of the Big Rip (LSBR). We classify the interactions which can possibly avoid this late-time abrupt event. We also study the parameter space of the model that is consistent with the interaction between DM and DE energy densities at present as indicated by recent studies based on BAO and SDSS data. In the later stage, we observationally distinguish those interactions using the statefinder hierarchy parameters S3(1), S4(1), S3(1), S5(1). We also compute the growth factor parameter ɛ(z) for the various interactions we consider herein and use the composite null diagnostic (CND) S3(1), ɛ(z) } as a tool to characterise those interactions by measuring their departures from the concordance model. In addition, we make a preliminary analysis of our model in light of the recently released data by SDSS III on the measurement of the linear growth rate of structure.

Evaluation of several two-step scoring functions based on linear interaction energy, effective ligand size, and empirical pair potentials for prediction of protein-ligand binding geometry and free energy.

PubMed

Rahaman, Obaidur; Estrada, Trilce P; Doren, Douglas J; Taufer, Michela; Brooks, Charles L; Armen, Roger S

2011-09-26

The performances of several two-step scoring approaches for molecular docking were assessed for their ability to predict binding geometries and free energies. Two new scoring functions designed for "step 2 discrimination" were proposed and compared to our CHARMM implementation of the linear interaction energy (LIE) approach using the Generalized-Born with Molecular Volume (GBMV) implicit solvation model. A scoring function S1 was proposed by considering only "interacting" ligand atoms as the "effective size" of the ligand and extended to an empirical regression-based pair potential S2. The S1 and S2 scoring schemes were trained and 5-fold cross-validated on a diverse set of 259 protein-ligand complexes from the Ligand Protein Database (LPDB). The regression-based parameters for S1 and S2 also demonstrated reasonable transferability in the CSARdock 2010 benchmark using a new data set (NRC HiQ) of diverse protein-ligand complexes. The ability of the scoring functions to accurately predict ligand geometry was evaluated by calculating the discriminative power (DP) of the scoring functions to identify native poses. The parameters for the LIE scoring function with the optimal discriminative power (DP) for geometry (step 1 discrimination) were found to be very similar to the best-fit parameters for binding free energy over a large number of protein-ligand complexes (step 2 discrimination). Reasonable performance of the scoring functions in enrichment of active compounds in four different protein target classes established that the parameters for S1 and S2 provided reasonable accuracy and transferability. Additional analysis was performed to definitively separate scoring function performance from molecular weight effects. This analysis included the prediction of ligand binding efficiencies for a subset of the CSARdock NRC HiQ data set where the number of ligand heavy atoms ranged from 17 to 35. This range of ligand heavy atoms is where improved accuracy of predicted ligand efficiencies is most relevant to real-world drug design efforts.

A Low-threshold Analysis of Data from the Cryogenic Dark Matter Search Experiment

NASA Astrophysics Data System (ADS)

Bunker, Raymond A., III

Although dark matter appears to constitute over 80% of the matter in the Universe, its composition is a mystery. Astrophysical observations suggest that the luminous portions of the Galaxy are embedded in a halo of darkmatter particles. Weakly Interacting Massive Particles (WIMPs) are the most studied class of dark-matter candidates and arise naturally within the context of many weak-scale supersymmetric theories. Direct-detection experiments like the Cryogenic Dark Matter Search (CDMS) strive to discern the kinetic energy of recoiling nuclei resulting from WIMP interactions with terrestrial matter. This is a considerable challenge in which the low (expected) rate of WIMP interactions must be distinguished from an overwhelming rate due to known types of radiation. An incontrovertible positive detection has remained elusive. However, a few experiments have recorded data that appear consistent with a low-mass WIMP. This thesis describes an attempt to probe the favored parameter space. To increase sensitivity to low-mass WIMPs, a low-threshold technique with improved sensitivity to small energy depositions is applied to CDMS shallow-site data. Four germanium and two silicon detectors were operated between December 2001 and June 2002, yielding 118 days of exposure. By sacrificing some of the CDMS detectors' ability to discriminate signal from background, energy thresholds of ˜1 and ˜2 keV were achieved for three of the germanium and both silicon detectors, respectively. A large number of WIMP candidate events are observed, most of which can be accounted for by misidentification of background sources. No conclusive evidence for a low-mass WIMP signal is found. The observed event rates are used to set upper limits on the WIMPnucleon scattering cross section as a function of WIMP mass. Interesting parameter space is excluded for WIMPs with masses below ˜9GeV/c 2. Under standard assumptions, the parameter space favored by interpretations of other experiments' data as low-mass WIMP signals is partially excluded, and new parameter space is excluded for WIMP masses between 3 and 4GeV/ c2.

Effects of filtration through Sephadex columns improve overall quality parameters and "in vivo" fertility of subfertile refrigerated boar-semen.

PubMed

Ramió-Lluch, L; Balasch, S; Bonet, S; Briz, M; Pinart, E; Rodríguez-Gil, J E

2009-10-01

This study was performed to test the effects of filtration through several chromatographic resins on the semen quality parameters (percentages of viability, altered acrosomes and morphological abnormalities, motion characteristics and the response to the Osmotic Resistance Test) of boar ejaculates of poor quality. Our results indicate that filtration through a non-ionic Sephadex resin bed (Sephadex G-15), combined with a glasswool subjection bed, induced an overall improvement of semen quality parameters, especially seen in a significant (P<0.05) decrease in the percentages of morphological abnormalities and an increase of several motility parameters related to velocity and linearity. Similar results, although less intense, were observed when the filtration through G-15 resin was accompanied by an ionically neutral polypropylene disk bed instead of glasswool. On the other hand, filtration through two separate ion-exchange Sephadex resins, cationic C-50 and anionic A-50, have less beneficial, and even detrimental, effects on boar-semen quality. In all cases, filtration was accompanied by a significant (P<0.01) decrease in the final concentration of the samples. Ultrastructural and lectin studies showed that the interaction between sperm and chromatographic resins depends on the resin type utilized, and in the case of G-15 it seems that it works by trapping that sperm with not enough strength to overcome the physical resistance associated with chromatographic particles. When semen of poor quality was filtered through G-15 resin and then was utilized for "in vivo" fertility trials, a significant (P<0.05) increase in the percentage of fertility was observed, when compared with the same, but unfiltered, samples. In summary, our results strongly indicate that filtration through ionically inert, Sephadex chromatographic resins could be a very useful and practical method to improve both boar-semen quality and fertilizing ability, especially from mediocre and/or subfertile samples.

Improving estimation of kinetic parameters in dynamic force spectroscopy using cluster analysis

NASA Astrophysics Data System (ADS)

Yen, Chi-Fu; Sivasankar, Sanjeevi

2018-03-01

Dynamic Force Spectroscopy (DFS) is a widely used technique to characterize the dissociation kinetics and interaction energy landscape of receptor-ligand complexes with single-molecule resolution. In an Atomic Force Microscope (AFM)-based DFS experiment, receptor-ligand complexes, sandwiched between an AFM tip and substrate, are ruptured at different stress rates by varying the speed at which the AFM-tip and substrate are pulled away from each other. The rupture events are grouped according to their pulling speeds, and the mean force and loading rate of each group are calculated. These data are subsequently fit to established models, and energy landscape parameters such as the intrinsic off-rate (koff) and the width of the potential energy barrier (xβ) are extracted. However, due to large uncertainties in determining mean forces and loading rates of the groups, errors in the estimated koff and xβ can be substantial. Here, we demonstrate that the accuracy of fitted parameters in a DFS experiment can be dramatically improved by sorting rupture events into groups using cluster analysis instead of sorting them according to their pulling speeds. We test different clustering algorithms including Gaussian mixture, logistic regression, and K-means clustering, under conditions that closely mimic DFS experiments. Using Monte Carlo simulations, we benchmark the performance of these clustering algorithms over a wide range of koff and xβ, under different levels of thermal noise, and as a function of both the number of unbinding events and the number of pulling speeds. Our results demonstrate that cluster analysis, particularly K-means clustering, is very effective in improving the accuracy of parameter estimation, particularly when the number of unbinding events are limited and not well separated into distinct groups. Cluster analysis is easy to implement, and our performance benchmarks serve as a guide in choosing an appropriate method for DFS data analysis.

Heat transfer modelling of pulsed laser-tissue interaction

NASA Astrophysics Data System (ADS)

Urzova, J.; Jelinek, M.

2018-03-01

Due to their attributes, the application of medical lasers is on the rise in numerous medical fields. From a biomedical point of view, the most interesting applications are the thermal interactions and the photoablative interactions, which effectively remove tissue without excessive heat damage to the remaining tissue. The objective of this work is to create a theoretical model for heat transfer in the tissue following its interaction with the laser beam to predict heat transfer during medical laser surgery procedures. The dimensions of the ablated crater (shape and ablation depth) were determined by computed tomography imaging. COMSOL Multiphysics software was used for temperature modelling. The parameters of tissue and blood, such as density, specific heat capacity, thermal conductivity and diffusivity, were calculated from the chemical ratio. The parameters of laser-tissue interaction, such as absorption and reflection coefficients, were experimentally determined. The parameters of the laser beam were power density, repetition frequency, pulse length and spot dimensions. Heat spreading after laser interaction with tissue was captured using a Fluke thermal camera. The model was verified for adipose tissue, skeletal muscle tissue and heart muscle tissue.

A scalable method for computing quadruplet wave-wave interactions

NASA Astrophysics Data System (ADS)

Van Vledder, Gerbrant

2017-04-01

Non-linear four-wave interactions are a key physical process in the evolution of wind generated ocean waves. The present generation operational wave models use the Discrete Interaction Approximation (DIA), but it accuracy is poor. It is now generally acknowledged that the DIA should be replaced with a more accurate method to improve predicted spectral shapes and derived parameters. The search for such a method is challenging as one should find a balance between accuracy and computational requirements. Such a method is presented here in the form of a scalable and adaptive method that can mimic both the time consuming exact Snl4 approach and the fast but inaccurate DIA, and everything in between. The method provides an elegant approach to improve the DIA, not by including more arbitrarily shaped wave number configurations, but by a mathematically consistent reduction of an exact method, viz. the WRT method. The adaptiveness is to adapt the abscissa of the locus integrand in relation to the magnitude of the known terms. The adaptiveness is extended to the highest level of the WRT method to select interacting wavenumber configurations in a hierarchical way in relation to their importance. This adaptiveness results in a speed-up of one to three orders of magnitude depending on the measure of accuracy. This definition of accuracy should not be expressed in terms of the quality of the transfer integral for academic spectra but rather in terms of wave model performance in a dynamic run. This has consequences for the balance between the required accuracy and the computational workload for evaluating these interactions. The performance of the scalable method on different scales is illustrated with results from academic spectra, simple growth curves to more complicated field cases using a 3G-wave model.

An information driven strategy to support multidisciplinary design

NASA Technical Reports Server (NTRS)

Rangan, Ravi M.; Fulton, Robert E.

1990-01-01

The design of complex engineering systems such as aircraft, automobiles, and computers is primarily a cooperative multidisciplinary design process involving interactions between several design agents. The common thread underlying this multidisciplinary design activity is the information exchange between the various groups and disciplines. The integrating component in such environments is the common data and the dependencies that exist between such data. This may be contrasted to classical multidisciplinary analyses problems where there is coupling between distinct design parameters. For example, they may be expressed as mathematically coupled relationships between aerodynamic and structural interactions in aircraft structures, between thermal and structural interactions in nuclear plants, and between control considerations and structural interactions in flexible robots. These relationships provide analytical based frameworks leading to optimization problem formulations. However, in multidisciplinary design problems, information based interactions become more critical. Many times, the relationships between different design parameters are not amenable to analytical characterization. Under such circumstances, information based interactions will provide the best integration paradigm, i.e., there is a need to model the data entities and their dependencies between design parameters originating from different design agents. The modeling of such data interactions and dependencies forms the basis for integrating the various design agents.

Biasing and the search for primordial non-Gaussianity beyond the local type

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

Gleyzes, Jérôme; De Putter, Roland; Doré, Olivier

Primordial non-Gaussianity encodes valuable information about the physics of inflation, including the spectrum of particles and interactions. Significant improvements in our understanding of non-Gaussanity beyond Planck require information from large-scale structure. The most promising approach to utilize this information comes from the scale-dependent bias of halos. For local non-Gaussanity, the improvements available are well studied but the potential for non-Gaussianity beyond the local type, including equilateral and quasi-single field inflation, is much less well understood. In this paper, we forecast the capabilities of large-scale structure surveys to detect general non-Gaussianity through galaxy/halo power spectra. We study how non-Gaussanity can bemore » distinguished from a general biasing model and where the information is encoded. For quasi-single field inflation, significant improvements over Planck are possible in some regions of parameter space. We also show that the multi-tracer technique can significantly improve the sensitivity for all non-Gaussianity types, providing up to an order of magnitude improvement for equilateral non-Gaussianity over the single-tracer measurement.« less

Including gauge-group parameters into the theory of interactions: an alternative mass-generating mechanism for gauge fields

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

Aldaya, V.; Lopez-Ruiz, F. F.; Sanchez-Sastre, E.

2006-11-03

We reformulate the gauge theory of interactions by introducing the gauge group parameters into the model. The dynamics of the new 'Goldstone-like' bosons is accomplished through a non-linear {sigma}-model Lagrangian. They are minimally coupled according to a proper prescription which provides mass terms to the intermediate vector bosons without spoiling gauge invariance. The present formalism is explicitly applied to the Standard Model of electroweak interactions.

Design, Packaging and Reliability of MEMS S&A Components and Systems

DTIC Science & Technology

2006-12-26

different parameters on stiction likelihood has been studied. The parameters are relative humidity, contact angles, surface roughness, Hamaker constant...cutoff distance of the attractive Van der Waals interaction d, =.2 nm Ah. is the Hamaker media of the materials of the sphere and the half space...interaction in air. Ah.. is the Hamaker media of the materials of the sphere and the half space interaction in water. Hamaker constant can be found using

Ghost Dark Energy with Non-Linear Interaction Term

NASA Astrophysics Data System (ADS)

Ebrahimi, E.

2016-06-01

Here we investigate ghost dark energy (GDE) in the presence of a non-linear interaction term between dark matter and dark energy. To this end we take into account a general form for the interaction term. Then we discuss about different features of three choices of the non-linear interacting GDE. In all cases we obtain equation of state parameter, w D = p/ ρ, the deceleration parameter and evolution equation of the dark energy density parameter (Ω D ). We find that in one case, w D cross the phantom line ( w D < -1). However in two other classes w D can not cross the phantom divide. The coincidence problem can be solved in these models completely and there exist good agreement between the models and observational values of w D , q. We study squared sound speed {vs2}, and find that for one case of non-linear interaction term {vs2} can achieves positive values at late time of evolution.

Interactions between vortex tubes and magnetic-flux rings at high kinetic and magnetic Reynolds numbers

NASA Astrophysics Data System (ADS)

Kivotides, Demosthenes

2018-03-01

The interactions between vortex tubes and magnetic-flux rings in incompressible magnetohydrodynamics are investigated at high kinetic and magnetic Reynolds numbers, and over a wide range of the interaction parameter. The latter is a measure of the turnover time of the large-scale fluid motions in units of the magnetic damping time, or of the strength of the Lorentz force in units of the inertial force. The small interaction parameter results, which are related to kinematic turbulent dynamo studies, indicate the evolution of magnetic rings into flattened spirals wrapped around the vortex tubes. This process is also observed at intermediate interaction parameter values, only now the Lorentz force creates new vortical structures at the magnetic spiral edges, which have a striking solenoid vortex-line structure, and endow the flattened magnetic-spiral surfaces with a curvature. At high interaction parameter values, the decisive physical factor is Lorentz force effects. The latter create two (adjacent to the magnetic ring) vortex rings that reconnect with the vortex tube by forming an intriguing, serpentinelike, vortex-line structure, and generate, in turn, two new magnetic rings, adjacent to the initial one. In this regime, the morphologies of the vorticity and magnetic field structures are similar. The effects of these structures on kinetic and magnetic energy spectra, as well as on the direction of energy transfer between flow and magnetic fields, are also indicated.

Beyond Control Panels: Direct Manipulation for Visual Analytics

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

Endert, Alexander; Bradel, Lauren; North, Chris

2013-07-19

Information Visualization strives to provide visual representations through which users can think about and gain insight into information. By leveraging the visual and cognitive systems of humans, complex relationships and phenomena occurring within datasets can be uncovered by exploring information visually. Interaction metaphors for such visualizations are designed to enable users direct control over the filters, queries, and other parameters controlling how the data is visually represented. Through the evolution of information visualization, more complex mathematical and data analytic models are being used to visualize relationships and patterns in data – creating the field of Visual Analytics. However, the expectationsmore » for how users interact with these visualizations has remained largely unchanged – focused primarily on the direct manipulation of parameters of the underlying mathematical models. In this article we present an opportunity to evolve the methodology for user interaction from the direct manipulation of parameters through visual control panels, to interactions designed specifically for visual analytic systems. Instead of focusing on traditional direct manipulation of mathematical parameters, the evolution of the field can be realized through direct manipulation within the visual representation – where users can not only gain insight, but also interact. This article describes future directions and research challenges that fundamentally change the meaning of direct manipulation with regards to visual analytics, advancing the Science of Interaction.« less

Lifestyle Factors and Metabolic Syndrome among Workers: The Role of Interactions between Smoking and Alcohol to Nutrition and Exercise

PubMed Central

Huang, Jui-Hua; Li, Ren-Hau; Huang, Shu-Ling; Sia, Hon-Ke; Chen, Yu-Ling; Tang, Feng-Cheng

2015-01-01

This study aimed to investigate (1) relations of smoking and alcohol to metabolic syndrome (MetS) and its components, with nutrition and exercise controlled; and (2) interactions between smoking/alcohol and nutrition/exercise on MetS. This cross-sectional study enrolled 4025 workers. Self-reported lifestyles, anthropometric values, blood pressure (BP), and biochemical determinations were obtained. Among males, smoking significantly increased the risk of low high-density lipoprotein cholesterol (HDL-C), high triglyceride, abdominal obesity (AO), and MetS. Additionally, smoking showed significant interaction effects with nutrition on high BP, AO, and MetS; after further analysis, nutrition did not decrease above-mentioned risks for smokers. However, there was no significant interaction of smoking with exercise on any metabolic parameter. Alcohol increased the risk of AO, but decreased low HDL-C. It also showed an interaction effect with exercise on AO; after further analysis, exercise decreased AO risk for drinkers. Among females, alcohol significantly decreased the risk of high fasting blood glucose, but did not show significant interaction with nutrition/exercise on any metabolic parameter. In conclusion, in males, smoking retained significant associations with MetS and its components, even considering benefits of nutrition; exercise kept predominance on lipid parameters regardless of smoking status. Alcohol showed inconsistencies on metabolic parameters for both genders. PMID:26694434

Lifestyle Factors and Metabolic Syndrome among Workers: The Role of Interactions between Smoking and Alcohol to Nutrition and Exercise.

PubMed

Huang, Jui-Hua; Li, Ren-Hau; Huang, Shu-Ling; Sia, Hon-Ke; Chen, Yu-Ling; Tang, Feng-Cheng

2015-12-16

This study aimed to investigate (1) relations of smoking and alcohol to metabolic syndrome (MetS) and its components, with nutrition and exercise controlled; and (2) interactions between smoking/alcohol and nutrition/exercise on MetS. This cross-sectional study enrolled 4025 workers. Self-reported lifestyles, anthropometric values, blood pressure (BP), and biochemical determinations were obtained. Among males, smoking significantly increased the risk of low high-density lipoprotein cholesterol (HDL-C), high triglyceride, abdominal obesity (AO), and MetS. Additionally, smoking showed significant interaction effects with nutrition on high BP, AO, and MetS; after further analysis, nutrition did not decrease above-mentioned risks for smokers. However, there was no significant interaction of smoking with exercise on any metabolic parameter. Alcohol increased the risk of AO, but decreased low HDL-C. It also showed an interaction effect with exercise on AO; after further analysis, exercise decreased AO risk for drinkers. Among females, alcohol significantly decreased the risk of high fasting blood glucose, but did not show significant interaction with nutrition/exercise on any metabolic parameter. In conclusion, in males, smoking retained significant associations with MetS and its components, even considering benefits of nutrition; exercise kept predominance on lipid parameters regardless of smoking status. Alcohol showed inconsistencies on metabolic parameters for both genders.

Search for Muonic Dark Forces at BABAR

NASA Astrophysics Data System (ADS)

Godang, Romulus

2017-04-01

Many models of physics beyond Standard Model predict the existence of light Higgs states, dark photons, and new gauge bosons mediating interactions between dark sectors and the Standard Model. Using a full data sample collected with the BABAR detector at the PEP-II e+e- collider, we report searches for a light non-Standard Model Higgs boson, dark photon, and a new muonic dark force mediated by a gauge boson (Z') coupling only to the second and third lepton families. Our results significantly improve upon the current bounds and further constrain the remaining region of the allowed parameter space.

Relationship of the Williams-Poulios and Manning-Rosen Potential Energy Models for Diatomic Molecules

NASA Astrophysics Data System (ADS)

Jia, Chun-Sheng; Liang, Guang-Chuan; Peng, Xiao-Long; Tang, Hong-Ming; Zhang, Lie-Hui

2014-06-01

By employing the dissociation energy and the equilibrium bond length for a diatomic molecule as explicit parameters, we generate an improved form of the Williams-Poulios potential energy model. It is found that the negative Williams-Poulios potential model is equivalent to the Manning-Rosen potential model for diatomic molecules. We observe that the Manning-Rosen potential is superior to the Morse potential in reproducing the interaction potential energy curves for the {{a}3 Σu+} state of the 6Li2 molecule and the {{X}1 sum+} state of the SiF+ molecule.

An application of synthetic seismicity in earthquake statistics - The Middle America Trench

NASA Technical Reports Server (NTRS)

Ward, Steven N.

1992-01-01

The way in which seismicity calculations which are based on the concept of fault segmentation incorporate the physics of faulting through static dislocation theory can improve earthquake recurrence statistics and hone the probabilities of hazard is shown. For the Middle America Trench, the spread parameters of the best-fitting lognormal or Weibull distributions (about 0.75) are much larger than the 0.21 intrinsic spread proposed in the Nishenko Buland (1987) hypothesis. Stress interaction between fault segments disrupts time or slip predictability and causes earthquake recurrence to be far more aperiodic than has been suggested.

Alternatives for jet engine control

NASA Technical Reports Server (NTRS)

Sain, M. K.

1981-01-01

Research centered on basic topics in the modeling and feedback control of nonlinear dynamical systems is reported. Of special interest were the following topics: (1) the role of series descriptions, especially insofar as they relate to questions of scheduling, in the control of gas turbine engines; (2) the use of algebraic tensor theory as a technique for parameterizing such descriptions; (3) the relationship between tensor methodology and other parts of the nonlinear literature; (4) the improvement of interactive methods for parameter selection within a tensor viewpoint; and (5) study of feedback gain representation as a counterpart to these modeling and parameterization ideas.

Cardioproteomics: advancing the discovery of signaling mechanisms involved in cardiovascular diseases

PubMed Central

Cui, Ziyou; Dewey, Shannamar; Gomes, Aldrin V

2011-01-01

Cardioproteomics (Cardiovascular proteomics) is fast becoming an indispensible technique in deciphering changes in signaling pathways that occur in cardiovascular diseases (CVDs). The quality and availability of the instruments and bioinformatics software used for cardioproteomics continues to improve, and these techniques are now available to most cardiovascular researchers either directly or indirectly via university core centers. The heart and aorta are specialized tissues which present unique challenges to investigate. Currently, the diverse range of proteomic techniques available for cardiovascular research makes the choice of the best method or best combination of methods for the disease parameter(s) being investigated as important as the equipment used. This review focuses on proteomic techniques and their applications which have advanced our understanding of the signaling mechanisms involved in CVDs at the levels of protein complex/protein-protein interaction, post-translational modifications and signaling induced protein changes. PMID:22254205

Mangifera indica L. leaf extract alleviates doxorubicin induced cardiac stress

PubMed Central

Bhatt, Laxit; Joshi, Viraj

2017-01-01

Aim: The study was undertaken to evaluate the cardioprotective effect of the alcoholic leaf extract of Mangifera indica L. against cardiac stress caused by doxorubicin (DOX). Materials and Methods: Rats were treated with 100 mg/kg of M. indica leaf extract (MILE) in alone and interactive groups for 21 days. Apart from the normal and MILE control groups, all the groups were subjected to DOX (15 mg/kg, i.p.) toxicity for 21 days and effects of different treatments were analyzed by changes in serum biomarkers, tissue antioxidant levels, electrocardiographic parameters, lipid profile, and histopathological evaluation. Results: The MILE treated group showed decrease in serum biomarker enzyme levels and increase in tissue antioxidants levels. Compared to DOX control group, MILE treated animals showed improvement in lipid profile, electrocardiographic parameters, histological score, and mortality. Conclusion: These findings clearly suggest the protective role of alcoholic leaf extract of M. indica against oxidative stress induced by DOX. PMID:28894627

Enhancement of L-asparaginase production by isolated Bacillus circulans (MTCC 8574) using response surface methodology.

PubMed

Hymavathi, M; Sathish, T; Subba Rao, Ch; Prakasham, R S

2009-10-01

L-asparaginase production was optimized using isolated Bacillus circulans (MTCC 8574) under solid-state fermentation (SSF) using locally available agricultural waste materials. Among different agricultural materials (red gram husk, bengal gram husk, coconut, and groundnut cake), red gram husk gave the maximum enzyme production. A wide range of SSF parameters were optimized for maximize the production of L-asparaginase. Preliminary studies revealed that incubation temperature, moisture content, inoculum level, glucose, and L-asparagine play a vital role in enzyme yield. The interactive behavior of each of these parameters along with their significance on enzyme yield was analyzed using fractional factorial central composite design (FFCCD). The observed correlation coefficient (R(2)) was 0.9714. Only L-asparagine and incubation temperature, were significant in linear and quadratic terms. L-asparaginase yield improved from 780 to 2,322 U/gds which is more than 300% using FFCCD as a means of optimizing conditions.

Measurements and calculations of H2-broadening and shift parameters of water vapour transitions of the ν1 + ν2 + ν3 band

NASA Astrophysics Data System (ADS)

Petrova, T. M.; Solodov, A. M.; Solodov, A. A.; Deichuli, V. M.; Starikov, V. I.

2018-05-01

The water vapour line broadening and shifting for 97 lines in the ν1 + ν2 + ν3 band induced by hydrogen pressure are measured with Bruker IFS 125 HR FTIR spectrometer. The measurements were performed at room temperature, at the spectral resolution of 0.01 cm-1 and in a wide pressure range of H2. The calculations of the broadening γ and shift δ coefficients were performed in the semi-classical method framework with use of an effective vibrationally depended interaction potential. Two potential parameters were optimised to improve the quality of calculations. Good agreements with measured broadening coefficients were achieved. The comparison of calculated broadening coefficients γ with the previous measurements is discussed. The analytical expressions that reproduce these coefficients for rotational, ν2, ν1, and ν3 vibrational bands are presented.

A judicious multiple hypothesis tracker with interacting feature extraction

NASA Astrophysics Data System (ADS)

McAnanama, James G.; Kirubarajan, T.

2009-05-01

The multiple hypotheses tracker (mht) is recognized as an optimal tracking method due to the enumeration of all possible measurement-to-track associations, which does not involve any approximation in its original formulation. However, its practical implementation is limited by the NP-hard nature of this enumeration. As a result, a number of maintenance techniques such as pruning and merging have been proposed to bound the computational complexity. It is possible to improve the performance of a tracker, mht or not, using feature information (e.g., signal strength, size, type) in addition to kinematic data. However, in most tracking systems, the extraction of features from the raw sensor data is typically independent of the subsequent association and filtering stages. In this paper, a new approach, called the Judicious Multi Hypotheses Tracker (jmht), whereby there is an interaction between feature extraction and the mht, is presented. The measure of the quality of feature extraction is input into measurement-to-track association while the prediction step feeds back the parameters to be used in the next round of feature extraction. The motivation for this forward and backward interaction between feature extraction and tracking is to improve the performance in both steps. This approach allows for a more rational partitioning of the feature space and removes unlikely features from the assignment problem. Simulation results demonstrate the benefits of the proposed approach.

Local and System Level Considerations for Plasma-Based Techniques in Hypersonic Flight

NASA Astrophysics Data System (ADS)

Suchomel, Charles; Gaitonde, Datta

2007-01-01

The harsh environment encountered due to hypersonic flight, particularly when air-breathing propulsion devices are utilized, poses daunting challenges to successful maturation of suitable technologies. This has spurred the quest for revolutionary solutions, particularly those exploiting the fact that air under these conditions can become electrically conducting either naturally or through artificial enhancement. Optimized development of such concepts must emphasize not only the detailed physics by which the fluid interacts with the imposed electromagnetic fields, but must also simultaneously identify system level issues integration and efficiencies that provide the greatest leverage. This paper presents some recent advances at both levels. At the system level, an analysis is summarized that incorporates the interdependencies occurring between weight, power and flow field performance improvements. Cruise performance comparisons highlight how one drag reduction device interacts with the vehicle to improve range. Quantified parameter interactions allow specification of system requirements and energy consuming technologies that affect overall flight vehicle performance. Results based on on the fundamental physics are presented by distilling numerous computational studies into a few guiding principles. These highlight the complex non-intuitive relationships between the various fluid and electromagnetic fields, together with thermodynamic considerations. Generally, energy extraction is an efficient process, while the reverse is accompanied by significant dissipative heating and inefficiency. Velocity distortions can be detrimental to plasma operation, but can be exploited to tailor flows through innovative electromagnetic configurations.

The genetics of human longevity: an intricacy of genes, environment, culture and microbiome.

PubMed

Dato, Serena; Rose, Giuseppina; Crocco, Paolina; Monti, Daniela; Garagnani, Paolo; Franceschi, Claudio; Passarino, Giuseppe

2017-07-01

Approximately one-quarter of the variation in lifespan in developed countries can be attributed to genetic factors. However, even large population based studies investigating genetic influence on human lifespan have been disappointing, identifying only a few genes accounting for genetic susceptibility to longevity. Some environmental and lifestyle determinants associated with longevity have been identified, which interplay with genetic factors in an intricate way. The study of gene-environment and gene-gene interactions can significantly improve our chance to disentangle this complex scenario. In this review, we first describe the most recent approaches for genetic studies of longevity, from those enriched with health parameters and frailty measures to pathway-based and SNP-SNP interaction analyses. Then, we go deeper into the concept of "environmental influences" in human aging and longevity, focusing on the contribution of life style changes, social and cultural influences, as important determinants of survival differences among individuals in a population. Finally, we discuss the contribution of the microbiome in human longevity, as an example of complex interaction between organism and environment. In conclusion, evidences collected from the latest studies on human longevity provide a support for the collection of life-long genetic and environmental/lifestyle variables with beneficial or detrimental effects on health, to improve our understanding of the determinants of human lifespan. Copyright © 2017 Elsevier B.V. All rights reserved.

Discovering graphical Granger causality using the truncating lasso penalty

PubMed Central

Shojaie, Ali; Michailidis, George

2010-01-01

Motivation: Components of biological systems interact with each other in order to carry out vital cell functions. Such information can be used to improve estimation and inference, and to obtain better insights into the underlying cellular mechanisms. Discovering regulatory interactions among genes is therefore an important problem in systems biology. Whole-genome expression data over time provides an opportunity to determine how the expression levels of genes are affected by changes in transcription levels of other genes, and can therefore be used to discover regulatory interactions among genes. Results: In this article, we propose a novel penalization method, called truncating lasso, for estimation of causal relationships from time-course gene expression data. The proposed penalty can correctly determine the order of the underlying time series, and improves the performance of the lasso-type estimators. Moreover, the resulting estimate provides information on the time lag between activation of transcription factors and their effects on regulated genes. We provide an efficient algorithm for estimation of model parameters, and show that the proposed method can consistently discover causal relationships in the large p, small n setting. The performance of the proposed model is evaluated favorably in simulated, as well as real, data examples. Availability: The proposed truncating lasso method is implemented in the R-package ‘grangerTlasso’ and is freely available at http://www.stat.lsa.umich.edu/∼shojaie/ Contact: shojaie@umich.edu PMID:20823316

Electronic Structure, Dielectric Response, and Surface Charge Distribution of RGD (1FUV) Peptide

PubMed Central

Adhikari, Puja; Wen, Amy M.; French, Roger H.; Parsegian, V. Adrian; Steinmetz, Nicole F.; Podgornik, Rudolf; Ching, Wai-Yim

2014-01-01

Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor. PMID:25001596

In-vivo viscous properties of the heel pad by stress-relaxation experiment based on a spherical indentation.

PubMed

Suzuki, Ryo; Ito, Kohta; Lee, Taeyong; Ogihara, Naomichi

2017-12-01

Identifying the viscous properties of the plantar soft tissue is crucial not only for understanding the dynamic interaction of the foot with the ground during locomotion, but also for development of improved footwear products and therapeutic footwear interventions. In the present study, the viscous and hyperelastic material properties of the plantar soft tissue were experimentally identified using a spherical indentation test and an analytical contact model of the spherical indentation test. Force-relaxation curves of the heel pads were obtained from the indentation experiment. The curves were fit to the contact model incorporating a five-element Maxwell model to identify the viscous material parameters. The finite element method with the experimentally identified viscoelastic parameters could successfully reproduce the measured force-relaxation curves, indicating the material parameters were correctly estimated using the proposed method. Although there are some methodological limitations, the proposed framework to identify the viscous material properties may facilitate the development of subject-specific finite element modeling of the foot and other biological materials. Copyright © 2017 IPEM. Published by Elsevier Ltd. All rights reserved.

Predicted Spatial Spread of Canine Rabies in Australia

PubMed Central

Fleming, Peter J. S.; Ward, Michael P.; Davis, Stephen A.

2017-01-01

Modelling disease dynamics is most useful when data are limited. We present a spatial transmission model for the spread of canine rabies in the currently rabies-free wild dog population of Australia. The introduction of a sub-clinically infected dog from Indonesia is a distinct possibility, as is the spillover infection of wild dogs. Ranges for parameters were estimated from the literature and expert opinion, or set to span an order of magnitude. Rabies was judged to have spread spatially if a new infectious case appeared 120 km from the index case. We found 21% of initial value settings resulted in canine rabies spreading 120km, and on doing so at a median speed of 67 km/year. Parameters governing dog movements and behaviour, around which there is a paucity of knowledge, explained most of the variance in model outcomes. Dog density, especially when interactions with other parameters were included, explained some of the variance in whether rabies spread 120km, but dog demography (mean lifespan and mean replacement period) had minimal impact. These results provide a clear research direction if Australia is to improve its preparedness for rabies. PMID:28114327

A consistent S-Adenosylmethionine force field improved by dynamic Hirshfeld-I atomic charges for biomolecular simulation

NASA Astrophysics Data System (ADS)

Saez, David Adrian; Vöhringer-Martinez, Esteban

2015-10-01

S-Adenosylmethionine (AdoMet) is involved in many biological processes as cofactor in enzymes transferring its sulfonium methyl group to various substrates. Additionally, it is used as drug and nutritional supplement to reduce the pain in osteoarthritis and against depression. Due to the biological relevance of AdoMet it has been part of various computational simulation studies and will also be in the future. However, to our knowledge no rigorous force field parameter development for its simulation in biological systems has been reported. Here, we use electronic structure calculations combined with molecular dynamics simulations in explicit solvent to develop force field parameters compatible with the AMBER99 force field. Additionally, we propose new dynamic Hirshfeld-I atomic charges which are derived from the polarized electron density of AdoMet in aqueous solution to describe its electrostatic interactions in biological systems. The validation of the force field parameters and the atomic charges is performed against experimental interproton NOE distances of AdoMet in aqueous solution and crystal structures of AdoMet in the cavity of three representative proteins.

Investigations on high speed machining of EN-353 steel alloy under different machining environments

NASA Astrophysics Data System (ADS)

Venkata Vishnu, A.; Jamaleswara Kumar, P.

2018-03-01

The addition of Nano Particles into conventional cutting fluids enhances its cooling capabilities; in the present paper an attempt is made by adding nano sized particles into conventional cutting fluids. Taguchi Robust Design Methodology is employed in order to study the performance characteristics of different turning parameters i.e. cutting speed, feed rate, depth of cut and type of tool under different machining environments i.e. dry machining, machining with lubricant - SAE 40 and machining with mixture of nano sized particles of Boric acid and base fluid SAE 40. A series of turning operations were performed using L27 (3)13 orthogonal array, considering high cutting speeds and the other machining parameters to measure hardness. The results are compared among the different machining environments, and it is concluded that there is considerable improvement in the machining performance using lubricant SAE 40 and mixture of SAE 40 + boric acid compared with dry machining. The ANOVA suggests that the selected parameters and the interactions are significant and cutting speed has most significant effect on hardness.

Development of response models for the Earth Radiation Budget Experiment (ERBE) sensors. Part 1: Dynamic models and computer simulations for the ERBE nonscanner, scanner and solar monitor sensors

NASA Technical Reports Server (NTRS)

Halyo, Nesim; Choi, Sang H.; Chrisman, Dan A., Jr.; Samms, Richard W.

1987-01-01

Dynamic models and computer simulations were developed for the radiometric sensors utilized in the Earth Radiation Budget Experiment (ERBE). The models were developed to understand performance, improve measurement accuracy by updating model parameters and provide the constants needed for the count conversion algorithms. Model simulations were compared with the sensor's actual responses demonstrated in the ground and inflight calibrations. The models consider thermal and radiative exchange effects, surface specularity, spectral dependence of a filter, radiative interactions among an enclosure's nodes, partial specular and diffuse enclosure surface characteristics and steady-state and transient sensor responses. Relatively few sensor nodes were chosen for the models since there is an accuracy tradeoff between increasing the number of nodes and approximating parameters such as the sensor's size, material properties, geometry, and enclosure surface characteristics. Given that the temperature gradients within a node and between nodes are small enough, approximating with only a few nodes does not jeopardize the accuracy required to perform the parameter estimates and error analyses.

Influence of Van der Waals interaction on the thermodynamics properties of NaCl

NASA Astrophysics Data System (ADS)

Marcondes, M. L.; Wentzcovitch, R. M.; Assali, L. V. C.

2016-12-01

Equations of state (EoS) are extremely important in several scientific domains. However, many applications require EoS parameters at high pressures and temperatures. Experimental determination of these parameters is limited in such conditions and ab initio calculations have become important in computing them. Density Functional Theory (DFT) with its various approximations for exchange and correlation energy is the method of choice, but lack of a good description of the exchange-correlation energy results in large errors in EoS parameters. It is well known that the alkali halides have been problematic from the onset and the quest for DFT functionals appropriate for such ionic and relatively weakly bonded systems has remained an active topic of research. Here we use DFT + van der Waals functionals to calculate the thermal equation of state and thermodynamic properties of the B1 NaCl phase. Our results show a remarkable improvement over the performance of standard the LDA and GGA functionals. This is hardly surprising given that ions in this system have nearly closed shell configurations.

Environmental confounding in gene-environment interaction studies.

PubMed

Vanderweele, Tyler J; Ko, Yi-An; Mukherjee, Bhramar

2013-07-01

We show that, in the presence of uncontrolled environmental confounding, joint tests for the presence of a main genetic effect and gene-environment interaction will be biased if the genetic and environmental factors are correlated, even if there is no effect of either the genetic factor or the environmental factor on the disease. When environmental confounding is ignored, such tests will in fact reject the joint null of no genetic effect with a probability that tends to 1 as the sample size increases. This problem with the joint test vanishes under gene-environment independence, but it still persists if estimating the gene-environment interaction parameter itself is of interest. Uncontrolled environmental confounding will bias estimates of gene-environment interaction parameters even under gene-environment independence, but it will not do so if the unmeasured confounding variable itself does not interact with the genetic factor. Under gene-environment independence, if the interaction parameter without controlling for the environmental confounder is nonzero, then there is gene-environment interaction either between the genetic factor and the environmental factor of interest or between the genetic factor and the unmeasured environmental confounder. We evaluate several recently proposed joint tests in a simulation study and discuss the implications of these results for the conduct of gene-environment interaction studies.

Interaction Junk: User Interaction-Based Evaluation of Visual Analytic Systems

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

Endert, Alexander; North, Chris

2012-10-14

With the growing need for visualization to aid users in understanding large, complex datasets, the ability for users to interact and explore these datasets is critical. As visual analytic systems have advanced to leverage powerful computational models and data analytics capabilities, the modes by which users engage and interact with the information are limited. Often, users are taxed with directly manipulating parameters of these models through traditional GUIs (e.g., using sliders to directly manipulate the value of a parameter). However, the purpose of user interaction in visual analytic systems is to enable visual data exploration – where users can focusmore » on their task, as opposed to the tool or system. As a result, users can engage freely in data exploration and decision-making, for the purpose of gaining insight. In this position paper, we discuss how evaluating visual analytic systems can be approached through user interaction analysis, where the goal is to minimize the cognitive translation between the visual metaphor and the mode of interaction (i.e., reducing the “Interactionjunk”). We motivate this concept through a discussion of traditional GUIs used in visual analytics for direct manipulation of model parameters, and the importance of designing interactions the support visual data exploration.« less

Interactive vs. Non-Interactive Multi-Model Ensembles

NASA Astrophysics Data System (ADS)

Duane, G. S.

2013-12-01

If the members of an ensemble of different models are allowed to interact with one another in run time, predictive skill can be improved as compared to that of any individual model or any average of indvidual model outputs. Inter-model connections in such an interactive ensemble can be trained, using historical data, so that the resulting ``supermodel' synchronizes with reality when used in weather-prediction mode, where the individual models perform data assimilation from each other (with trainable inter-model 'observation error') as well as from real observations. In climate-projection mode, parameters of the individual models are changed, as might occur from an increase in GHG levels, and one obtains relevant statistical properties of the new supermodel attractor. In simple cases, it has been shown that training of the inter-model connections with the old parameter values gives a supermodel that is still predictive when the parameter values are changed. Here we inquire as to the circumstances under which supermodel performance can be expected to exceed that of the customary weighted average of model outputs. We consider a supermodel formed from quasigeostrophic (QG) channel models with different forcing coefficients, and introduce an effective training scheme for the inter-model connections. We show that the blocked-zonal index cycle is reproduced better by the supermodel than by any non-interactive ensemble in the extreme case where the forcing coefficients of the different models are very large or very small. With realistic differences in forcing coefficients, as would be representative of actual differences among IPCC-class models, the usual linearity assumption is justified and a weighted average of model outputs is adequate. It is therefore hypothesized that supermodeling is likely to be useful in situations where there are qualitative model differences, as arising from sub-gridscale parameterizations, that affect overall model behavior. Otherwise the usual ex post facto averaging will probably suffice. The advantage of supermodeling is seen in statistics such as anticorrelation between blocking activity in the Atlantic and Pacific sectors, in the case of the QG channel model, rather than in overall blocking frequency. Likewise in climate models, the advantage of supermodeling is typically manifest in higher-order statistics rather than in quantities such as mean temperature.

UV fatigue investigations with non-destructive tools in silica

NASA Astrophysics Data System (ADS)

Natoli, Jean-Yves; Beaudier, Alexandre; Wagner, Frank R.

2017-08-01

A fatigue effect is often observed under multiple laser irradiations, overall in UV. This decrease of LIDT, is a critical parameter for laser sources with high repetition rates and with a need of long-term life, as in spatial applications at 355nm. A challenge is also to replace excimer lasers by solid laser sources, this challenge requires to improve drastically the lifetime of optical materials at 266nm. Main applications of these sources are devoted to material surface nanostructuration, spectroscopy and medical surgeries. In this work we focus on the understanding of the laser matter interaction at 266nm in silica in order to predict the lifetime of components and study parameters links to these lifetimes to give keys of improvement for material suppliers. In order to study the mechanism involved in the case of multiple irradiations, an interesting approach is to involve the evolution of fluorescence, in order to observe the first stages of material changes just before breakdown. We will show that it is sometime possible to estimate the lifetime of component only with the fluorescence measurement, saving time and materials. Moreover, the data from the diagnostics give relevant informations to highlight "defects" induced by multiple laser irradiations.

Transfer effects of fall training on balance performance and spatiotemporal gait parameters in healthy community-dwelling older adults: a pilot study.

PubMed

Donath, Lars; Faude, Oliver; Bridenbaugh, Stephanie A; Roth, Ralf; Soltermann, Martin; Kressig, Reto W; Zahner, Lukas

2014-07-01

This study examined transfer effects of fall training on fear of falling (Falls Efficacy Scale-International [FES-I]), balance performance, and spatiotemporal gait characteristics in older adults. Eighteen community-dwelling older adults (ages 65-85) were randomly assigned to an intervention or control group. The intervention group completed 12 training sessions (60 min, 6 weeks). During pre- and posttesting, we measured FES-I, balance performance (double limb, closed eyes; single limb, open eyes; double limb, open eyes with motor-interfered task), and gait parameters (e.g., velocity; cadence; stride time, stride width, and stride length; variability of stride time and stride length) under single- and motor-interfered tasks. Dual tasks were applied to appraise improvements of cognitive processing during balance and gait. FES-I (p = .33) and postural sway did not significantly change (0.36 < p < .79). Trends toward significant interaction effects were found for step width during normal walking and stride length variability during the motor dual task (p = .05, ηp 2 = .22). Fall training did not sufficiently improve fear of falling, balance, or gait performance under single- or dual-task conditions in healthy older adults.

Ride performance of a high speed rail vehicle using controlled semi active suspension system

NASA Astrophysics Data System (ADS)

Sharma, Sunil Kumar; Kumar, Anil

2017-05-01

The rail-wheel interaction in a rail vehicle running at high speed results in large amplitude vibration of carbody that deteriorates the ride comfort of travellers. The role of suspension system is crucial to provide an acceptable level of ride performance. In this context, an existing rail vehicle is modelled in vertical, pitch and roll motions of carbody and bogies. Additionally, nonlinear stiffness and damping parameters of passive suspension system are defined based on experimental data. In the secondary vertical suspension system, a magneto-rheological (MR) damper is included to improve the ride quality and comfort. The parameters of MR damper depend on the current, amplitude and frequency of excitations. At different running speeds, three semi-active suspension strategies with MR damper are analysed for periodic track irregularity and the resulting performance indices are juxtaposed with the nonlinear passive suspension system. The disturbance rejection and force tracking damper controller algorithms are applied to control the desired force of MR damper. This study reveals that the vertical vibrations of a vehicle can be reduced significantly by using the proposed semi-active suspension strategies. Moreover, it naturally results in improved ride quality and passenger’s comfort in comparison to the existing passive system.

Controlling the transmitted information of a multi-photon interacting with a single-Cooper pair box

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

Kadry, Heba, E-mail: hkadry1@yahoo.com; Abdel-Aty, Abdel-Haleem, E-mail: hkadry1@yahoo.com; Zakaria, Nordin, E-mail: hkadry1@yahoo.com

2014-10-24

We study a model of a multi-photon interaction of a single Cooper pair box with a cavity field. The exchange of the information using this system is studied. We quantify the fidelity of the transmitted information. The effect of the system parameters (detuning parameter, field photons, state density and mean photon number) in the fidelity of the transmitted information is investigated. We found that the fidelity of the transmitted information can be controlled using the system parameters.

Development of a Thermodynamic Model for the Hanford Tank Waste Operations Simulator - 12193

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

Carter, Robert; Seniow, Kendra

The Hanford Tank Waste Operations Simulator (HTWOS) is the current tool used by the Hanford Tank Operations Contractor for system planning and assessment of different operational strategies. Activities such as waste retrievals in the Hanford tank farms and washing and leaching of waste in the Waste Treatment and Immobilization Plant (WTP) are currently modeled in HTWOS. To predict phase compositions during these activities, HTWOS currently uses simple wash and leach factors that were developed many years ago. To improve these predictions, a rigorous thermodynamic framework has been developed based on the multi-component Pitzer ion interaction model for use with severalmore » important chemical species in Hanford tank waste. These chemical species are those with the greatest impact on high-level waste glass production in the WTP and whose solubility depends on the processing conditions. Starting with Pitzer parameter coefficients and species chemical potential coefficients collated from open literature sources, reconciliation with published experimental data led to a self-consistent set of coefficients known as the HTWOS Pitzer database. Using Gibbs energy minimization with the Pitzer ion interaction equations in Microsoft Excel,1 a number of successful predictions were made for the solubility of simple mixtures of the chosen species. Currently, this thermodynamic framework is being programmed into HTWOS as the mechanism for determining the solid-liquid phase distributions for the chosen species, replacing their simple wash and leach factors. Starting from a variety of open literature sources, a collection of Pitzer parameters and species chemical potentials, as functions of temperature, was tested for consistency and accuracy by comparison with available experimental thermodynamic data (e.g., osmotic coefficients and solubility). Reconciliation of the initial set of parameter coefficients with the experimental data led to the development of the self-consistent set known as the HTWOS Pitzer database. Using Microsoft Excel to formulate the Gibbs energy minimization method and the multi-component Pitzer ion interaction equations, several predictions of the solubility of solute mixtures at various temperatures were made using the HTWOS Pitzer database coefficients. Examples of these predictions are shown in Figure 3 and Figure 4. A listing of the entire HTWOS Pitzer database can be found in RPP-RPT-50703. Currently, work is underway to install the Pitzer ion interaction model in HTWOS as the mechanism for determining the solid-liquid phase distributions of select waste constituents during tank retrievals and subsequent washing and leaching of the waste. Validation of the Pitzer ion interaction model in HTWOS will be performed with analytical laboratory data of actual tank waste. This change in HTWOS is expected to elicit shifts in mission criteria, such as mission end date and quantity of high-level waste glass produced by WTP, as predicted by HTWOS. These improvements to the speciation calculations in HTWOS, however, will establish a better planning basis and facilitate more effective and efficient future operations of the WTP. (authors)« less

Color separation in forensic image processing using interactive differential evolution.

PubMed

Mushtaq, Harris; Rahnamayan, Shahryar; Siddiqi, Areeb

2015-01-01

Color separation is an image processing technique that has often been used in forensic applications to differentiate among variant colors and to remove unwanted image interference. This process can reveal important information such as covered text or fingerprints in forensic investigation procedures. However, several limitations prevent users from selecting the appropriate parameters pertaining to the desired and undesired colors. This study proposes the hybridization of an interactive differential evolution (IDE) and a color separation technique that no longer requires users to guess required control parameters. The IDE algorithm optimizes these parameters in an interactive manner by utilizing human visual judgment to uncover desired objects. A comprehensive experimental verification has been conducted on various sample test images, including heavily obscured texts, texts with subtle color variations, and fingerprint smudges. The advantage of IDE is apparent as it effectively optimizes the color separation parameters at a level indiscernible to the naked eyes. © 2014 American Academy of Forensic Sciences.

Identification of an Interaction between VWF rs7965413 and Platelet Count as a Novel Risk Marker for Metabolic Syndrome: An Extensive Search of Candidate Polymorphisms in a Case-Control Study

PubMed Central

Nakatochi, Masahiro; Ushida, Yasunori; Yasuda, Yoshinari; Yoshida, Yasuko; Kawai, Shun; Kato, Ryuji; Nakashima, Toru; Iwata, Masamitsu; Kuwatsuka, Yachiyo; Ando, Masahiko; Hamajima, Nobuyuki; Kondo, Takaaki; Oda, Hiroaki; Hayashi, Mutsuharu; Kato, Sawako; Yamaguchi, Makoto; Maruyama, Shoichi; Matsuo, Seiichi; Honda, Hiroyuki

2015-01-01

Although many single nucleotide polymorphisms (SNPs) have been identified to be associated with metabolic syndrome (MetS), there was only a slight improvement in the ability to predict future MetS by the simply addition of SNPs to clinical risk markers. To improve the ability to predict future MetS, combinational effects, such as SNP—SNP interaction, SNP—environment interaction, and SNP—clinical parameter (SNP × CP) interaction should be also considered. We performed a case-control study to explore novel SNP × CP interactions as risk markers for MetS based on health check-up data of Japanese male employees. We selected 99 SNPs that were previously reported to be associated with MetS and components of MetS; subsequently, we genotyped these SNPs from 360 cases and 1983 control subjects. First, we performed logistic regression analyses to assess the association of each SNP with MetS. Of these SNPs, five SNPs were significantly associated with MetS (P < 0.05): LRP2 rs2544390, rs1800592 between UCP1 and TBC1D9, APOA5 rs662799, VWF rs7965413, and rs1411766 between MYO16 and IRS2. Furthermore, we performed multiple logistic regression analyses, including an SNP term, a CP term, and an SNP × CP interaction term for each CP and SNP that was significantly associated with MetS. We identified a novel SNP × CP interaction between rs7965413 and platelet count that was significantly associated with MetS [SNP term: odds ratio (OR) = 0.78, P = 0.004; SNP × CP interaction term: OR = 1.33, P = 0.001]. This association of the SNP × CP interaction with MetS remained nominally significant in multiple logistic regression analysis after adjustment for either the number of MetS components or MetS components excluding obesity. Our results reveal new insight into platelet count as a risk marker for MetS. PMID:25646961

Identification of an interaction between VWF rs7965413 and platelet count as a novel risk marker for metabolic syndrome: an extensive search of candidate polymorphisms in a case-control study.

PubMed

Nakatochi, Masahiro; Ushida, Yasunori; Yasuda, Yoshinari; Yoshida, Yasuko; Kawai, Shun; Kato, Ryuji; Nakashima, Toru; Iwata, Masamitsu; Kuwatsuka, Yachiyo; Ando, Masahiko; Hamajima, Nobuyuki; Kondo, Takaaki; Oda, Hiroaki; Hayashi, Mutsuharu; Kato, Sawako; Yamaguchi, Makoto; Maruyama, Shoichi; Matsuo, Seiichi; Honda, Hiroyuki

2015-01-01

Although many single nucleotide polymorphisms (SNPs) have been identified to be associated with metabolic syndrome (MetS), there was only a slight improvement in the ability to predict future MetS by the simply addition of SNPs to clinical risk markers. To improve the ability to predict future MetS, combinational effects, such as SNP-SNP interaction, SNP-environment interaction, and SNP-clinical parameter (SNP × CP) interaction should be also considered. We performed a case-control study to explore novel SNP × CP interactions as risk markers for MetS based on health check-up data of Japanese male employees. We selected 99 SNPs that were previously reported to be associated with MetS and components of MetS; subsequently, we genotyped these SNPs from 360 cases and 1983 control subjects. First, we performed logistic regression analyses to assess the association of each SNP with MetS. Of these SNPs, five SNPs were significantly associated with MetS (P < 0.05): LRP2 rs2544390, rs1800592 between UCP1 and TBC1D9, APOA5 rs662799, VWF rs7965413, and rs1411766 between MYO16 and IRS2. Furthermore, we performed multiple logistic regression analyses, including an SNP term, a CP term, and an SNP × CP interaction term for each CP and SNP that was significantly associated with MetS. We identified a novel SNP × CP interaction between rs7965413 and platelet count that was significantly associated with MetS [SNP term: odds ratio (OR) = 0.78, P = 0.004; SNP × CP interaction term: OR = 1.33, P = 0.001]. This association of the SNP × CP interaction with MetS remained nominally significant in multiple logistic regression analysis after adjustment for either the number of MetS components or MetS components excluding obesity. Our results reveal new insight into platelet count as a risk marker for MetS.

Interactive model evaluation tool based on IPython notebook

NASA Astrophysics Data System (ADS)

Balemans, Sophie; Van Hoey, Stijn; Nopens, Ingmar; Seuntjes, Piet

2015-04-01

In hydrological modelling, some kind of parameter optimization is mostly performed. This can be the selection of a single best parameter set, a split in behavioural and non-behavioural parameter sets based on a selected threshold or a posterior parameter distribution derived with a formal Bayesian approach. The selection of the criterion to measure the goodness of fit (likelihood or any objective function) is an essential step in all of these methodologies and will affect the final selected parameter subset. Moreover, the discriminative power of the objective function is also dependent from the time period used. In practice, the optimization process is an iterative procedure. As such, in the course of the modelling process, an increasing amount of simulations is performed. However, the information carried by these simulation outputs is not always fully exploited. In this respect, we developed and present an interactive environment that enables the user to intuitively evaluate the model performance. The aim is to explore the parameter space graphically and to visualize the impact of the selected objective function on model behaviour. First, a set of model simulation results is loaded along with the corresponding parameter sets and a data set of the same variable as the model outcome (mostly discharge). The ranges of the loaded parameter sets define the parameter space. A selection of the two parameters visualised can be made by the user. Furthermore, an objective function and a time period of interest need to be selected. Based on this information, a two-dimensional parameter response surface is created, which actually just shows a scatter plot of the parameter combinations and assigns a color scale corresponding with the goodness of fit of each parameter combination. Finally, a slider is available to change the color mapping of the points. Actually, the slider provides a threshold to exclude non behaviour parameter sets and the color scale is only attributed to the remaining parameter sets. As such, by interactively changing the settings and interpreting the graph, the user gains insight in the model structural behaviour. Moreover, a more deliberate choice of objective function and periods of high information content can be identified. The environment is written in an IPython notebook and uses the available interactive functions provided by the IPython community. As such, the power of the IPython notebook as a development environment for scientific computing is illustrated (Shen, 2014).

Combining Genome-Wide Information with a Functional Structural Plant Model to Simulate 1-Year-Old Apple Tree Architecture.

PubMed

Migault, Vincent; Pallas, Benoît; Costes, Evelyne

2016-01-01

In crops, optimizing target traits in breeding programs can be fostered by selecting appropriate combinations of architectural traits which determine light interception and carbon acquisition. In apple tree, architectural traits were observed to be under genetic control. However, architectural traits also result from many organogenetic and morphological processes interacting with the environment. The present study aimed at combining a FSPM built for apple tree, MAppleT, with genetic determinisms of architectural traits, previously described in a bi-parental population. We focused on parameters related to organogenesis (phyllochron and immediate branching) and morphogenesis processes (internode length and leaf area) during the first year of tree growth. Two independent datasets collected in 2004 and 2007 on 116 genotypes, issued from a 'Starkrimson' × 'Granny Smith' cross, were used. The phyllochron was estimated as a function of thermal time and sylleptic branching was modeled subsequently depending on phyllochron. From a genetic map built with SNPs, marker effects were estimated on four MAppleT parameters with rrBLUP, using 2007 data. These effects were then considered in MAppleT to simulate tree development in the two climatic conditions. The genome wide prediction model gave consistent estimations of parameter values with correlation coefficients between observed values and estimated values from SNP markers ranging from 0.79 to 0.96. However, the accuracy of the prediction model following cross validation schemas was lower. Three integrative traits (the number of leaves, trunk length, and number of sylleptic laterals) were considered for validating MAppleT simulations. In 2007 climatic conditions, simulated values were close to observations, highlighting the correct simulation of genetic variability. However, in 2004 conditions which were not used for model calibration, the simulations differed from observations. This study demonstrates the possibility of integrating genome-based information in a FSPM for a perennial fruit tree. It also showed that further improvements are required for improving the prediction ability. Especially temperature effect should be extended and other factors taken into account for modeling GxE interactions. Improvements could also be expected by considering larger populations and by testing other genome wide prediction models. Despite these limitations, this study opens new possibilities for supporting plant breeding by in silico evaluations of the impact of genotypic polymorphisms on plant integrative phenotypes.

Comparative 4f-4f absorption spectral study for the interactions of Nd(III) with some amino acids: Preliminary thermodynamics and kinetic studies of interaction of Nd(III):glycine with Ca(II)

NASA Astrophysics Data System (ADS)

Moaienla, T.; Bendangsenla, N.; David Singh, Th.; Sumitra, Ch.; Rajmuhon Singh, N.; Indira Devi, M.

2012-02-01

Spectral analysis of Nd(III) complexes with some amino acids viz.; glycine, L-alanine, L-phenylalanine and L-aspartic acid in the presence and absence of Ca 2+ was carried out in some organic solvents; CH 3OH, CH 3CN, DMF and dioxane using comparative absorption spectra of 4f-4f transitions. The study was carried out by evaluating various energy interaction parameters like Slator-Condon ( Fk), Lande factor ( ξ4f), nephelauxetic ratio ( β), bonding parameter ( b1/2), percent-covalency ( δ) by applying partial and multiple regression analysis. The values of oscillator strength ( Pobs) and Judd-Ofelt electric dipole intensity parameter Tλ ( λ = 2, 4, 6) for different 4f-4f transitions have been calculated. On analysis of the variation of the various energy interaction parameters as well as the changes in the oscillator strength ( Pobs) and Tλ values, reveal the mode of binding with the different ligands. Kinetic studies for the complexation of Nd(III):glycine:Ca(II) have also been discussed at different temperatures in DMF medium and from it the values of activation energy ( Ea) and thermodynamic parameters like Δ H°, Δ S° and Δ G° for the complexation are evaluated.

Three-dimensional visualization of nanostructured surfaces and bacterial attachment using Autodesk® Maya®.

PubMed

Boshkovikj, Veselin; Fluke, Christopher J; Crawford, Russell J; Ivanova, Elena P

2014-02-28

There has been a growing interest in understanding the ways in which bacteria interact with nano-structured surfaces. As a result, there is a need for innovative approaches to enable researchers to visualize the biological processes taking place, despite the fact that it is not possible to directly observe these processes. We present a novel approach for the three-dimensional visualization of bacterial interactions with nano-structured surfaces using the software package Autodesk Maya. Our approach comprises a semi-automated stage, where actual surface topographic parameters, obtained using an atomic force microscope, are imported into Maya via a custom Python script, followed by a 'creative stage', where the bacterial cells and their interactions with the surfaces are visualized using available experimental data. The 'Dynamics' and 'nDynamics' capabilities of the Maya software allowed the construction and visualization of plausible interaction scenarios. This capability provides a practical aid to knowledge discovery, assists in the dissemination of research results, and provides an opportunity for an improved public understanding. We validated our approach by graphically depicting the interactions between the two bacteria being used for modeling purposes, Staphylococcus aureus and Pseudomonas aeruginosa, with different titanium substrate surfaces that are routinely used in the production of biomedical devices.

Three-dimensional visualization of nanostructured surfaces and bacterial attachment using Autodesk® Maya®

NASA Astrophysics Data System (ADS)

Boshkovikj, Veselin; Fluke, Christopher J.; Crawford, Russell J.; Ivanova, Elena P.

2014-02-01

There has been a growing interest in understanding the ways in which bacteria interact with nano-structured surfaces. As a result, there is a need for innovative approaches to enable researchers to visualize the biological processes taking place, despite the fact that it is not possible to directly observe these processes. We present a novel approach for the three-dimensional visualization of bacterial interactions with nano-structured surfaces using the software package Autodesk Maya. Our approach comprises a semi-automated stage, where actual surface topographic parameters, obtained using an atomic force microscope, are imported into Maya via a custom Python script, followed by a `creative stage', where the bacterial cells and their interactions with the surfaces are visualized using available experimental data. The `Dynamics' and `nDynamics' capabilities of the Maya software allowed the construction and visualization of plausible interaction scenarios. This capability provides a practical aid to knowledge discovery, assists in the dissemination of research results, and provides an opportunity for an improved public understanding. We validated our approach by graphically depicting the interactions between the two bacteria being used for modeling purposes, Staphylococcus aureus and Pseudomonas aeruginosa, with different titanium substrate surfaces that are routinely used in the production of biomedical devices.

Within-brain classification for brain tumor segmentation.

PubMed

Havaei, Mohammad; Larochelle, Hugo; Poulin, Philippe; Jodoin, Pierre-Marc

2016-05-01

In this paper, we investigate a framework for interactive brain tumor segmentation which, at its core, treats the problem of interactive brain tumor segmentation as a machine learning problem. This method has an advantage over typical machine learning methods for this task where generalization is made across brains. The problem with these methods is that they need to deal with intensity bias correction and other MRI-specific noise. In this paper, we avoid these issues by approaching the problem as one of within brain generalization. Specifically, we propose a semi-automatic method that segments a brain tumor by training and generalizing within that brain only, based on some minimum user interaction. We investigate how adding spatial feature coordinates (i.e., i, j, k) to the intensity features can significantly improve the performance of different classification methods such as SVM, kNN and random forests. This would only be possible within an interactive framework. We also investigate the use of a more appropriate kernel and the adaptation of hyper-parameters specifically for each brain. As a result of these experiments, we obtain an interactive method whose results reported on the MICCAI-BRATS 2013 dataset are the second most accurate compared to published methods, while using significantly less memory and processing power than most state-of-the-art methods.

Multifactor-Dimensionality Reduction Reveals High-Order Interactions among Estrogen-Metabolism Genes in Sporadic Breast Cancer

PubMed Central

Ritchie, Marylyn D.; Hahn, Lance W.; Roodi, Nady; Bailey, L. Renee; Dupont, William D.; Parl, Fritz F.; Moore, Jason H.

2001-01-01

One of the greatest challenges facing human geneticists is the identification and characterization of susceptibility genes for common complex multifactorial human diseases. This challenge is partly due to the limitations of parametric-statistical methods for detection of gene effects that are dependent solely or partially on interactions with other genes and with environmental exposures. We introduce multifactor-dimensionality reduction (MDR) as a method for reducing the dimensionality of multilocus information, to improve the identification of polymorphism combinations associated with disease risk. The MDR method is nonparametric (i.e., no hypothesis about the value of a statistical parameter is made), is model-free (i.e., it assumes no particular inheritance model), and is directly applicable to case-control and discordant-sib-pair studies. Using simulated case-control data, we demonstrate that MDR has reasonable power to identify interactions among two or more loci in relatively small samples. When it was applied to a sporadic breast cancer case-control data set, in the absence of any statistically significant independent main effects, MDR identified a statistically significant high-order interaction among four polymorphisms from three different estrogen-metabolism genes. To our knowledge, this is the first report of a four-locus interaction associated with a common complex multifactorial disease. PMID:11404819

Three-dimensional visualization of nanostructured surfaces and bacterial attachment using Autodesk® Maya®

PubMed Central

Boshkovikj, Veselin; Fluke, Christopher J.; Crawford, Russell J.; Ivanova, Elena P.

2014-01-01

There has been a growing interest in understanding the ways in which bacteria interact with nano-structured surfaces. As a result, there is a need for innovative approaches to enable researchers to visualize the biological processes taking place, despite the fact that it is not possible to directly observe these processes. We present a novel approach for the three-dimensional visualization of bacterial interactions with nano-structured surfaces using the software package Autodesk Maya. Our approach comprises a semi-automated stage, where actual surface topographic parameters, obtained using an atomic force microscope, are imported into Maya via a custom Python script, followed by a ‘creative stage', where the bacterial cells and their interactions with the surfaces are visualized using available experimental data. The ‘Dynamics' and ‘nDynamics' capabilities of the Maya software allowed the construction and visualization of plausible interaction scenarios. This capability provides a practical aid to knowledge discovery, assists in the dissemination of research results, and provides an opportunity for an improved public understanding. We validated our approach by graphically depicting the interactions between the two bacteria being used for modeling purposes, Staphylococcus aureus and Pseudomonas aeruginosa, with different titanium substrate surfaces that are routinely used in the production of biomedical devices. PMID:24577105

Numerical studies on alpha production from high energy proton beam interaction with Boron

NASA Astrophysics Data System (ADS)

Moustaizis, S. D.; Lalousis, P.; Hora, H.; Korn, G.

2017-05-01

Numerical investigations on high energy proton beam interaction with high density Boron plasma allows to simulate conditions concerning the alpha production from recent experimental measurements . The experiments measure the alpha production due to p11B nuclear fusion reactions when a laser-driven high energy proton beam interacts with Boron plasma produced by laser beam interaction with solid Boron. The alpha production and consequently the efficiency of the process depends on the initial proton beam energy, proton beam density, the Boron plasma density and temperature, and their temporal evolution. The main advantage for the p11B nuclear fusion reaction is the production of three alphas with total energy of 8.9 MeV, which could enhance the alpha heating effect and improve the alpha production. This particular effect is termed in the international literature as the alpha avalanche effect. Numerical results using a multi-fluid, global particle and energy balance, code shows the alpha production efficiency as a function of the initial energy of the proton beam, the Boron plasma density, the initial Boron plasma temperature and the temporal evolution of the plasma parameters. The simulations enable us to determine the interaction conditions (proton beam - B plasma) for which the alpha heating effect becomes important.

Prognostic relevance of the interaction between short-term, metronome-paced heart rate variability, and inflammation: results from the population-based CARLA cohort study.

PubMed

Medenwald, Daniel; Swenne, Cees A; Loppnow, Harald; Kors, Jan A; Pietzner, Diana; Tiller, Daniel; Thiery, Joachim; Nuding, Sebastian; Greiser, Karin H; Haerting, Johannes; Werdan, Karl; Kluttig, Alexander

2017-01-01

To determine the interaction between HRV and inflammation and their association with cardiovascular/all-cause mortality in the general population. Subjects of the CARLA study (n = 1671; 778 women, 893 men, 45-83 years of age) were observed for an average follow-up period of 8.8 years (226 deaths, 70 cardiovascular deaths). Heart rate variability parameters were calculated from 5-min segments of 20-min resting electrocardiograms. High-sensitivity C-reactive protein (hsCRP), interleukin-6 (IL-6), and soluble tumour necrosis factor-alpha receptor type 1 (sTNF-R1) were measured as inflammation parameters. The HRV parameters determined included the standard deviation of normal-to-normal intervals (SDNN), the root-mean-square of successive normal-interval differences (RMSSD), the low- and high-frequency (HF) power, the ratio of both, and non-linear parameters [Poincaré plot (SD1, SD2, SD1/SD2), short-term detrended fluctuation analysis]. We estimated hazard ratios by using covariate-adjusted Cox regression for cardiovascular and all-cause mortality incorporating an interaction term of HRV/inflammation parameters. Relative excess risk due to interactions (RERIs) were computed. We found an interaction effect of sTNF-R1 with SDNN (RERI: 0.5; 99% confidence interval (CI): 0.1-1.0), and a weaker effect with RMSSD (RERI: 0.4; 99% CI: 0.0-0.9) and HF (RERI: 0.4; 99% CI: 0.0-0.9) with respect to cardiovascular mortality on an additive scale after covariate adjustment. Neither IL-6 nor hsCRP showed a significant interaction with the HRV parameters. A change in TNF-α levels or the autonomic nervous system influences the mortality risk through both entities simultaneously. Thus, TNF-α and HRV need to be considered when predicating mortality. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2016. For permissions please email: journals.permissions@oup.com.

Three-dimensional, virtual reality vestibular rehabilitation for chronic imbalance problem caused by Ménière's disease: a pilot study^.

PubMed

Hsu, Su-Yi; Fang, Te-Yung; Yeh, Shih-Ching; Su, Mu-Chun; Wang, Pa-Chun; Wang, Victoria Y

2017-08-01

The purpose of this study was to evaluate a three-dimensional, virtual reality system for vestibular rehabilitation in patients with intractable Ménière's disease and chronic vestibular dysfunction. We included 70 patients (36 for study, 34 as control) with a chronic imbalance problem caused by uncompensated Ménière's disease. The virtual reality vestibular rehabilitation comprised four training tasks (modified Cawthorne-Cooksey exercises: eye, head, extension, and coordination exercises) performed in six training sessions (in 4 weeks). Measurements of the task scores and balance parameters obtained at the baseline and after final training sessions were compared. A significant improvement was observed in extension and coordination scores. Patients in the early stages of Ménière's disease had a significantly greater improvement in the center of gravity sway and trajectory excursion in the mediolateral direction than did patients in the late stages of Ménière's disease. Mild functional disability attributable to Ménière's disease was a predictor of improvement in the statokinesigram and maximum trajectory excursion in the anteroposterior direction after rehabilitation. The control group showed no significant improvement in almost all parameters. Virtual reality vestibular rehabilitation may be useful in patients with Ménière's disease, particular those in the early stages or having mild functional disability. Implication for rehabilitation Chronic imbalance caused by uncompensated Ménière's disease is an indication for vestibular rehabilitation. The interactive virtual reality video game, when integrated into vestibular rehabilitation exercise protocol, may assist patients who have mild disability Ménière's disease and who cannot benefit from treatment with drugs or surgery. The initial data from this study support the applicability of three-dimensional virtual reality technology in vestibular rehabilitation programs. The technology gives professionals a new tool to guide patients for vestibular rehabilitation exercises through three-dimensional virtual reality video game playing. The virtual reality vestibular exercise game can provide patients a step-wise, interactive, dynamic, three-dimensional, and interesting rehabilitation environment.

Mean-field and linear regime approach to magnetic hyperthermia of core-shell nanoparticles: can tiny nanostructures fight cancer?

NASA Astrophysics Data System (ADS)

Carrião, Marcus S.; Bakuzis, Andris F.

2016-04-01

The phenomenon of heat dissipation by magnetic materials interacting with an alternating magnetic field, known as magnetic hyperthermia, is an emergent and promising therapy for many diseases, mainly cancer. Here, a magnetic hyperthermia model for core-shell nanoparticles is developed. The theoretical calculation, different from previous models, highlights the importance of heterogeneity by identifying the role of surface and core spins on nanoparticle heat generation. We found that the most efficient nanoparticles should be obtained by selecting materials to reduce the surface to core damping factor ratio, increasing the interface exchange parameter and tuning the surface to core anisotropy ratio for each material combination. From our results we propose a novel heat-based hyperthermia strategy with the focus on improving the heating efficiency of small sized nanoparticles instead of larger ones. This approach might have important implications for cancer treatment and could help improving clinical efficacy.The phenomenon of heat dissipation by magnetic materials interacting with an alternating magnetic field, known as magnetic hyperthermia, is an emergent and promising therapy for many diseases, mainly cancer. Here, a magnetic hyperthermia model for core-shell nanoparticles is developed. The theoretical calculation, different from previous models, highlights the importance of heterogeneity by identifying the role of surface and core spins on nanoparticle heat generation. We found that the most efficient nanoparticles should be obtained by selecting materials to reduce the surface to core damping factor ratio, increasing the interface exchange parameter and tuning the surface to core anisotropy ratio for each material combination. From our results we propose a novel heat-based hyperthermia strategy with the focus on improving the heating efficiency of small sized nanoparticles instead of larger ones. This approach might have important implications for cancer treatment and could help improving clinical efficacy. Electronic supplementary information (ESI) available: Unit cells per region calculation; core-shell Hamiltonian; magnetisation description functions; energy argument of Brillouin function; polydisperse models; details of experimental procedure; LRT versus core-shell model; model calculation software; and shell thickness study. See DOI: 10.1039/C5NR09093H

Ischemia reperfusion dysfunction changes model-estimated kinetics of myofilament interaction due to inotropic drugs in isolated hearts

PubMed Central

Rhodes, Samhita S; Camara, Amadou KS; Ropella, Kristina M; Audi, Said H; Riess, Matthias L; Pagel, Paul S; Stowe, David F

2006-01-01

Background The phase-space relationship between simultaneously measured myoplasmic [Ca2+] and isovolumetric left ventricular pressure (LVP) in guinea pig intact hearts is altered by ischemic and inotropic interventions. Our objective was to mathematically model this phase-space relationship between [Ca2+] and LVP with a focus on the changes in cross-bridge kinetics and myofilament Ca2+ sensitivity responsible for alterations in Ca2+-contraction coupling due to inotropic drugs in the presence and absence of ischemia reperfusion (IR) injury. Methods We used a four state computational model to predict LVP using experimentally measured, averaged myoplasmic [Ca2+] transients from unpaced, isolated guinea pig hearts as the model input. Values of model parameters were estimated by minimizing the error between experimentally measured LVP and model-predicted LVP. Results We found that IR injury resulted in reduced myofilament Ca2+ sensitivity, and decreased cross-bridge association and dissociation rates. Dopamine (8 μM) reduced myofilament Ca2+ sensitivity before, but enhanced it after ischemia while improving cross-bridge kinetics before and after IR injury. Dobutamine (4 μM) reduced myofilament Ca2+ sensitivity while improving cross-bridge kinetics before and after ischemia. Digoxin (1 μM) increased myofilament Ca2+ sensitivity and cross-bridge kinetics after but not before ischemia. Levosimendan (1 μM) enhanced myofilament Ca2+ affinity and cross-bridge kinetics only after ischemia. Conclusion Estimated model parameters reveal mechanistic changes in Ca2+-contraction coupling due to IR injury, specifically the inefficient utilization of Ca2+ for contractile function with diastolic contracture (increase in resting diastolic LVP). The model parameters also reveal drug-induced improvements in Ca2+-contraction coupling before and after IR injury. PMID:16512898

Differential Mobility Spectrometry for Improved Selectivity in Hydrophilic Interaction Liquid Chromatography-Tandem Mass Spectrometry Analysis of Paralytic Shellfish Toxins

NASA Astrophysics Data System (ADS)

Beach, Daniel G.

2017-08-01

Paralytic shellfish toxins (PSTs) are neurotoxins produced by dinoflagellates and cyanobacteria that cause paralytic shellfish poisoning in humans. PST quantitation by LC-MS is challenging because of their high polarity, lability as gas-phase ions, and large number of potentially interfering analogues. Differential mobility spectrometry (DMS) has the potential to improve the performance of LC-MS methods for PSTs in terms of selectivity and limits of detection. This work describes a comprehensive investigation of the separation of 16 regulated PSTs by DMS and the development of highly selective LC-DMS-MS methods for PST quantitation. The effects of all DMS parameters on the separation of PSTs from one another were first investigated in detail. The labile nature of 11α-gonyautoxin epimers gave unique insight into fragmentation of labile analytes before, during, and after the DMS analyzer. Two sets of DMS parameters were identified that either optimized the resolution of PSTs from one another or transmitted them at a limited number of compensation voltage (CV) values corresponding to structural subclasses. These were used to develop multidimensional LC-DMS-MS/MS methods using existing HILIC-MS/MS parameters. In both cases, improved selectivity was observed when using DMS, and the quantitative capabilities of a rapid UPLC-DMS-MS/MS method were evaluated. Limits of detection of the developed method were similar to those without DMS, and differences were highly analyte-dependant. Analysis of shellfish matrix reference materials showed good agreement with established methods. The developed methods will be useful in cases where specific matrix interferences are encountered in the LC-MS/MS analysis of PSTs in complex biological samples.

U (1 ) -symmetric infinite projected entangled-pair states study of the spin-1/2 square J1-J2 Heisenberg model

NASA Astrophysics Data System (ADS)

Haghshenas, R.; Sheng, D. N.

2018-05-01

We develop an improved variant of U (1 ) -symmetric infinite projected entangled-pair states (iPEPS) ansatz to investigate the ground-state phase diagram of the spin-1 /2 square J1-J2 Heisenberg model. In order to improve the accuracy of the ansatz, we discuss a simple strategy to select automatically relevant symmetric sectors and also introduce an optimization method to treat second-neighbor interactions more efficiently. We show that variational ground-state energies of the model obtained by the U (1 ) -symmetric iPEPS ansatz (for a fixed bond dimension D ) set a better upper bound, improving previous tensor-network-based results. By studying the finite-D scaling of the magnetically order parameter, we find a Néel phase for J2/J1<0.53 . For 0.53

Can poly-parameter linear-free energy relationships (pp-LFERs) improve modelling bioaccumulation in fish?

PubMed

Zhao, Shizhen; Jones, Kevin C; Sweetman, Andrew J

2018-01-01

A wide range of studies have characterized different types of biosorbent, with regard to their interactions with chemicals. This has resulted in the development of poly-parameter linear free energy relationships (pp-LFERs) for the estimation of partitioning of neutral organic compounds to biological phases (e.g., storage lipids, phospholipids and serum albumins). The aims of this study were to explore and evaluate the influence of implementing pp-LFERs both into a one-compartment fish model and a multi-compartment physiologically based toxicokinetic (PBTK) fish model and the associated implications for chemical risk assessment. For this purpose, fish was used as reference biota, due to their important role in aquatic food chains and dietary exposure to humans. The bioconcentration factor (BCF) was utilized as the evaluation metric. Overall, our results indicated that models incorporating pp-LFERs (R 2  = 0.75) slightly outperformed the single parameter (sp) LFERs approach in the one-compartmental fish model (R 2  = 0.72). A pronounced enhancement was achieved for compounds with log K OW between 4 and 5 with increased R 2 from 0.52 to 0.71. The minimal improvement was caused by the overestimation of lipid contribution and underestimation of protein contribution by the sp-approach, which cancelled each other out. Meanwhile, a greater improvement was observed for multi-compartmental PBTK models with consideration of metabolism, making all predictions fall within a factor of 10 compared with measured data. For screening purposes, the K OW -based (sp-LFERs) approach should be sufficient to quantify the main partitioning characteristics. Further developments are required for the consideration of ionization and more accurate quantification of biotransformation in biota. Copyright © 2017 Elsevier Ltd. All rights reserved.

Combined effects of metal mixtures and predator stress on the freshwater isopod Asellus aquaticus.

PubMed

Van Ginneken, M; Blust, R; Bervoets, L

2018-04-30

Biotic stressors have been demonstrated to change the toxicity of pollutants. While the combined effects of predator cues and pesticides are well documented, the interaction of predator stress with metals is a topic that has remained largely unexplored. In this laboratory experiment, the freshwater isopod Asellus aquaticus is exposed to predator cues and metal mixtures of Cd, Cu and Pb. We examined the effects on growth, respiration and, as behavioral parameters, feeding rate and activity. These were linked to the free ion activities (FIAs) in the water and the metal body concentrations. The findings reveal that Cu accumulation significantly influenced the growth rate, the feeding rate and the activity of isopods exposed to predator stress. Furthermore, we found a concentration-dependent interaction of the Cd + Pb mixtures on the feeding rate and a lower feeding rate for Cd and Pb predator exposed asellids. As several interactions were found between metals and predator stress, it demonstrates the importance of investigating how organisms and whole ecosystems respond to multiple stressors. A better understanding of these interactions will undoubtedly improve risk assessment and management. Copyright © 2018 Elsevier B.V. All rights reserved.

A Statistical Method of Identifying Interactions in Neuron–Glia Systems Based on Functional Multicell Ca2+ Imaging

PubMed Central

Nakae, Ken; Ikegaya, Yuji; Ishikawa, Tomoe; Oba, Shigeyuki; Urakubo, Hidetoshi; Koyama, Masanori; Ishii, Shin

2014-01-01

Crosstalk between neurons and glia may constitute a significant part of information processing in the brain. We present a novel method of statistically identifying interactions in a neuron–glia network. We attempted to identify neuron–glia interactions from neuronal and glial activities via maximum-a-posteriori (MAP)-based parameter estimation by developing a generalized linear model (GLM) of a neuron–glia network. The interactions in our interest included functional connectivity and response functions. We evaluated the cross-validated likelihood of GLMs that resulted from the addition or removal of connections to confirm the existence of specific neuron-to-glia or glia-to-neuron connections. We only accepted addition or removal when the modification improved the cross-validated likelihood. We applied the method to a high-throughput, multicellular in vitro Ca2+ imaging dataset obtained from the CA3 region of a rat hippocampus, and then evaluated the reliability of connectivity estimates using a statistical test based on a surrogate method. Our findings based on the estimated connectivity were in good agreement with currently available physiological knowledge, suggesting our method can elucidate undiscovered functions of neuron–glia systems. PMID:25393874

Two-Player 2 × 2 Quantum Game in Spin System

NASA Astrophysics Data System (ADS)

Huang, Zhiming; Situ, Haozhen

2017-05-01

In this work, we study the payoffs of quantum Samaritan's dilemma played with the thermal entangled state of XXZ spin model in the presence of Dzyaloshinskii-Moriya (DM) interaction. We discuss the effect of anisotropy parameter, strength of DM interaction and temperature on quantum Samaritan's dilemma. It is shown that although increasing DM interaction and anisotropy parameter generate entanglement, players payoffs are not simply decided by entanglement and depend on other game components such as strategy and payoff measurement. In general, Entanglement and Alice's payoff evolve to a relatively stable value with anisotropy parameter, and develop to a fixed value with DM interaction strength, while Bob's payoff changes in the reverse direction. It is noted that the augment of Alice's payoff compensates for the loss of Bob's payoff. For different strategies, payoffs have different changes with temperature. Our results and discussions can be analogously generalized to other 2 × 2 quantum static games in various spin models.

Modeling the cooperative and competitive contagions in online social networks

NASA Astrophysics Data System (ADS)

Zhuang, Yun-Bei; Chen, J. J.; Li, Zhi-hong

2017-10-01

The wide adoption of social media has increased the interaction among different pieces of information, and this interaction includes cooperation and competition for our finite attention. While previous research focus on fully competition, this paper extends the interaction to be both "cooperation" and "competition", by employing an IS1S2 R model. To explore how two different pieces of information interact with each other, the IS1S2 R model splits the agents into four parts-(Ignorant-Spreader I-Spreader II-Stifler), based on SIR epidemic spreading model. Using real data from Weibo.com, a social network site similar to Twitter, we find some parameters, like decaying rates, can both influence the cooperative diffusion process and the competitive process, while other parameters, like infectious rates only have influence on the competitive diffusion process. Besides, the parameters' effect are more significant in the competitive diffusion than in the cooperative diffusion.

TRIP-ID: A tool for a smart and interactive identification of Magic Formula tyre model parameters from experimental data acquired on track or test rig

NASA Astrophysics Data System (ADS)

Farroni, Flavio; Lamberti, Raffaele; Mancinelli, Nicolò; Timpone, Francesco

2018-03-01

Tyres play a key role in ground vehicles' dynamics because they are responsible for traction, braking and cornering. A proper tyre-road interaction model is essential for a useful and reliable vehicle dynamics model. In the last two decades Pacejka's Magic Formula (MF) has become a standard in simulation field. This paper presents a Tool, called TRIP-ID (Tyre Road Interaction Parameters IDentification), developed to characterize and to identify with a high grade of accuracy and reliability MF micro-parameters from experimental data deriving from telemetry or from test rig. The tool guides interactively the user through the identification process on the basis of strong diagnostic considerations about the experimental data made evident by the tool itself. A motorsport application of the tool is shown as a case study.

Effects of intermittent theta burst stimulation on spasticity after stroke.

PubMed

Kim, Dae Hyun; Shin, Ji Cheol; Jung, Seungsoo; Jung, Tae-Min; Kim, Deog Young

2015-07-08

Spasticity is a common cause of long-term disability in poststroke hemiplegic patients. We investigated whether intermittent theta burst stimulation (iTBS) could reduce upper-limb spasticity after a stroke. Fifteen hemiplegic stroke patients were recruited for a double-blind sham-controlled cross-over design study. A single session of iTBS or sham stimulation was delivered on the motor hotspot of the affected flexor carpi radialis muscle in a random and counterbalanced order with a 1-week interval. Modified Ashworth scale (MAS), modified Tardieu scale (MTS), H-wave/M-wave amplitude ratio, peak torque (PT), peak torque angle (PTA), work of affected wrist flexor, and rectified integrated electromyographic activity of the flexor carpi radialis muscle were measured before, immediately after, 30 min after, and 1 week after iTBS or sham stimulation. Repeated-measures analysis of variance showed a significant interaction between time and intervention for the MAS, MTS, PT, PTA, and rectified integrated electromyographic activity (P<0.05), indicating that these parameters were significantly improved by iTBS compared with sham stimulation. However, the H-wave/M-wave amplitude ratio and work were not affected. MAS and MTS significantly improved for at least 30 min after iTBS, but the other parameters only improved immediately after iTBS (P<0.05). In conclusion, iTBS on the affected hemisphere may help to reduce poststroke spasticity transiently.

Beth-Uhlenbeck approach for repulsive interactions between baryons in a hadron gas

NASA Astrophysics Data System (ADS)

Vovchenko, Volodymyr; Motornenko, Anton; Gorenstein, Mark I.; Stoecker, Horst

2018-03-01

The quantum mechanical Beth-Uhlenbeck (BU) approach for repulsive hard-core interactions between baryons is applied to the thermodynamics of a hadron gas. The second virial coefficient a2—the "excluded volume" parameter—calculated within the BU approach is found to be temperature dependent, and it differs dramatically from the classical excluded volume (EV) model result. At temperatures T =100 -200 MeV, the widely used classical EV model underestimates the EV parameter for nucleons at a given value of the nucleon hard-core radius by large factors of 3-4. Previous studies, which employed the hard-core radii of hadrons as an input into the classical EV model, have to be re-evaluated using the appropriately rescaled EV parameters. The BU approach is used to model the repulsive baryonic interactions in the hadron resonance gas (HRG) model. Lattice data for the second- and fourth-order net baryon susceptibilities are described fairly well when the temperature dependent BU baryonic excluded volume parameter corresponds to nucleon hard-core radii of rc=0.25 -0.3 fm. Role of the attractive baryonic interactions is also considered. It is argued that HRG model with a constant baryon-baryon EV parameter vN N≃1 fm3 provides a simple yet efficient description of baryon-baryon interaction in the crossover temperature region.

Optical absorption characteristics in the assessment of powder phosphor-based x-ray detectors: from nano- to micro-scale.

PubMed

Liaparinos, P F

2015-11-21

X-ray phosphor-based detectors have enormously improved the quality of medical imaging examinations through the optimization of optical diffusion. In recent years, with the development of science and technology in the field of materials, improved powder phosphors require structural and optical properties that contribute to better optical signal propagation. The purpose of this paper was to provide a quantitative and qualitative understanding of the optical absorption characteristics in the assessment of powder phosphor-based detectors (from nano- scale up to micro-scale). Variations on the optical absorption parameters (i.e. the light extinction coefficient [Formula: see text] and the percentage probability of light absorption p%) were evaluated based on Mie calculations examining a wide range of light wavelengths, particle refractive indices and sizes. To model and assess the effects of the aforementioned parameters on optical diffusion, Monte Carlo simulation techniques were employed considering: (i) phosphors of different layer thickness, 100 μm (thin layer) and 300 μm (thick layer), respectively, (ii) light extinction coefficient values, 1, 3 and 6 μm(-1), and (iii) percentage probability of light absorption p% in the range 10(-4)-10(-2). Results showed that the [Formula: see text] coefficient is high for phosphor grains in the submicron scale and for low light wavelengths. At higher wavelengths (above 650 nm), optical quanta follow approximately similar depths until interaction for grain diameter 500 nm and 1 μm. Regarding the variability of the refractive index, high variations of the [Formula: see text] coefficient occurred above 1.6. Furthermore, results derived from Monte Carlo modeling showed that high spatial resolution phosphors can be accomplished by increasing the [Formula: see text] parameter. More specifically, the FWHM was found to decrease (i.e. higher resolution): (i) 4.8% at 100 μm and (ii) 9.5%, at 300 μm layer thickness. This study attempted to examine the role of the optical absorption parameters on optical diffusion studies. A significant outcome of the present investigation was that the improvement of phosphor spatial resolution without decreasing the light collection efficiency too much can be better achieved by increasing the parameter [Formula: see text] rather than the parameter p%.

Selecting the optimal synthesis parameters of InP/CdxZn1-xSe quantum dots for a hybrid remote phosphor white LED for general lighting applications.

PubMed

Ryckaert, Jana; Correia, António; Tessier, Mickael D; Dupont, Dorian; Hens, Zeger; Hanselaer, Peter; Meuret, Youri

2017-11-27

Quantum dots can be used in white LEDs for lighting applications to fill the spectral gaps in the combined emission spectrum of the blue pumping LED and a broad band phosphor, in order to improve the source color rendering properties. Because quantum dots are low scattering materials, their use can also reduce the amount of backscattered light which can increase the overall efficiency of the white LED. The absorption spectrum and narrow emission spectrum of quantum dots can be easily tuned by altering their synthesis parameters. Due to the re-absorption events between the different luminescent materials and the light interaction with the LED package, determining the optimal quantum dot properties is a highly non-trivial task. In this paper we propose a methodology to select the optimal quantum dot to be combined with a broad band phosphor in order to realize a white LED with optimal luminous efficacy and CRI. The methodology is based on accurate and efficient simulations using the extended adding-doubling approach that take into account all the optical interactions. The method is elaborated for the specific case of a hybrid, remote phosphor white LED with YAG:Ce phosphor in combination with InP/CdxZn 1-x Se type quantum dots. The absorption and emission spectrum of the quantum dots are generated in function of three synthesis parameters (core size, shell size and cadmium fraction) by a semi-empirical 'quantum dot model' to include the continuous tunability of these spectra. The sufficiently fast simulations allow to scan the full parameter space consisting of these synthesis parameters and luminescent material concentrations in terms of CRI and efficacy. A conclusive visualization of the final performance allows to make a well-considered trade-off between these performance parameters. For the hybrid white remote phosphor LED with YAG:Ce and InP/CdxZn 1-x Se quantum dots a CRI Ra = 90 (with R9>50) and an overall efficacy of 110 lm/W is found.

Spectral Study of the Interaction of Myoglobin with Tannin

NASA Astrophysics Data System (ADS)

Grigoryan, K. R.; Sargsyan, L. S.

2016-07-01

The interaction of myoglobin with tannin (tannic acid) at 298.15 and 303.15 K was studied by fluorescence and absorption spectroscopy in the UV region. The physicochemical and thermodynamic binding parameters (the fluorescence quenching mechanism, the bonding constant, the number of binding sites, the type of interaction) and parameters of the formed complex were determined. It was found that binding of myoglobin with tannic acid does not lead to significant changes in the electronic state of the heme ring of myoglobin.

A new methodology based on sensitivity analysis to simplify the recalibration of functional-structural plant models in new conditions.

PubMed

Mathieu, Amélie; Vidal, Tiphaine; Jullien, Alexandra; Wu, QiongLi; Chambon, Camille; Bayol, Benoit; Cournède, Paul-Henry

2018-06-19

Functional-structural plant models (FSPMs) describe explicitly the interactions between plants and their environment at organ to plant scale. However, the high level of description of the structure or model mechanisms makes this type of model very complex and hard to calibrate. A two-step methodology to facilitate the calibration process is proposed here. First, a global sensitivity analysis method was applied to the calibration loss function. It provided first-order and total-order sensitivity indexes that allow parameters to be ranked by importance in order to select the most influential ones. Second, the Akaike information criterion (AIC) was used to quantify the model's quality of fit after calibration with different combinations of selected parameters. The model with the lowest AIC gives the best combination of parameters to select. This methodology was validated by calibrating the model on an independent data set (same cultivar, another year) with the parameters selected in the second step. All the parameters were set to their nominal value; only the most influential ones were re-estimated. Sensitivity analysis applied to the calibration loss function is a relevant method to underline the most significant parameters in the estimation process. For the studied winter oilseed rape model, 11 out of 26 estimated parameters were selected. Then, the model could be recalibrated for a different data set by re-estimating only three parameters selected with the model selection method. Fitting only a small number of parameters dramatically increases the efficiency of recalibration, increases the robustness of the model and helps identify the principal sources of variation in varying environmental conditions. This innovative method still needs to be more widely validated but already gives interesting avenues to improve the calibration of FSPMs.

Developing force fields when experimental data is sparse: AMBER/GAFF-compatible parameters for inorganic and alkyl oxoanions.

PubMed

Kashefolgheta, Sadra; Vila Verde, Ana

2017-08-09

We present a set of Lennard-Jones parameters for classical, all-atom models of acetate and various alkylated and non-alkylated forms of sulfate, sulfonate and phosphate ions, optimized to reproduce their interactions with water and with the physiologically relevant sodium, ammonium and methylammonium cations. The parameters are internally consistent and are fully compatible with the Generalized Amber Force Field (GAFF), the AMBER force field for proteins, the accompanying TIP3P water model and the sodium model of Joung and Cheatham. The parameters were developed primarily relying on experimental information - hydration free energies and solution activity derivatives at 0.5 m concentration - with ab initio, gas phase calculations being used for the cases where experimental information is missing. The ab initio parameterization scheme presented here is distinct from other approaches because it explicitly connects gas phase binding energies to intermolecular interactions in solution. We demonstrate that the original GAFF/AMBER parameters often overestimate anion-cation interactions, leading to an excessive number of contact ion pairs in solutions of carboxylate ions, and to aggregation in solutions of divalent ions. GAFF/AMBER parameters lead to excessive numbers of salt bridges in proteins and of contact ion pairs between sodium and acidic protein groups, issues that are resolved by using the optimized parameters presented here.

Evaluation of kinetic constants of biomolecular interaction on optical surface plasmon resonance sensor with Newton Iteration Method

NASA Astrophysics Data System (ADS)

Zhao, Yuanyuan; Jiang, Guoliang; Hu, Jiandong; Hu, Fengjiang; Wei, Jianguang; Shi, Liang

2010-10-01

In the immunology, there are two important types of biomolecular interaction: antigens-antibodies and receptors-ligands. Monitoring the response rate and affinity of biomolecular interaction can help analyze the protein function, drug discover, genomics and proteomics research. Moreover the association rate constant and dissociation rate constant of receptors-ligands are the important parameters for the study of signal transmission between cells. Recent advances in bioanalyzer instruments have greatly simplified the measurement of the kinetics of molecular interactions. Non-destructive and real-time monitoring the response to evaluate the parameters between antigens and antibodies can be performed by using optical surface plasmon resonance (SPR) biosensor technology. This technology provides a quantitative analysis that is carried out rapidly with label-free high-throughput detection using the binding curves of antigens-antibodies. Consequently, the kinetic parameters of interaction between antigens and antibodies can be obtained. This article presents a low cost integrated SPR-based bioanalyzer (HPSPR-6000) designed by ourselves. This bioanalyzer is mainly composed of a biosensor TSPR1K23, a touch-screen monitor, a microprocessor PIC24F128, a microflow cell with three channels, a clamp and a photoelectric conversion device. To obtain the kinetic parameters, sensorgrams may be modeled using one of several binding models provided with BIAevaluation software 3.0, SensiQ or Autolab. This allows calculation of the association rate constant (ka) and the dissociation rate constant (kd). The ratio of ka to kd can be used to estimate the equilibrium constant. Another kind is the analysis software OriginPro, which can process the obtained data by nonlinear fitting and then get some correlative parameters, but it can't be embedded into the bioanalyzer, so the bioanalyzer don't support the use of OriginPro. This paper proposes a novel method to evaluate the kinetic parameters of biomolecular interaction by using Newton Iteration Method and Least Squares Method. First, the pseudo first order kinetic model of biomolecular interaction was established. Then the data of molecular interaction of HBsAg and HBsAb was obtained by bioanalyzer. Finally, we used the optical SPR bioanalyzer software which was written by ourselves to make nonlinear fit about the association and dissociation curves. The correlation coefficient R-squared is 0.99229 and 0.99593, respectively. Furthermore, the kinetic parameters and affinity constants were evaluated using the obtained data from the fitting results.

A study of the pulsatile flow and its interaction with rectangular leaflets

NASA Astrophysics Data System (ADS)

Ledesma, Rene; Zenit, Roberto; Pulos, Guillermo

2009-11-01

To avoid the complexity and limited understanding of the 3D pulsatile flow field through heart valves, a cardiac-like flow circuit and a test channel were designed to study the behavior of bidimensional leaflets made of hyperelastic materials. We study a simple 2D arrangement to understand the basic physics of the flow-leaflet interaction. Creating a periodic pressure gradient, measurements of leaflet deflection were obtained for different flow conditions, geometries and materials. Using PIV and Phase Locking techniques, we have obtained the leaflet motion and the time-dependent flow velocity fields. The results show that two dimensionless parameters determine the performance of a simple bi-dimensional valve, in accordance with the flow conditions applied: π1=f(sw)^1/2(E/ρ)^1/2 and π2=V/(2slw), where f is the pulsation frequency, V is the stroke volume, s, w and l are the dimensions on the leaftlet and E and ρ are the elastic modulus and density of the material, respectively. Furthermore, we have identified the conditions for which the fluid stresses can be minimized. With these results we propose a new set of parameters to improve the performance of prosthetic heart valves and, in consequence, to reduce blood damage.

Application of two-level factorial design to investigate the effect of process parameters on the sonocrystallization of sulfathiazole

NASA Astrophysics Data System (ADS)

Kuo, Peng-Hsuan; Zhang, Bo-Cong; Su, Chie-Shaan; Liu, Jun-Jen; Sheu, Ming-Thau

2017-08-01

In this study, cooling sonocrystallization was used to recrystallize an active pharmaceutical ingredient, sulfathiazole, using methanol as the solvent. The effects of three operating parameters-sonication intensity, sonication duration, and solution concentration-on the recrystallization were investigated by using a 2k factorial design. The solid-state properties of sulfathiazole, including the mean particle size, crystal habit, and polymorphic form, were analyzed. Analysis of variance showed that the effect of the sonication intensity, cross-interaction effect of sonication intensity/sonication duration, and cross-interaction effect of sonication intensity/solution concentration on the recrystallization were significant. The results obtained using the 2k factorial design indicated that a combination of high sonication intensity and long sonication duration is not favorable for sonocrystallization, especially at a high solution concentration. A comparison of the solid-state properties of the original and the recrystallized sulfathiazole revealed that the crystal habit of the recrystallized sulfathiazole was more regular and that its mean particle size could be reduced to approximately 10 μm. Furthermore, the analytical results obtained using the PXRD, DSC, and FTIR spectroscopy indicated that the polymorphic purity of sulfathiazole improved from the original Form III/IV mixture to Form III after sonocrystallization.

Control of Chemical Effects in the Separation Process of a Differential Mobility / Mass Spectrometer System

PubMed Central

Schneider, Bradley B.; Coy, Stephen L.; Krylov, Evgeny V.; Nazarov, Erkinjon G.

2013-01-01

Differential mobility spectrometry (DMS) separates ions on the basis of the difference in their migration rates under high versus low electric fields. Several models describing the physical nature of this field mobility dependence have been proposed but emerging as a dominant effect is the clusterization model sometimes referred to as the dynamic cluster-decluster model. DMS resolution and peak capacity is strongly influenced by the addition of modifiers which results in the formation and dissociation of clusters. This process increases selectivity due to the unique chemical interactions that occur between an ion and neutral gas phase molecules. It is thus imperative to bring the parameters influencing the chemical interactions under control and find ways to exploit them in order to improve the analytical utility of the device. In this paper we describe three important areas that need consideration in order to stabilize and capitalize on the chemical processes that dominate a DMS separation. The first involves means of controlling the dynamic equilibrium of the clustering reactions with high concentrations of specific reagents. The second area involves a means to deal with the unwanted heterogeneous cluster ion populations emitted from the electrospray ionization process that degrade resolution and sensitivity. The third involves fine control of parameters that affect the fundamental collision processes, temperature and pressure. PMID:20065515

An investigation of the thermodynamic miscibility between VeTPGS and polymers.

PubMed

Li, Jinjiang; Chiappetta, Doris

2008-02-28

Within the past decade, more than half of the drug candidates generated are poorly water soluble and therefore overcoming the low aqueous solubility of drug candidates becomes critical for product development. Vitamin E TPGS (VeTPGS), a non-ionic surfactant, has been used in both liquid and solid dosage forms to solubilize compounds and improve their bioavailability. To prepare solid dosage forms using VeTPGS, VeTPGS is often mixed with other excipients, mostly polymers. However, there is still a lack of understanding of miscibility between VeTPGS and polymers from a thermodynamic point of view. In this paper, the miscibility of VeTPGS with polymers has been studied in the light of the Flory-Huggins (F-H) theory with an objective to understand the effect of dispersion forces (solubility parameter) and nondispersive interactions on the miscibility between VeTPGS and polymers. A series of polymers with similar solubility parameters and structure similarity were selected. Binary blends of polymers and VeTPGS were prepared using a vapor evaporation technique followed by XRPD, DSC, and SEM characterization. Results suggest that the miscibility between VeTPGS and PMMA is very likely due to a specific interaction between the hydrophobic portion of VeTPGS (Vitamin E) and PMMA.

Hot-crack test for aluminium alloys welds using TIG process

NASA Astrophysics Data System (ADS)

Niel, A.; Deschaux-Beaume, F.; Bordreuil, C.; Fras, G.

2010-06-01

Hot cracking is a critical defect frequently observed during welding of aluminium alloys. In order to better understand the interaction between cracking phenomenon, process parameters, mechanical factors and microstructures resulting from solidification after welding, an original hot-cracking test during welding is developed. According to in-situ observations and post mortem analyses, hot cracking mechanisms are investigated, taking into account the interaction between microstructural parameters, depending on the thermal cycles, and mechanical parameters, depending on geometry and clamping conditions of the samples and on the thermal field on the sample. Finally, a process map indicating the limit between cracking and non-cracking zones according to welding parameters is presented.

Bayesian Methods for Effective Field Theories

NASA Astrophysics Data System (ADS)

Wesolowski, Sarah

Microscopic predictions of the properties of atomic nuclei have reached a high level of precision in the past decade. This progress mandates improved uncertainty quantification (UQ) for a robust comparison of experiment with theory. With the uncertainty from many-body methods under control, calculations are now sensitive to the input inter-nucleon interactions. These interactions include parameters that must be fit to experiment, inducing both uncertainty from the fit and from missing physics in the operator structure of the Hamiltonian. Furthermore, the implementation of the inter-nucleon interactions is not unique, which presents the additional problem of assessing results using different interactions. Effective field theories (EFTs) take advantage of a separation of high- and low-energy scales in the problem to form a power-counting scheme that allows the organization of terms in the Hamiltonian based on their expected contribution to observable predictions. This scheme gives a natural framework for quantification of uncertainty due to missing physics. The free parameters of the EFT, called the low-energy constants (LECs), must be fit to data, but in a properly constructed EFT these constants will be natural-sized, i.e., of order unity. The constraints provided by the EFT, namely the size of the systematic uncertainty from truncation of the theory and the natural size of the LECs, are assumed information even before a calculation is performed or a fit is done. Bayesian statistical methods provide a framework for treating uncertainties that naturally incorporates prior information as well as putting stochastic and systematic uncertainties on an equal footing. For EFT UQ Bayesian methods allow the relevant EFT properties to be incorporated quantitatively as prior probability distribution functions (pdfs). Following the logic of probability theory, observable quantities and underlying physical parameters such as the EFT breakdown scale may be expressed as pdfs that incorporate the prior pdfs. Problems of model selection, such as distinguishing between competing EFT implementations, are also natural in a Bayesian framework. In this thesis we focus on two complementary topics for EFT UQ using Bayesian methods--quantifying EFT truncation uncertainty and parameter estimation for LECs. Using the order-by-order calculations and underlying EFT constraints as prior information, we show how to estimate EFT truncation uncertainties. We then apply the result to calculating truncation uncertainties on predictions of nucleon-nucleon scattering in chiral effective field theory. We apply model-checking diagnostics to our calculations to ensure that the statistical model of truncation uncertainty produces consistent results. A framework for EFT parameter estimation based on EFT convergence properties and naturalness is developed which includes a series of diagnostics to ensure the extraction of the maximum amount of available information from data to estimate LECs with minimal bias. We develop this framework using model EFTs and apply it to the problem of extrapolating lattice quantum chromodynamics results for the nucleon mass. We then apply aspects of the parameter estimation framework to perform case studies in chiral EFT parameter estimation, investigating a possible operator redundancy at fourth order in the chiral expansion and the appropriate inclusion of truncation uncertainty in estimating LECs.

Improvement of localised corrosion resistance of AISI 2205 Duplex Stainless Steel joints made by gas metal arc welding under electromagnetic interaction of low intensity

NASA Astrophysics Data System (ADS)

García-Rentería, M. A.; López-Morelos, V. H.; García-Hernández, R.; Dzib-Pérez, L.; García-Ochoa, E. M.; González-Sánchez, J.

2014-12-01

The resistance to localised corrosion of AISI 2205 duplex stainless steel plates joined by Gas Metal Arc Welding (GMAW) under the effect of electromagnetic interaction of low intensity (EMILI) was evaluated with sensitive electrochemical methods. Welds were made using two shielding gas mixtures: 98% Ar + 2% O2 (M1) and 97% Ar + 3% N2 (M2). Plates were welded under EMILI using the M1 gas with constant welding parameters. The modified microstructural evolution in the high temperature heat affected zone and at the fusion zone induced by application of EMILI during welding is associated with the increase of resistance to localised corrosion of the welded joints. Joints made by GMAW using the shielding gas M2 without the application of magnetic field presented high resistance to general corrosion but high susceptibility to undergo localised attack.

Thermal expansion in dispersion-bound molecular crystals

DOE PAGES

Ko, Hsin -Yu; DiStasio, Robert A.; Santra, Biswajit; ...

2018-05-18

In this paper, we explore how anharmonicity, nuclear quantum effects (NQE), many-body dispersion interactions, and Pauli repulsion influence thermal properties of dispersion-bound molecular crystals. Accounting for anharmonicity with ab initio molecular dynamics yields cell parameters accurate to within 2% of experiment for a set of pyridinelike molecular crystals at finite temperatures and pressures. From the experimental thermal expansion curve, we find that pyridine-I has a Debye temperature just above its melting point, indicating sizable NQE across the entire crystalline range of stability. We find that NQE lead to a substantial volume increase in pyridine-I (≈ 40% more than classical thermalmore » expansion at 153 K) and attribute this to intermolecular Pauli repulsion promoted by intramolecular quantum fluctuations. Finally, when predicting delicate properties such as the thermal expansivity, we show that many-body dispersion interactions and more sophisticated density functional approximations improve the accuracy of the theoretical model.« less

Monte Carlo modeling of light-tissue interactions in narrow band imaging.

PubMed

Le, Du V N; Wang, Quanzeng; Ramella-Roman, Jessica C; Pfefer, T Joshua

2013-01-01

Light-tissue interactions that influence vascular contrast enhancement in narrow band imaging (NBI) have not been the subject of extensive theoretical study. In order to elucidate relevant mechanisms in a systematic and quantitative manner we have developed and validated a Monte Carlo model of NBI and used it to study the effect of device and tissue parameters, specifically, imaging wavelength (415 versus 540 nm) and vessel diameter and depth. Simulations provided quantitative predictions of contrast-including up to 125% improvement in small, superficial vessel contrast for 415 over 540 nm. Our findings indicated that absorption rather than scattering-the mechanism often cited in prior studies-was the dominant factor behind spectral variations in vessel depth-selectivity. Narrow-band images of a tissue-simulating phantom showed good agreement in terms of trends and quantitative values. Numerical modeling represents a powerful tool for elucidating the factors that affect the performance of spectral imaging approaches such as NBI.

GLobal Integrated Design Environment (GLIDE): A Concurrent Engineering Application

NASA Technical Reports Server (NTRS)

McGuire, Melissa L.; Kunkel, Matthew R.; Smith, David A.

2010-01-01

The GLobal Integrated Design Environment (GLIDE) is a client-server software application purpose-built to mitigate issues associated with real time data sharing in concurrent engineering environments and to facilitate discipline-to-discipline interaction between multiple engineers and researchers. GLIDE is implemented in multiple programming languages utilizing standardized web protocols to enable secure parameter data sharing between engineers and researchers across the Internet in closed and/or widely distributed working environments. A well defined, HyperText Transfer Protocol (HTTP) based Application Programming Interface (API) to the GLIDE client/server environment enables users to interact with GLIDE, and each other, within common and familiar tools. One such common tool, Microsoft Excel (Microsoft Corporation), paired with its add-in API for GLIDE, is discussed in this paper. The top-level examples given demonstrate how this interface improves the efficiency of the design process of a concurrent engineering study while reducing potential errors associated with manually sharing information between study participants.

Thermal expansion in dispersion-bound molecular crystals

NASA Astrophysics Data System (ADS)

Ko, Hsin-Yu; DiStasio, Robert A.; Santra, Biswajit; Car, Roberto

2018-05-01

We explore how anharmonicity, nuclear quantum effects (NQE), many-body dispersion interactions, and Pauli repulsion influence thermal properties of dispersion-bound molecular crystals. Accounting for anharmonicity with ab initio molecular dynamics yields cell parameters accurate to within 2 % of experiment for a set of pyridinelike molecular crystals at finite temperatures and pressures. From the experimental thermal expansion curve, we find that pyridine-I has a Debye temperature just above its melting point, indicating sizable NQE across the entire crystalline range of stability. We find that NQE lead to a substantial volume increase in pyridine-I (≈40 % more than classical thermal expansion at 153 K) and attribute this to intermolecular Pauli repulsion promoted by intramolecular quantum fluctuations. When predicting delicate properties such as the thermal expansivity, we show that many-body dispersion interactions and more sophisticated density functional approximations improve the accuracy of the theoretical model.

Pedestal cleaning for high laser pulse contrast ratio with a 100 TW class laser system.

PubMed

Fourmaux, S; Payeur, S; Buffechoux, S; Lassonde, P; St-Pierre, C; Martin, F; Kieffer, J C

2011-04-25

Laser matter interaction at relativistic intensities using 100 TW class laser systems or higher is becoming more and more widespread. One of the critical issues of such laser systems is to let the laser pulse interact at high intensity with the solid target and avoid any pre-plasma. Thus, a high Laser Pulse Contrast Ratio (LPCR) parameter is of prime importance. We present the LPCR characterization of a high repetition 100 TW class laser system. We demonstrate that the generated Amplified Spontaneous Emission (ASE) degrades the overall LPCR performance. We propose a simple way to clean the pulse after the first amplification stage by introducing a solid state saturable absorber which results in a LPCR improvement to better than 10(10) with only a 30% energy loss at a 10 Hz repetition rate. We finally correlated this cleaning method with experimental results.

Mutualisms and Population Regulation: Mechanism Matters

PubMed Central

Jha, Shalene; Allen, David; Liere, Heidi; Perfecto, Ivette; Vandermeer, John

2012-01-01

For both applied and theoretical ecological science, the mutualism between ants and their hemipteran partners is iconic. In this well-studied interaction, ants are assumed to provide hemipterans protection from natural enemies in exchange for nutritive honeydew. Despite decades of research and the potential importance in pest control, the precise mechanism producing this mutualism remains contested. By analyzing maximum likelihood parameter estimates of a hemipteran population model, we show that the mechanism of the mutualism is direct, via improved hemipteran growth rates, as opposed to the frequently assumed indirect mechanism, via harassment of the specialist parasites and predators of the hemipterans. Broadly, this study demonstrates that the management of mutualism-based ecosystem services requires a mechanistic understanding of mutualistic interactions. A consequence of this finding is the counter intuitive demonstration that preserving ant participation in the ant-hemipteran mutualism may be the best way of insuring pest control. PMID:22927978

Thermal expansion in dispersion-bound molecular crystals

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

Ko, Hsin -Yu; DiStasio, Robert A.; Santra, Biswajit

In this paper, we explore how anharmonicity, nuclear quantum effects (NQE), many-body dispersion interactions, and Pauli repulsion influence thermal properties of dispersion-bound molecular crystals. Accounting for anharmonicity with ab initio molecular dynamics yields cell parameters accurate to within 2% of experiment for a set of pyridinelike molecular crystals at finite temperatures and pressures. From the experimental thermal expansion curve, we find that pyridine-I has a Debye temperature just above its melting point, indicating sizable NQE across the entire crystalline range of stability. We find that NQE lead to a substantial volume increase in pyridine-I (≈ 40% more than classical thermalmore » expansion at 153 K) and attribute this to intermolecular Pauli repulsion promoted by intramolecular quantum fluctuations. Finally, when predicting delicate properties such as the thermal expansivity, we show that many-body dispersion interactions and more sophisticated density functional approximations improve the accuracy of the theoretical model.« less

Simulation of Orientation in Injection Molding of High Aspect Ratio Particle Thermoplastic Composites

NASA Astrophysics Data System (ADS)

Vélez-García, Gregorio M.; Ortman, Kevin C.; Eberle, Aaron P. R.; Wapperom, Peter; Baird, Donald G.

2008-07-01

A 2D coupled Hele-Shaw flow approximation for predicting the flow-induced orientation of high aspect ratio particles in injection molded composite parts is presented. For a highly concentrated short glass fiber PBT suspension, the impact of inter-particle interactions and the orientation at the gate is investigated for a center-gated disk using material parameters determined from rheometry. Experimental orientation is determined from confocal laser micrographs using the methods of ellipses. The constitutive equations are discretized using discontinuous Galerkin Finite Elements. Model predictions are significantly improved by using a localized orientation measured experimentally at the gate region instead of random or averaged gapwise measured orientation assumed in previous studies. The predicted profile in different radial positions can be related to the layered structure along the gapwise direction. Model modifications including interactions have lower impact than the initial conditions.

Gravity Wave Interactions with Fine Structures in the Mesosphere and Lower Thermosphere

NASA Astrophysics Data System (ADS)

Mixa, Tyler; Fritts, David; Bossert, Katrina; Laughman, Brian; Wang, Ling; Lund, Thomas; Kantha, Lakshmi

2017-04-01

An anelastic numerical model is used to probe the influences of fine layering structures on gravity wave propagation in the Mesosphere and Lower Thermosphere (MLT). Recent lidar observations confirm the presence of persistent layered structures in the MLT that have sharp stratification and vertical scales below 1km. Gravity waves propagating through finely layered environments can excite and modulate the evolution of small scale instabilities that redefine the layering structure in these regions. Such layers in turn filter the outgoing wave spectra, promote ducting or reflection, hasten the onset of self-acceleration dynamics, and encourage wave/mean-flow interactions via energy and momentum transport. Using high resolution simulations of a localized gravity wave packet in a deep atmosphere, we identify the relative impacts of various wave and mean flow parameters to improve our understanding of these dynamics and complement recent state-of-the-art observations.

Sensitivity Analysis in Agent-Based Models of Socio-Ecological Systems: An Example in Agricultural Land Conservation for Lake Water Quality Improvement

NASA Astrophysics Data System (ADS)

Ligmann-Zielinska, A.; Kramer, D. B.; Spence Cheruvelil, K.; Soranno, P.

2012-12-01

Socio-ecological systems are dynamic and nonlinear. To account for this complexity, we employ agent-based models (ABMs) to study macro-scale phenomena resulting from micro-scale interactions among system components. Because ABMs typically have many parameters, it is challenging to identify which parameters contribute to the emerging macro-scale patterns. In this paper, we address the following question: What is the extent of participation in agricultural land conservation programs given heterogeneous landscape, economic, social, and individual decision making criteria in complex lakesheds? To answer this question, we: [1] built an ABM for our model system; [2] simulated land use change resulting from agent decision making, [3] estimated the uncertainty of the model output, decomposed it and apportioned it to each of the parameters in the model. Our model system is a freshwater socio-ecological system - that of farmland and lake water quality within a region containing a large number of lakes and high proportions of agricultural lands. Our study focuses on examining how agricultural land conversion from active to fallow reduces freshwater nutrient loading and improves water quality. Consequently, our ABM is composed of farmer agents who make decisions related to participation in a government-sponsored Conservation Reserve Program (CRP) managed by the Farm Service Agency (FSA). We also include an FSA agent, who selects enrollment offers made by farmers and announces the signup results leading to land use change. The model is executed in a Monte Carlo simulation framework to generate a distribution of maps of fallow lands that are used for calculating nutrient loading to lakes. What follows is a variance-based sensitivity analysis of the results. We compute sensitivity indices for individual parameters and their combinations, allowing for identification of the most influential as well as the insignificant inputs. In the case study, we observe that farmland conservation is first and foremost driven by the FSA signup choices. Environmental criteria used in FSA offer selection play a secondary role in farmland-to-fallow-land conversion. Farmer decision making is mainly influenced by the willingness to reduce the potential annual rental payments. As the case study demonstrates, our approach leads to ABM simplification without the loss of outcome variability. It also shows how to represent the magnitude of ABM complexity and isolate the effects of the interconnected explanatory variables on the simulated emergent phenomena. More importantly, the results of our research indicate that some of the parameters exert influence on model outcomes only if analyzed in combination with other parameters. Without evaluating the interaction effects among inputs, we risk losing important functional relationships among ABM components and, consequently, we potentially reduce its explanatory power.

Interactions Between Item Content And Group Membership on Achievement Test Items.

ERIC Educational Resources Information Center

Linn, Robert L.; Harnisch, Delwyn L.

The purpose of this investigation was to examine the interaction of item content and group membership on achievement test items. Estimates of the parameters of the three parameter logistic model were obtained on the 46 item math test for the sample of eighth grade students (N = 2055) participating in the Illinois Inventory of Educational Progress,…

Automated optimization of water-water interaction parameters for a coarse-grained model.

PubMed

Fogarty, Joseph C; Chiu, See-Wing; Kirby, Peter; Jakobsson, Eric; Pandit, Sagar A

2014-02-13

We have developed an automated parameter optimization software framework (ParOpt) that implements the Nelder-Mead simplex algorithm and applied it to a coarse-grained polarizable water model. The model employs a tabulated, modified Morse potential with decoupled short- and long-range interactions incorporating four water molecules per interaction site. Polarizability is introduced by the addition of a harmonic angle term defined among three charged points within each bead. The target function for parameter optimization was based on the experimental density, surface tension, electric field permittivity, and diffusion coefficient. The model was validated by comparison of statistical quantities with experimental observation. We found very good performance of the optimization procedure and good agreement of the model with experiment.

Chimera regimes in a ring of oscillators with local nonlinear interaction

NASA Astrophysics Data System (ADS)

Shepelev, Igor A.; Zakharova, Anna; Vadivasova, Tatiana E.

2017-03-01

One of important problems concerning chimera states is the conditions of their existence and stability. Until now, it was assumed that chimeras could arise only in ensembles with nonlocal character of interactions. However, this assumption is not exactly right. In some special cases chimeras can be realized for local type of coupling [1-3]. We propose a simple model of ensemble with local coupling when chimeras are realized. This model is a ring of linear oscillators with the local nonlinear unidirectional interaction. Chimera structures in the ring are found using computer simulations for wide area of values of parameters. Diagram of the regimes on plane of control parameters is plotted and scenario of chimera destruction are studied when the parameters are changed.

Accurate estimation of motion blur parameters in noisy remote sensing image

NASA Astrophysics Data System (ADS)

Shi, Xueyan; Wang, Lin; Shao, Xiaopeng; Wang, Huilin; Tao, Zhong

2015-05-01

The relative motion between remote sensing satellite sensor and objects is one of the most common reasons for remote sensing image degradation. It seriously weakens image data interpretation and information extraction. In practice, point spread function (PSF) should be estimated firstly for image restoration. Identifying motion blur direction and length accurately is very crucial for PSF and restoring image with precision. In general, the regular light-and-dark stripes in the spectrum can be employed to obtain the parameters by using Radon transform. However, serious noise existing in actual remote sensing images often causes the stripes unobvious. The parameters would be difficult to calculate and the error of the result relatively big. In this paper, an improved motion blur parameter identification method to noisy remote sensing image is proposed to solve this problem. The spectrum characteristic of noisy remote sensing image is analyzed firstly. An interactive image segmentation method based on graph theory called GrabCut is adopted to effectively extract the edge of the light center in the spectrum. Motion blur direction is estimated by applying Radon transform on the segmentation result. In order to reduce random error, a method based on whole column statistics is used during calculating blur length. Finally, Lucy-Richardson algorithm is applied to restore the remote sensing images of the moon after estimating blur parameters. The experimental results verify the effectiveness and robustness of our algorithm.

Automatic Calibration of a Semi-Distributed Hydrologic Model Using Particle Swarm Optimization

NASA Astrophysics Data System (ADS)

Bekele, E. G.; Nicklow, J. W.

2005-12-01

Hydrologic simulation models need to be calibrated and validated before using them for operational predictions. Spatially-distributed hydrologic models generally have a large number of parameters to capture the various physical characteristics of a hydrologic system. Manual calibration of such models is a very tedious and daunting task, and its success depends on the subjective assessment of a particular modeler, which includes knowledge of the basic approaches and interactions in the model. In order to alleviate these shortcomings, an automatic calibration model, which employs an evolutionary optimization technique known as Particle Swarm Optimizer (PSO) for parameter estimation, is developed. PSO is a heuristic search algorithm that is inspired by social behavior of bird flocking or fish schooling. The newly-developed calibration model is integrated to the U.S. Department of Agriculture's Soil and Water Assessment Tool (SWAT). SWAT is a physically-based, semi-distributed hydrologic model that was developed to predict the long term impacts of land management practices on water, sediment and agricultural chemical yields in large complex watersheds with varying soils, land use, and management conditions. SWAT was calibrated for streamflow and sediment concentration. The calibration process involves parameter specification, whereby sensitive model parameters are identified, and parameter estimation. In order to reduce the number of parameters to be calibrated, parameterization was performed. The methodology is applied to a demonstration watershed known as Big Creek, which is located in southern Illinois. Application results show the effectiveness of the approach and model predictions are significantly improved.

Path integrals with higher order actions: Application to realistic chemical systems

NASA Astrophysics Data System (ADS)

Lindoy, Lachlan P.; Huang, Gavin S.; Jordan, Meredith J. T.

2018-02-01

Quantum thermodynamic parameters can be determined using path integral Monte Carlo (PIMC) simulations. These simulations, however, become computationally demanding as the quantum nature of the system increases, although their efficiency can be improved by using higher order approximations to the thermal density matrix, specifically the action. Here we compare the standard, primitive approximation to the action (PA) and three higher order approximations, the Takahashi-Imada action (TIA), the Suzuki-Chin action (SCA) and the Chin action (CA). The resulting PIMC methods are applied to two realistic potential energy surfaces, for H2O and HCN-HNC, both of which are spectroscopically accurate and contain three-body interactions. We further numerically optimise, for each potential, the SCA parameter and the two free parameters in the CA, obtaining more significant improvements in efficiency than seen previously in the literature. For both H2O and HCN-HNC, accounting for all required potential and force evaluations, the optimised CA formalism is approximately twice as efficient as the TIA formalism and approximately an order of magnitude more efficient than the PA. The optimised SCA formalism shows similar efficiency gains to the CA for HCN-HNC but has similar efficiency to the TIA for H2O at low temperature. In H2O and HCN-HNC systems, the optimal value of the a1 CA parameter is approximately 1/3 , corresponding to an equal weighting of all force terms in the thermal density matrix, and similar to previous studies, the optimal α parameter in the SCA was ˜0.31. Importantly, poor choice of parameter significantly degrades the performance of the SCA and CA methods. In particular, for the CA, setting a1 = 0 is not efficient: the reduction in convergence efficiency is not offset by the lower number of force evaluations. We also find that the harmonic approximation to the CA parameters, whilst providing a fourth order approximation to the action, is not optimal for these realistic potentials: numerical optimisation leads to better approximate cancellation of the fifth order terms, with deviation between the harmonic and numerically optimised parameters more marked in the more quantum H2O system. This suggests that numerically optimising the CA or SCA parameters, which can be done at high temperature, will be important in fully realising the efficiency gains of these formalisms for realistic potentials.

Improvement in the physiological function and standing stability based on kinect multimedia for older people

PubMed Central

Chen, Chih-Chen

2016-01-01

[Purpose] The increase in the Taiwanese older population is associated with age-related inconveniences. Finding adequate and simple physical activities to help the older people maintaining their physiological function and preventing them from falls has become an urgent social issue. [Subjects and Methods] This study aimed to design a virtual exercise training game suitable for Taiwanese older people. This system will allow for the maintenance of the physiological function and standing stability through physical exercise, while using a virtual reality game. The participants can easily exercise in a carefree, interactive environment. This study will use Kinect for Windows for physical movement detection and Unity software for virtual world development. [Results] Group A and B subjects were involved in the exercise training method of Kinect interactive multimedia for 12 weeks. The results showed that the functional reach test and the unipedal stance test improved significantly. [Conclusion] The physiological function and standing stability of the group A subjects were examined at six weeks post training. The results showed that these parameters remained constant. This proved that the proposed system provide substantial support toward the preservation of the Taiwanese older people’ physiological function and standing stability. PMID:27190480

Improvement in the physiological function and standing stability based on kinect multimedia for older people.

PubMed

Chen, Chih-Chen

2016-04-01

[Purpose] The increase in the Taiwanese older population is associated with age-related inconveniences. Finding adequate and simple physical activities to help the older people maintaining their physiological function and preventing them from falls has become an urgent social issue. [Subjects and Methods] This study aimed to design a virtual exercise training game suitable for Taiwanese older people. This system will allow for the maintenance of the physiological function and standing stability through physical exercise, while using a virtual reality game. The participants can easily exercise in a carefree, interactive environment. This study will use Kinect for Windows for physical movement detection and Unity software for virtual world development. [Results] Group A and B subjects were involved in the exercise training method of Kinect interactive multimedia for 12 weeks. The results showed that the functional reach test and the unipedal stance test improved significantly. [Conclusion] The physiological function and standing stability of the group A subjects were examined at six weeks post training. The results showed that these parameters remained constant. This proved that the proposed system provide substantial support toward the preservation of the Taiwanese older people' physiological function and standing stability.

Review of Top Quark Physics Results

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

Kehoe, R.; Narain, M.; Kumar, A.

2007-12-01

As the heaviest known fundamental particle, the top quark has taken a central role in the study of fundamental interactions. Production of top quarks in pairs provides an important probe of strong interactions. The top quark mass is a key fundamental parameter which places a valuable constraint on the Higgs boson mass and electroweak symmetry breaking. Observations of the relative rates and kinematics of top quark final states constrain potential new physics. In many cases, the tests available with study of the top quark are both critical and unique. Large increases in data samples from the Fermilab Tevatron have beenmore » coupled with major improvements in experimental techniques to produce many new precision measurements of the top quark. The first direct evidence for electroweak production of top quarks has been obtained, with a resulting direct determination of V{sub tb}. Several of the properties of the top quark have been measured. Progress has also been made in obtaining improved limits on potential anomalous production and decay mechanisms. This review presents an overview of recent theoretical and experimental developments in this field. We also provide a brief discussion of the implications for further efforts.« less

Theoretical study of bismuth-doped cadmium telluride

NASA Astrophysics Data System (ADS)

Menendez-Proupin, E.; Rios-Gonzalez, J. A.; Pena, J. L.

Cadmium telluride heavily doped with bismuth has been proposed as an absorber with an intermediate band for solar cells. Increase in the photocurrent has been shown recently, although the overall cell efficiency has not improved. In this work, we study the electronic structure and the formation energies of the defects associated to bismuth impurities. We have performed electronic structure calculations within generalized density functional theory, using the exchange-correlation functional HSE(w) , where the range-separation parameter w has been tuned to reproduce the CdTe bandgap. Improving upon previous reports, we have included the spin-orbit interaction, which modifies the structure of the valence band and the energy levels of bismuth. We have found that interstitial Bi (Bii) tends to occupy Cd vacancies, cadmium substitution (BiCd) creates single donor level, while tellurium substitution (BiTe) is a shallow single acceptor. We investigate the interaction between these point defects and how can they be combined to create a partially filled intermediate band. Supported by FONDECYT Grant 1130437, CONACYT-SENER SUSTENTABILIDAD ENERGETICA/project CeMIE-Sol PY-207450/25 and PY-207450/26. JARG acknowledges CONACYT fellowship for research visit. Powered@NLHPC (ECM-02).

Developing the professional competence of future doctors in the instructional setting of higher medical educational institutions.

PubMed

Morokhovets, Halyna Yu; Lysanets, Yuliia V

The main objectives of higher medical education is the continuous professional improvement of physicians to meet the needs dictated by the modern world both at undergraduate and postgraduate levels. In this respect, the system of higher medical education has undergone certain changes - from determining the range of professional competences to the adoption of new standards of education in medicine. The article aims to analyze the parameters of doctor's professionalism in the context of competence-based approach and to develop practical recommendations for the improvement of instruction techniques. The authors reviewed the psycho-pedagogical materials and summarized the acquired experience of teachers at higher medical institutions as to the development of instruction techniques in the modern educational process. The study is based on the results of testing via the technique developed by T.I. Ilyina. Analytical and biblio-semantic methods were used in the paper. It has been found that the training process at medical educational institution should be focused on the learning outcomes. The authors defined the quality parameters of doctors' training and suggested the model for developing the professional competence of medical students. This model explains the cause-and-effect relationships between the forms of instruction, teaching techniques and specific components of professional competence in future doctors. The paper provides practical recommendations on developing the core competencies which a qualified doctor should master. The analysis of existing interactive media in Ukraine and abroad has been performed. It has been found that teaching the core disciplines with the use of latest technologies and interactive means keeps abreast of the times, while teaching social studies and humanities to medical students still involves certain difficulties.

sin2 θ W estimate and bounds on nonstandard interactions at source and detector in the solar neutrino low-energy regime

NASA Astrophysics Data System (ADS)

Khan, Amir N.; McKay, Douglas W.

2017-07-01

We explore the implications of the Borexino experiment's real time measurements of the lowest energy part of the neutrino spectrum from the primary pp fusion process up to 0.420 MeV through the 7Be decay at 0.862 MeV to the pep reaction at 1.44 MeV. We exploit the fact that at such low energies, the large mixing angle solution to the Mikheyev-Smirnov-Wolfenstein matter effects in the sun are small for 7Be and pep and negligible for pp. Consequently, the neutrinos produced in the sun change their flavor almost entirely through vacuum oscillations during propagation from the sun's surface and through possible nonstandard interactions acting at the solar source and Borexino detector. We combine the different NSI effects at source and detector in a single framework and use the current Borexino data to bound NSI non-universal and flavor-changing parameters at energies below the reach of reactor neutrino experiments. We also study the implication of the current data for the weak-mixing angle at this "low-energy frontier" data from the Borexino experiment, where it is expected to be slightly larger than its value at the Z mass. We find sin2 θ W = 0.224 ± 0.016, the lowest energy-scale estimate to date. Looking to the future, we use projected sensitivities to solar neutrinos in next generation dedicated solar experiments and direct dark matter detection experiments and find a potential factor five improvement in determination of the weak-mixing angle and up to an order of magnitude improvement in probing the NSI parameters space.

Impact of Optimized land Surface Parameters on the Land-Atmosphere Coupling in WRF Simulations of Dry and Wet Extremes

NASA Technical Reports Server (NTRS)

Kumar, Sujay; Santanello, Joseph; Peters-Lidard, Christa; Harrison, Ken

2011-01-01

Land-atmosphere (L-A) interactions play a critical role in determining the diurnal evolution of both planetary boundary layer (PBL) and land surface temperature and moisture budgets, as well as controlling feedbacks with clouds and precipitation that lead to the persistence of dry and wet regimes. Recent efforts to quantify the strength of L-A coupling in prediction models have produced diagnostics that integrate across both the land and PBL components of the system. In this study, we examine the impact of improved specification of land surface states, anomalies, and fluxes on coupled WRF forecasts during the summers of extreme dry (2006) and wet (2007) conditions in the U.S. Southern Great Plains. The improved land initialization and surface flux parameterizations are obtained through the use of a new optimization and uncertainty module in NASA's Land Information System (LIS-OPT), whereby parameter sets are calibrated in the Noah land surface model and classified according to the land cover and soil type mapping of the observations and the full domain. The impact of the calibrated parameters on the a) spin up of land surface states used as initial conditions, and b) heat and moisture fluxes of the coupled (LIS-WRF) simulations are then assessed in terms of ambient weather, PBL budgets, and precipitation along with L-A coupling diagnostics. In addition, the sensitivity of this approach to the period of calibration (dry, wet, normal) is investigated. Finally, tradeoffs of computational tractability and scientific validity (e.g.,. relating to the representation of the spatial dependence of parameters) and the feasibility of calibrating to multiple observational datasets are also discussed.

Sensitivities to charged-current nonstandard neutrino interactions at DUNE

NASA Astrophysics Data System (ADS)

Bakhti, Pouya; Khan, Amir N.; Wang, W.

2017-12-01

We investigate the effects of charged-current (CC) nonstandard neutrino interactions (NSIs) at the source and at the detector in the simulated data for the planned Deep Underground Neutrino Experiment (DUNE). We neglect the neutral-current NSIs at the propagation because several solutions have already been proposed for resolving the degeneracies posed by neutral-current NSIs but no solutions exist for the degeneracies due to the CC NSIs. We study the effects of CC NSIs on the simultaneous measurements of {θ }23 and {δ }{{CP}} in DUNE. The analysis reveals that 3σ C.L. measurement of the correct octant of {θ }23 in the standard mixing scenario is spoiled if the CC NSIs are taken into account. Likewise, the CC NSIs can deteriorate the uncertainty of the {δ }{{CP}} measurement by a factor of two relative to that in the standard oscillation scenario. We also show that the source and the detector CC NSIs can induce a significant amount of fake CP-violation and the CP-conserving case can be excluded by more than 80% C.L. in the presence of fake CP-violation. We further find DUNE’s potential for constraining the relevant CC NSI parameters from the single parameter fits for both neutrino and antineutrino appearance and disappearance channels at both the near and far detectors. The results show that there could be improvements in the current bounds by at least one order of magnitude at DUNE’s near and far detectors, except for a few parameters which remain weaker at the far detector.

Semiparametric Bayesian analysis of gene-environment interactions with error in measurement of environmental covariates and missing genetic data.

PubMed

Lobach, Iryna; Mallick, Bani; Carroll, Raymond J

2011-01-01

Case-control studies are widely used to detect gene-environment interactions in the etiology of complex diseases. Many variables that are of interest to biomedical researchers are difficult to measure on an individual level, e.g. nutrient intake, cigarette smoking exposure, long-term toxic exposure. Measurement error causes bias in parameter estimates, thus masking key features of data and leading to loss of power and spurious/masked associations. We develop a Bayesian methodology for analysis of case-control studies for the case when measurement error is present in an environmental covariate and the genetic variable has missing data. This approach offers several advantages. It allows prior information to enter the model to make estimation and inference more precise. The environmental covariates measured exactly are modeled completely nonparametrically. Further, information about the probability of disease can be incorporated in the estimation procedure to improve quality of parameter estimates, what cannot be done in conventional case-control studies. A unique feature of the procedure under investigation is that the analysis is based on a pseudo-likelihood function therefore conventional Bayesian techniques may not be technically correct. We propose an approach using Markov Chain Monte Carlo sampling as well as a computationally simple method based on an asymptotic posterior distribution. Simulation experiments demonstrated that our method produced parameter estimates that are nearly unbiased even for small sample sizes. An application of our method is illustrated using a population-based case-control study of the association between calcium intake with the risk of colorectal adenoma development.

Uncertainty quantification and global sensitivity analysis of the Los Alamos sea ice model

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

Urrego-Blanco, Jorge Rolando; Urban, Nathan Mark; Hunke, Elizabeth Clare

Changes in the high-latitude climate system have the potential to affect global climate through feedbacks with the atmosphere and connections with midlatitudes. Sea ice and climate models used to understand these changes have uncertainties that need to be characterized and quantified. We present a quantitative way to assess uncertainty in complex computer models, which is a new approach in the analysis of sea ice models. We characterize parametric uncertainty in the Los Alamos sea ice model (CICE) in a standalone configuration and quantify the sensitivity of sea ice area, extent, and volume with respect to uncertainty in 39 individual modelmore » parameters. Unlike common sensitivity analyses conducted in previous studies where parameters are varied one at a time, this study uses a global variance-based approach in which Sobol' sequences are used to efficiently sample the full 39-dimensional parameter space. We implement a fast emulator of the sea ice model whose predictions of sea ice extent, area, and volume are used to compute the Sobol' sensitivity indices of the 39 parameters. Main effects and interactions among the most influential parameters are also estimated by a nonparametric regression technique based on generalized additive models. A ranking based on the sensitivity indices indicates that model predictions are most sensitive to snow parameters such as snow conductivity and grain size, and the drainage of melt ponds. Lastly, it is recommended that research be prioritized toward more accurately determining these most influential parameter values by observational studies or by improving parameterizations in the sea ice model.« less

Experiments for practical education in process parameter optimization for selective laser sintering to increase workpiece quality

NASA Astrophysics Data System (ADS)

Reutterer, Bernd; Traxler, Lukas; Bayer, Natascha; Drauschke, Andreas

2016-04-01

Selective Laser Sintering (SLS) is considered as one of the most important additive manufacturing processes due to component stability and its broad range of usable materials. However the influence of the different process parameters on mechanical workpiece properties is still poorly studied, leading to the fact that further optimization is necessary to increase workpiece quality. In order to investigate the impact of various process parameters, laboratory experiments are implemented to improve the understanding of the SLS limitations and advantages on an educational level. Experiments are based on two different workstations, used to teach students the fundamentals of SLS. First of all a 50 W CO2 laser workstation is used to investigate the interaction of the laser beam with the used material in accordance with varied process parameters to analyze a single-layered test piece. Second of all the FORMIGA P110 laser sintering system from EOS is used to print different 3D test pieces in dependence on various process parameters. Finally quality attributes are tested including warpage, dimension accuracy or tensile strength. For dimension measurements and evaluation of the surface structure a telecentric lens in combination with a camera is used. A tensile test machine allows testing of the tensile strength and the interpreting of stress-strain curves. The developed laboratory experiments are suitable to teach students the influence of processing parameters. In this context they will be able to optimize the input parameters depending on the component which has to be manufactured and to increase the overall quality of the final workpiece.

Uncertainty quantification and global sensitivity analysis of the Los Alamos sea ice model

DOE PAGES

Urrego-Blanco, Jorge Rolando; Urban, Nathan Mark; Hunke, Elizabeth Clare; ...

2016-04-01

Changes in the high-latitude climate system have the potential to affect global climate through feedbacks with the atmosphere and connections with midlatitudes. Sea ice and climate models used to understand these changes have uncertainties that need to be characterized and quantified. We present a quantitative way to assess uncertainty in complex computer models, which is a new approach in the analysis of sea ice models. We characterize parametric uncertainty in the Los Alamos sea ice model (CICE) in a standalone configuration and quantify the sensitivity of sea ice area, extent, and volume with respect to uncertainty in 39 individual modelmore » parameters. Unlike common sensitivity analyses conducted in previous studies where parameters are varied one at a time, this study uses a global variance-based approach in which Sobol' sequences are used to efficiently sample the full 39-dimensional parameter space. We implement a fast emulator of the sea ice model whose predictions of sea ice extent, area, and volume are used to compute the Sobol' sensitivity indices of the 39 parameters. Main effects and interactions among the most influential parameters are also estimated by a nonparametric regression technique based on generalized additive models. A ranking based on the sensitivity indices indicates that model predictions are most sensitive to snow parameters such as snow conductivity and grain size, and the drainage of melt ponds. Lastly, it is recommended that research be prioritized toward more accurately determining these most influential parameter values by observational studies or by improving parameterizations in the sea ice model.« less

Uncertainty quantification and global sensitivity analysis of the Los Alamos sea ice model

NASA Astrophysics Data System (ADS)

Urrego-Blanco, Jorge R.; Urban, Nathan M.; Hunke, Elizabeth C.; Turner, Adrian K.; Jeffery, Nicole

2016-04-01

Changes in the high-latitude climate system have the potential to affect global climate through feedbacks with the atmosphere and connections with midlatitudes. Sea ice and climate models used to understand these changes have uncertainties that need to be characterized and quantified. We present a quantitative way to assess uncertainty in complex computer models, which is a new approach in the analysis of sea ice models. We characterize parametric uncertainty in the Los Alamos sea ice model (CICE) in a standalone configuration and quantify the sensitivity of sea ice area, extent, and volume with respect to uncertainty in 39 individual model parameters. Unlike common sensitivity analyses conducted in previous studies where parameters are varied one at a time, this study uses a global variance-based approach in which Sobol' sequences are used to efficiently sample the full 39-dimensional parameter space. We implement a fast emulator of the sea ice model whose predictions of sea ice extent, area, and volume are used to compute the Sobol' sensitivity indices of the 39 parameters. Main effects and interactions among the most influential parameters are also estimated by a nonparametric regression technique based on generalized additive models. A ranking based on the sensitivity indices indicates that model predictions are most sensitive to snow parameters such as snow conductivity and grain size, and the drainage of melt ponds. It is recommended that research be prioritized toward more accurately determining these most influential parameter values by observational studies or by improving parameterizations in the sea ice model.

Photofragmentation, state interaction, and energetics of Rydberg and ion-pair states: Resonance enhanced multiphoton ionization of HI

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

Hróðmarsson, Helgi Rafn; Wang, Huasheng; Kvaran, Ágúst, E-mail: agust@hi.is

2014-06-28

Mass resolved resonance enhanced multiphoton ionization data for hydrogen iodide (HI), for two-photon resonance excitation to Rydberg and ion-pair states in the 69 600–72 400 cm{sup −1} region were recorded and analyzed. Spectral perturbations due to homogeneous and heterogeneous interactions between Rydberg and ion-pair states, showing as deformations in line-positions, line-intensities, and line-widths, were focused on. Parameters relevant to photodissociation processes, state interaction strengths and spectroscopic parameters for deperturbed states were derived. Overall interaction and dynamical schemes to describe the observations are proposed.

Collective firm bankruptcies and phase transition in rating dynamics

NASA Astrophysics Data System (ADS)

Sieczka, P.; Hołyst, J. A.

2009-10-01

We present a simple model of firm rating evolution. We consider two sources of defaults: individual dynamics of economic development and Potts-like interactions between firms. We show that such a defined model leads to phase transition, which results in collective defaults. The existence of the collective phase depends on the mean interaction strength. For small interaction strength parameters, there are many independent bankruptcies of individual companies. For large parameters, there are giant collective defaults of firm clusters. In the case when the individual firm dynamics favors dumping of rating changes, there is an optimal strength of the firm's interactions from the systemic risk point of view. in here

Sequential Exposure of Bortezomib and Vorinostat is Synergistic in Multiple Myeloma Cells

PubMed Central

Nanavati, Charvi; Mager, Donald E.

2018-01-01

Purpose To examine the combination of bortezomib and vorinostat in multiple myeloma cells (U266) and xenografts, and to assess the nature of their potential interactions with semi-mechanistic pharmacodynamic models and biomarkers. Methods U266 proliferation was examined for a range of bortezomib and vorinostat exposure times and concentrations (alone and in combination). A non-competitive interaction model was used with interaction parameters that reflect the nature of drug interactions after simultaneous and sequential exposures. p21 and cleaved PARP were measured using immunoblotting to assess critical biomarker dynamics. For xenografts, data were extracted from literature and modeled with a PK/PD model with an interaction parameter. Results Estimated model parameters for simultaneous in vitro and xenograft treatments suggested additive drug effects. The sequence of bortezomib preincubation for 24 hours, followed by vorinostat for 24 hours, resulted in an estimated interaction term significantly less than 1, suggesting synergistic effects. p21 and cleaved PARP were also up-regulated the most in this sequence. Conclusions Semi-mechanistic pharmacodynamic modeling suggests synergistic pharmacodynamic interactions for the sequential administration of bortezomib followed by vorinostat. Increased p21 and cleaved PARP expression can potentially explain mechanisms of their enhanced effects, which require further PK/PD systems analysis to suggest an optimal dosing regimen. PMID:28101809

Novel Hybrid Adaptive Controller for Manipulation in Complex Perturbation Environments

PubMed Central

Smith, Alex M. C.; Yang, Chenguang; Ma, Hongbin; Culverhouse, Phil; Cangelosi, Angelo; Burdet, Etienne

2015-01-01

In this paper we present a hybrid control scheme, combining the advantages of task-space and joint-space control. The controller is based on a human-like adaptive design, which minimises both control effort and tracking error. Our novel hybrid adaptive controller has been tested in extensive simulations, in a scenario where a Baxter robot manipulator is affected by external disturbances in the form of interaction with the environment and tool-like end-effector perturbations. The results demonstrated improved performance in the hybrid controller over both of its component parts. In addition, we introduce a novel method for online adaptation of learning parameters, using the fuzzy control formalism to utilise expert knowledge from the experimenter. This mechanism of meta-learning induces further improvement in performance and avoids the need for tuning through trial testing. PMID:26029916

Evaluation of Industry Standard Turbulence Models on an Axisymmetric Supersonic Compression Corner

NASA Technical Reports Server (NTRS)

DeBonis, James R.

2015-01-01

Reynolds-averaged Navier-Stokes computations of a shock-wave/boundary-layer interaction (SWBLI) created by a Mach 2.85 flow over an axisymmetric 30-degree compression corner were carried out. The objectives were to evaluate four turbulence models commonly used in industry, for SWBLIs, and to evaluate the suitability of this test case for use in further turbulence model benchmarking. The Spalart-Allmaras model, Menter's Baseline and Shear Stress Transport models, and a low-Reynolds number k- model were evaluated. Results indicate that the models do not accurately predict the separation location; with the SST model predicting the separation onset too early and the other models predicting the onset too late. Overall the Spalart-Allmaras model did the best job in matching the experimental data. However there is significant room for improvement, most notably in the prediction of the turbulent shear stress. Density data showed that the simulations did not accurately predict the thermal boundary layer upstream of the SWBLI. The effect of turbulent Prandtl number and wall temperature were studied in an attempt to improve this prediction and understand their effects on the interaction. The data showed that both parameters can significantly affect the separation size and location, but did not improve the agreement with the experiment. This case proved challenging to compute and should provide a good test for future turbulence modeling work.

Effectiveness of Wii-based rehabilitation in stroke: A randomized controlled study.

PubMed

Karasu, Ayça Utkan; Batur, Elif Balevi; Karataş, Gülçin Kaymak

2018-05-08

To investigate the efficacy of Nintendo Wii Fit®-based balance rehabilitation as an adjunc-tive therapy to conventional rehabilitation in stroke patients. During the study period, 70 stroke patients were evaluated. Of these, 23 who met the study criteria were randomly assigned to either the experimental group (n = 12) or the control group (n = 11) by block randomization. Primary outcome measures were Berg Balance Scale, Functional Reach Test, Postural Assessment Scale for Stroke Patients, Timed Up and Go Test and Static Balance Index. Secondary outcome measures were postural sway, as assessed with Emed-X, Functional Independence Measure Transfer and Ambulation Scores. An evaluator who was blinded to the groups made assessments immediately before (baseline), immediately after (post-treatment), and 4 weeks after completion of the study (follow-up). Group-time interaction was significant in the Berg Balance Scale, Functional Reach Test, anteroposterior and mediolateral centre of pressure displacement with eyes open, anteroposterior centre of pressure displacement with eyes closed, centre of pressure displacement during weight shifting to affected side, to unaffected side and total centre of pressure displacement during weight shifting. Demonstrating significant group-time interaction in those parameters suggests that, while both groups exhibited significant improvement, the experimental group showed greater improvement than the control group. Virtual reality exercises with the Nintendo Wii system could represent a useful adjunctive therapy to traditional treatment to improve static and dynamic balance in stroke patients.

Beyond conventional dose-response curves: Sensorgram comparison in SPR allows single concentration activity and similarity assessment.

PubMed

Gassner, C; Karlsson, R; Lipsmeier, F; Moelleken, J

2018-05-30

Previously we have introduced two SPR-based assay principles (dual-binding assay and bridging assay), which allow the determination of two out of three possible interaction parameters for bispecific molecules within one assay setup: two individual interactions to both targets, and/or one simultaneous/overall interaction, which potentially reflects the inter-dependency of both individual binding events. However, activity and similarity are determined by comparing report points over a concentration range, which also mirrors the way data is generated by conventional ELISA-based methods So far, binding kinetics have not been specifically considered in generic approaches for activity assessment. Here, we introduce an improved slope-ratio model which, together with a sensorgram comparison based similarity assessment, allows the development of a detailed, USP-conformal ligand binding assay using only a single sample concentration. We compare this novel analysis method to the usual concentration-range approach for both SPR-based assay principles and discuss its impact on data quality and increased sample throughput. Copyright © 2018 Elsevier B.V. All rights reserved.

Chytrid parasitism facilitates trophic transfer between bloom-forming cyanobacteria and zooplankton (Daphnia)

NASA Astrophysics Data System (ADS)

Agha, Ramsy; Saebelfeld, Manja; Manthey, Christin; Rohrlack, Thomas; Wolinska, Justyna

2016-10-01

Parasites are rarely included in food web studies, although they can strongly alter trophic interactions. In aquatic ecosystems, poorly grazed cyanobacteria often dominate phytoplankton communities, leading to the decoupling of primary and secondary production. Here, we addressed the interface between predator-prey and host-parasite interactions by conducting a life-table experiment, in which four Daphnia galeata genotypes were maintained on quantitatively comparable diets consisting of healthy cyanobacteria or cyanobacteria infected by a fungal (chytrid) parasite. In four out of five fitness parameters, at least one Daphnia genotype performed better on parasitised cyanobacteria than in the absence of infection. Further treatments consisting of purified chytrid zoospores and heterotrophic bacteria suspensions established the causes of improved fitness. First, Daphnia feed on chytrid zoospores which trophically upgrade cyanobacterial carbon. Second, an increase in heterotrophic bacterial biomass, promoted by cyanobacterial decay, provides an additional food source for Daphnia. In addition, chytrid infection induces fragmentation of cyanobacterial filaments, which could render cyanobacteria more edible. Our results demonstrate that chytrid parasitism can sustain zooplankton under cyanobacterial bloom conditions, and exemplify the potential of parasites to alter interactions between trophic levels.

An extended hybrid density functional (X3LYP) with improved descriptions of nonbond interactions and thermodynamic properties of molecular systems

NASA Astrophysics Data System (ADS)

Xu, Xin; Zhang, Qingsong; Muller, Richard P.; Goddard, William A.

2005-01-01

We derive here the form for the exact exchange energy density for a density that decays with Gaussian-type behavior at long range. This functional is intermediate between the B88 and the PW91 exchange functionals. Using this modified functional to match the form expected for Gaussian densities, we propose the X3LYP extended functional. We find that X3LYP significantly outperforms Becke three parameter Lee-Yang-Parr (B3LYP) for describing van der Waals and hydrogen bond interactions, while performing slightly better than B3LYP for predicting heats of formation, ionization potentials, electron affinities, proton affinities, and total atomic energies as validated with the extended G2 set of atoms and molecules. Thus X3LYP greatly enlarges the field of applications for density functional theory. In particular the success of X3LYP in describing the water dimer (with Re and De within the error bars of the most accurate determinations) makes it an excellent candidate for predicting accurate ligand-protein and ligand-DNA interactions.

Tunable Coarse Graining for Monte Carlo Simulations of Proteins via Smoothed Energy Tables: Direct and Exchange Simulations

PubMed Central

2015-01-01

Many commonly used coarse-grained models for proteins are based on simplified interaction sites and consequently may suffer from significant limitations, such as the inability to properly model protein secondary structure without the addition of restraints. Recent work on a benzene fluid (LettieriS.; ZuckermanD. M.J. Comput. Chem.2012, 33, 268−27522120971) suggested an alternative strategy of tabulating and smoothing fully atomistic orientation-dependent interactions among rigid molecules or fragments. Here we report our initial efforts to apply this approach to the polar and covalent interactions intrinsic to polypeptides. We divide proteins into nearly rigid fragments, construct distance and orientation-dependent tables of the atomistic interaction energies between those fragments, and apply potential energy smoothing techniques to those tables. The amount of smoothing can be adjusted to give coarse-grained models that range from the underlying atomistic force field all the way to a bead-like coarse-grained model. For a moderate amount of smoothing, the method is able to preserve about 70–90% of the α-helical structure while providing a factor of 3–10 improvement in sampling per unit computation time (depending on how sampling is measured). For a greater amount of smoothing, multiple folding–unfolding transitions of the peptide were observed, along with a factor of 10–100 improvement in sampling per unit computation time, although the time spent in the unfolded state was increased compared with less smoothed simulations. For a β hairpin, secondary structure is also preserved, albeit for a narrower range of the smoothing parameter and, consequently, for a more modest improvement in sampling. We have also applied the new method in a “resolution exchange” setting, in which each replica runs a Monte Carlo simulation with a different degree of smoothing. We obtain exchange rates that compare favorably to our previous efforts at resolution exchange (LymanE.; ZuckermanD. M.J. Chem. Theory Comput.2006, 2, 656−666). PMID:25400525

Tool Support for Parametric Analysis of Large Software Simulation Systems

NASA Technical Reports Server (NTRS)

Schumann, Johann; Gundy-Burlet, Karen; Pasareanu, Corina; Menzies, Tim; Barrett, Tony

2008-01-01

The analysis of large and complex parameterized software systems, e.g., systems simulation in aerospace, is very complicated and time-consuming due to the large parameter space, and the complex, highly coupled nonlinear nature of the different system components. Thus, such systems are generally validated only in regions local to anticipated operating points rather than through characterization of the entire feasible operational envelope of the system. We have addressed the factors deterring such an analysis with a tool to support envelope assessment: we utilize a combination of advanced Monte Carlo generation with n-factor combinatorial parameter variations to limit the number of cases, but still explore important interactions in the parameter space in a systematic fashion. Additional test-cases, automatically generated from models (e.g., UML, Simulink, Stateflow) improve the coverage. The distributed test runs of the software system produce vast amounts of data, making manual analysis impossible. Our tool automatically analyzes the generated data through a combination of unsupervised Bayesian clustering techniques (AutoBayes) and supervised learning of critical parameter ranges using the treatment learner TAR3. The tool has been developed around the Trick simulation environment, which is widely used within NASA. We will present this tool with a GN&C (Guidance, Navigation and Control) simulation of a small satellite system.

Self-tuning regulator for an interacting CSTR process

NASA Astrophysics Data System (ADS)

Rajendra Mungale, Niraj; Upadhyay, Akshay; Jaganatha Pandian, B.

2017-11-01

In the paper we have laid emphasis on STR that is Self Tuning Regulator and its application for an interacting process. CSTR has a great importance in Chemical Process when we deal with controlling different parameters of a process using CSTR. Basically CSTR is used to maintain a constant liquid temperature in the process. The proposed method called self-tuning regulator, is a different scheme where process parameters are updated and the controller parameters are obtained from the solution of a design problem. The paper deals with STR and methods associated with it.

Transitions induced by speed in self-propelled particles system with attractive interactions

NASA Astrophysics Data System (ADS)

Cambui, Dorilson. S.; Rosas, Alexandre

2018-05-01

In this work, we consider a system of self-propelled particles with attractive interactions in two dimensions. The model presents an order-disorder transition with the speed playing the role of the control parameter. In order to characterize the transition, we investigate the behavior of the order parameter and the Binder cumulant as a function of the speed. Our main finding is that the transition can be either continuous or discontinuous depending on two parameter of the model: the strength of the noise and the radius of attraction.

Evaluation of drug-carrier interactions in quaternary powder mixtures containing perindopril tert-butylamine and indapamide.

PubMed

Voelkel, Adam; Milczewska, Kasylda; Teżyk, Michał; Milanowski, Bartłomiej; Lulek, Janina

2016-04-30

Interactions occurring between components in the quaternary powder mixtures consisting of perindopril tert-butylamine, indapamide (active pharmaceutical ingredients), carrier substance and hydrophobic colloidal silica were examined. Two grades of lactose monohydrate: Spherolac(®) 100 and Granulac(®) 200 and two types of microcrystalline cellulose: M101D+ and Vivapur(®) 102 were used as carriers. We determined the size distribution (laser diffraction method), morphology (scanning electron microscopy) and a specific surface area of the powder particles (by nitrogen adsorption-desorption). For the determination of the surface energy of powder mixtures the method of inverse gas chromatography was applied. Investigated mixtures were characterized by surface parameters (dispersive component of surface energy, specific interactions parameters, specific surface area), work of adhesion and cohesion as well as Flory-Huggins parameter χ23('). Results obtained for all quaternary powder mixtures indicate existence of interactions between components. The strongest interactions occur for both blends with different types of microcrystalline cellulose (PM-1 and PM-4) while much weaker ones for powder mixtures with various types of lactose (PM-2 and PM-3). Published by Elsevier B.V.

A new approach to modeling aerosol effects on East Asian climate: Parametric uncertainties associated with emissions, cloud microphysics, and their interactions: AEROSOL EFFECTS ON EAST ASIAN CLIMATE

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

Yan, Huiping; Qian, Yun; Zhao, Chun

2015-09-09

In this study, we adopt a parametric sensitivity analysis framework that integrates the quasi-Monte Carlo parameter sampling approach and a surrogate model to examine aerosol effects on the East Asian Monsoon climate simulated in the Community Atmosphere Model (CAM5). A total number of 256 CAM5 simulations are conducted to quantify the model responses to the uncertain parameters associated with cloud microphysics parameterizations and aerosol (e.g., sulfate, black carbon (BC), and dust) emission factors and their interactions. Results show that the interaction terms among parameters are important for quantifying the sensitivity of fields of interest, especially precipitation, to the parameters. Themore » relative importance of cloud-microphysics parameters and emission factors (strength) depends on evaluation metrics or the model fields we focused on, and the presence of uncertainty in cloud microphysics imposes an additional challenge in quantifying the impact of aerosols on cloud and climate. Due to their different optical and microphysical properties and spatial distributions, sulfate, BC, and dust aerosols have very different impacts on East Asian Monsoon through aerosol-cloud-radiation interactions. The climatic effects of aerosol do not always have a monotonic response to the change of emission factors. The spatial patterns of both sign and magnitude of aerosol-induced changes in radiative fluxes, cloud, and precipitation could be different, depending on the aerosol types, when parameters are sampled in different ranges of values. We also identify the different cloud microphysical parameters that show the most significant impact on climatic effect induced by sulfate, BC and dust, respectively, in East Asia.« less

Using Heat Pulses for Quantifying 3d Seepage Velocity in Groundwater-Surface Water Interactions, Considering Source Size, Regime, and Dispersion

NASA Astrophysics Data System (ADS)

Zlotnik, V. A.; Tartakovsky, D. M.

2017-12-01

The study is motivated by rapid proliferation of field methods for measurements of seepage velocity using heat tracing and is directed to broadening their potential for studies of groundwater-surface water interactions, and hyporheic zone in particular. In vast majority, existing methods assume vertical or horizontal, uniform, 1D seepage velocity. Often, 1D transport assumed as well, and analytical models of heat transport by Suzuki-Stallman are heavily used to infer seepage velocity. However, both of these assumptions (1D flow and 1D transport) are violated due to the flow geometry, media heterogeneity, and localized heat sources. Attempts to apply more realistic conceptual models still lack full 3D view, and known 2D examples are treated numerically, or by making additional simplifying assumptions about velocity orientation. Heat pulse instruments and sensors already offer an opportunity to collect data sufficient for 3D seepage velocity identification at appropriate scale, but interpretation tools for groundwater-surface water interactions in 3D have not been developed yet. We propose an approach that can substantially improve capabilities of already existing field instruments without additional measurements. Proposed closed-form analytical solutions are simple and well suited for using in inverse modeling. Field applications and ramifications for applications, including data analysis are discussed. The approach simplifies data collection, determines 3D seepage velocity, and facilitates interpretation of relations between heat transport parameters, fluid flow, and media properties. Results are obtained using tensor properties of transport parameters, Green's functions, and rotational coordinate transformations using the Euler angles

DigitalHuman (DH): An Integrative Mathematical Model ofHuman Physiology

NASA Technical Reports Server (NTRS)

Hester, Robert L.; Summers, Richard L.; lIescu, Radu; Esters, Joyee; Coleman, Thomas G.

2010-01-01

Mathematical models and simulation are important tools in discovering the key causal relationships governing physiological processes and improving medical intervention when physiological complexity is a central issue. We have developed a model of integrative human physiology called DigitalHuman (DH) consisting of -5000 variables modeling human physiology describing cardiovascular, renal, respiratory, endocrine, neural and metabolic physiology. Users can view time-dependent solutions and interactively introduce perturbations by altering numerical parameters to investigate new hypotheses. The variables, parameters and quantitative relationships as well as all other model details are described in XML text files. All aspects of the model, including the mathematical equations describing the physiological processes are written in XML open source, text-readable files. Model structure is based upon empirical data of physiological responses documented within the peer-reviewed literature. The model can be used to understand proposed physiological mechanisms and physiological interactions that may not be otherwise intUitively evident. Some of the current uses of this model include the analyses of renal control of blood pressure, the central role of the liver in creating and maintaining insulin resistance, and the mechanisms causing orthostatic hypotension in astronauts. Additionally the open source aspect of the modeling environment allows any investigator to add detailed descriptions of human physiology to test new concepts. The model accurately predicts both qualitative and more importantly quantitative changes in clinically and experimentally observed responses. DigitalHuman provides scientists a modeling environment to understand the complex interactions of integrative physiology. This research was supported by.NIH HL 51971, NSF EPSCoR, and NASA

Comparative Clinical Pharmacokinetics of Midodrine and Its Active Metabolite Desglymidodrine in Cirrhotic Patients with Tense Ascites Versus Healthy Volunteers.

PubMed

Ali, Ahmed; Farid, Samar; Amin, Mona; Kassem, Mohamed; Al-Garem, Nouman; Al-Ghobashy, Medhat

2016-02-01

Midodrine is an α-agonist prodrug of desglymidodrine used for the management of hypotension, and can also be used for hepatorenal syndrome and cirrhotic patients with tense ascites. The objective of the present work was to study the clinical pharmacokinetic parameters of midodrine and its active metabolite desglymidodrine in cirrhotic patients with tense ascites, which may help in dose selection and improve treatment outcome. This was a prospective, open-label, single-dose, parallel-group study. At first, a pilot study was performed on one healthy volunteer by taking serial blood samples at scheduled time intervals to validate the method of analysis and sampling times. The full study was then conducted by selecting 12 cirrhotic patients with tense ascites in one group and taking nine blood samples. We also selected five healthy volunteers as the control group and took 11 blood samples. Statistically significant differences were observed between the healthy volunteer group and the patients group in the area under the concentration versus time curve (AUC0-t) and maximum plasma concentration (Cmax) values of midodrine and desglymidodrine. Based on the results of the pharmacokinetic analysis, the patient group was further subdivided into those receiving the interacting drug ranitidine (five patients) and those not receiving the interacting drug (seven patients). Pharmacokinetic parameters of midodrine can differ significantly in cirrhotic patients with tense ascites from those in healthy individuals. Drug monitoring, dose adjustments, and drug-drug interactions should all be considered during therapy in this vulnerable patient group.

Does an electronic continuum correction improve effective short-range ion-ion interactions in aqueous solution?

NASA Astrophysics Data System (ADS)

Bruce, Ellen E.; van der Vegt, Nico F. A.

2018-06-01

Non-polarizable force fields for hydrated ions not always accurately describe short-range ion-ion interactions, frequently leading to artificial ion clustering in bulk aqueous solutions. This can be avoided by adjusting the nonbonded anion-cation or cation-water Lennard-Jones parameters. This approach has been successfully applied to different systems, but the parameterization is demanding owing to the necessity of separate investigations of each ion pair. Alternatively, polarization effects may effectively be accounted for using the electronic continuum correction (ECC) of Leontyev et al. [J. Chem. Phys. 119, 8024 (2003)], which involves scaling the ionic charges with the inverse square-root of the water high-frequency dielectric permittivity. ECC has proven to perform well for monovalent salts as well as for divalent salts in water. Its performance, however, for multivalent salts with higher valency remains unexplored. The present work illustrates the applicability of the ECC model to trivalent K3PO4 and divalent K2HPO4 in water. We demonstrate that the ECC models, without additional tuning of force field parameters, provide an accurate description of water-mediated interactions between salt ions. This results in predictions of the osmotic coefficients of aqueous K3PO4 and K2HPO4 solutions in good agreement with experimental data. Analysis of ion pairing thermodynamics in terms of contact ion pair (CIP), solvent-separated ion pair, and double solvent-separated ion pair contributions shows that potassium-phosphate CIP formation is stronger with trivalent than with divalent phosphate ions.

Determination of the Nucleon-Nucleon Interaction in the ImQMD Model by Nuclear Reactions at Fermi Energy

NASA Astrophysics Data System (ADS)

Li, Cheng; Tian, Jun-Long; Wang, Ning

2013-11-01

The nucleon-nucleon interaction is investigated by using the ImQMD model with the three sets of parameters IQ1, IQ2 and IQ3 in which the corresponding incompressibility coefficients of nuclear matter are different. Fusion excitation function and the charge distribution of fragments are calculated for reaction systems 40Ca+40Ca at different incident energies. It is found that obvious differences in the charge distribution were observed at the energy region 10-25A MeV by adopting the three sets of parameters, while the results were close to each other at energy region of 30-45A MeV for the reaction system. It indicates that the Fermi energy region is a sensitive energy region to explore the N-N interaction. The fragment multiplicity spectrum for 238U+197Au at 15A MeV are reproduced by the ImQMD model with the set of parameter IQ3. It is concluded that charge distribution of the fragments and the fragment multiplicity spectrum are good observables for studying N-N interaction, and IQ3 is a suitable set of parameters for the ImQMD model.

Optimization of bump and blowing to control the flow through a transonic compressor blade cascade

NASA Astrophysics Data System (ADS)

Mazaheri, K.; Khatibirad, S.

2018-03-01

Shock control bump (SCB) and blowing are two flow control methods, used here to improve the aerodynamic performance of transonic compressors. Both methods are applied to a NASA rotor 67 blade section and are optimized to minimize the total pressure loss. A continuous adjoint algorithm is used for multi-point optimization of a SCB to improve the aerodynamic performance of the rotor blade section, for a range of operational conditions around its design point. A multi-point and two single-point optimizations are performed in the design and off-design conditions. It is shown that the single-point optimized shapes have the best performance for their respective operating conditions, but the multi-point one has an overall better performance over the whole operating range. An analysis is given regarding how similarly both single- and multi-point optimized SCBs change the wave structure between blade sections resulting in a more favorable flow pattern. Interactions of the SCB with the boundary layer and the wave structure, and its effects on the separation regions are also studied. We have also introduced the concept of blowing for control of shock wave and boundary-layer interaction. A geometrical model is introduced, and the geometrical and physical parameters of blowing are optimized at the design point. The performance improvements of blowing are compared with the SCB. The physical interactions of SCB with the boundary layer and the shock wave are analyzed. The effects of SCB on the wave structure in the flow domain outside the boundary-layer region are investigated. It is shown that the effects of the blowing mechanism are very similar to the SCB.

Four papers on transportation and the environment

NASA Astrophysics Data System (ADS)

Roth, Kevin Daniel

The main essay of this thesis, found in the first chapter, examines how two policies that are a priori equivalent, fuel economy standards and feebates, interact differently with complementary policies that also attempt to improve fuel economy. To examine these interactions I build a general equilibrium model of the automobile market that allows manufacturers to trade off horsepower, weight, and fuel economy of vehicles along a production possibility frontier (PPF). I also estimate household demand for vehicles and miles for a simulation model that includes the used car and scrappage markets. This model allows me to simulate the interaction of a research and development policy that increases the PPF of domestic firms, or a tax credit that increases demand for efficient vehicles, with either a CAFE standard or feebate. I find that vehicle emissions increase under all these interactions but the effects are muted under the feebate because it allows fuel economy to improve by 0.60% to 1.88%, while CAFE, by targeting an average fuel economy, will always offset these uncoordinated complementary policies. The second essay examines transportation systems with unpriced congestion where single-occupant low-emission vehicles are allowed into high occupancy vehicle (HOV) lanes to encourage their adoption exacerbates congestion costs for carpoolers. The resulting welfare effects of the policy are negative, with environmental benefits overwhelmingly dominated by the increased congestion costs. Exploiting the introduction of the Clean Air Vehicle Stickers policy in California with a regression discontinuity design, our results imply a best-case cost of 124 per ton of reductions in greenhouse gases, 606,000 dollars per ton of nitrogen oxides reduction, and $505,000 dollars per ton of hydrocarbon reduction, exceeding those of other options readily available to policymakers. The third essay examines the 'Energy Paradox.' From previous literature, it can be found that consumers tend to undervalue discounted future energy costs in their purchase decisions for energy-using durables. We show that this finding could, in part, result from ignoring consumer heterogeneity in empirical analyses as opposed to true undervaluation. The fourth essay examines used vehicle scrappage rates. We find that not only are vehicles lasting longer but that scrap rates are less responsive to changes in vehicle price than previously estimated. These parameters help to refine the parameters used to evaluate public policies like CAFE standards and gasoline taxes that are known to have important effects on used vehicles.

Modeling of the phase equilibria of polystyrene in methylcyclohexane with semi-empirical quantum mechanical methods I.

PubMed

Wilczura-Wachnik, Hanna; Jónsdóttir, Svava Osk

2003-04-01

A method for calculating interaction parameters traditionally used in phase-equilibrium computations in low-molecular systems has been extended for the prediction of solvent activities of aromatic polymer solutions (polystyrene+methylcyclohexane). Using ethylbenzene as a model compound for the repeating unit of the polymer, the intermolecular interaction energies between the solvent molecule and the polymer were simulated. The semiempirical quantum chemical method AM1, and a method for sampling relevant internal orientations for a pair of molecules developed previously were used. Interaction energies are determined for three molecular pairs, the solvent and the model molecule, two solvent molecules and two model molecules, and used to calculated UNIQUAC interaction parameters, a(ij) and a(ji). Using these parameters, the solvent activities of the polystyrene 90,000 amu+methylcyclohexane system, and the total vapor pressures of the methylcyclohexane+ethylbenzene system were calculated. The latter system was compared to experimental data, giving qualitative agreement. Figure Solvent activities for the methylcylcohexane(1)+polystyrene(2) system at 316 K. Parameters aij (blue line) obtained with the AM1 method; parameters aij (pink line) from VLE data for the ethylbenzene+methylcyclohexane system. The abscissa is the polymer weight fraction defined as y2(x1)=(1mx1)M2/[x1M1+(1mx1)M2], where x1 is the solvent mole fraction and Mi are the molecular weights of the components.

Computer-aided method for the determination of Hansen solubility parameters. Application to the miscibility of refrigerating lubricant and new refrigerant

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

Remigy, J.C.; Nakache, E.; Brechot, P.D.

This article presents a method which allows one to find the Hansen solubility parameters by means of data processing. In the first part, the authors present the thermodynamical principle of Hansen parameters, and then they explain the model used to find parameters from experimental data. They validate the method by studying the solubility parameters of CFC-12 (dichlorodifluoromethane), HFC-134a (1,1,1,2-tetrafluoroethane), neopentylglycol esters, trimethylolpropane esters, dipentaerythritol esters, and pentaerythritol esters. Then, the variation of Hansen parameters are studied as well as the relation between the miscibility temperature (the temperature at which a blend passes from the miscible state to the immiscible state)more » and the interaction distance. The authors establish the critical interaction distance of HFC-134a which determines the solubility limit and they study its variation with temperature.« less

Toward improved simulation of river operations through integration with a hydrologic model

USGS Publications Warehouse

Morway, Eric D.; Niswonger, Richard G.; Triana, Enrique

2016-01-01

Advanced modeling tools are needed for informed water resources planning and management. Two classes of modeling tools are often used to this end–(1) distributed-parameter hydrologic models for quantifying supply and (2) river-operation models for sorting out demands under rule-based systems such as the prior-appropriation doctrine. Within each of these two broad classes of models, there are many software tools that excel at simulating the processes specific to each discipline, but have historically over-simplified, or at worse completely neglected, aspects of the other. As a result, water managers reliant on river-operation models for administering water resources need improved tools for representing spatially and temporally varying groundwater resources in conjunctive-use systems. A new tool is described that improves the representation of groundwater/surface-water (GW-SW) interaction within a river-operations modeling context and, in so doing, advances evaluation of system-wide hydrologic consequences of new or altered management regimes.

Local and nonlocal order parameters in the Kitaev chain

NASA Astrophysics Data System (ADS)

Chitov, Gennady Y.

2018-02-01

We have calculated order parameters for the phases of the Kitaev chain with interaction and dimerization at a special symmetric point applying the Jordan-Wigner and other duality transformations. We use string order parameters (SOPs) defined via the correlation functions of the Majorana string operators. The SOPs are mapped onto the local order parameters of some dual Hamiltonians and easily calculated. We have shown that the phase diagram of the interacting dimerized chain comprises the phases with the conventional local order as well as the phases with nonlocal SOPs. From the results for the critical indices, we infer the two-dimensional Ising universality class of criticality at the particular symmetry point where the model is exactly solvable.

The geometric field (gravity) as an electro-chemical potential in a Ginzburg-Landau theory of superconductivity

NASA Astrophysics Data System (ADS)

Atanasov, Victor

2017-07-01

We extend the superconductor's free energy to include an interaction of the order parameter with the curvature of space-time. This interaction leads to geometry dependent coherence length and Ginzburg-Landau parameter which suggests that the curvature of space-time can change the superconductor's type. The curvature of space-time doesn't affect the ideal diamagnetism of the superconductor but acts as chemical potential. In a particular circumstance, the geometric field becomes order-parameter dependent, therefore the superconductor's order parameter dynamics affects the curvature of space-time and electrical or internal quantum mechanical energy can be channelled into the curvature of space-time. Experimental consequences are discussed.

Competing interactions in ferromagnetic/antiferromagnetic perovskite superlattices

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

Takamura, Y.; Biegalski, M.B.; Christen, H.M.

2009-10-22

Soft x-ray magnetic dichroism, magnetization, and magnetotransport measurements demonstrate that the competition between different magnetic interactions (exchange coupling, electronic reconstruction, and long-range interactions) in La{sub 0.7}Sr{sub 0.3}FeO{sub 3}(LSFO)/La{sub 0.7}Sr{sub 0.3}MnO{sub 3}(LSMO) perovskite oxide superlattices leads to unexpected functional properties. The antiferromagnetic order parameter in LSFO and ferromagnetic order parameter in LSMO show a dissimilar dependence on sublayer thickness and temperature, illustrating the high degree of tunability in these artificially layered materials.

Superconductivity in the Penson-Kolb Model on a Triangular Lattice

NASA Astrophysics Data System (ADS)

Ptok, A.; Mierzejewski, M.

2008-07-01

We investigate properties of the two-dimensional Penson-Kolb model with repulsive pair hopping interaction. In the case of a bipartite square lattice this interaction may lead to the η-type pairing, when the phase of superconducting order parameter changes from one lattice site to the neighboring one. We show that this interaction may be responsible for the onset of superconductivity also for a triangular lattice. We discuss the spatial dependence of the superconducting order parameter and demonstrate that the total momentum of the paired electrons is determined by the lattice geometry.

Early Recovery of Aphasia through Thrombolysis: The Significance of Spontaneous Speech.

PubMed

Furlanis, Giovanni; Ridolfi, Mariana; Polverino, Paola; Menichelli, Alina; Caruso, Paola; Naccarato, Marcello; Sartori, Arianna; Torelli, Lucio; Pesavento, Valentina; Manganotti, Paolo

2018-07-01

Aphasia is one of the most devastating stroke-related consequences for social interaction and daily activities. Aphasia recovery in acute stroke depends on the degree of reperfusion after thrombolysis or thrombectomy. As aphasia assessment tests are often time-consuming for patients with acute stroke, physicians have been developing rapid and simple tests. The aim of our study is to evaluate the improvement of language functions in the earliest stage in patients treated with thrombolysis and in nontreated patients using our rapid screening test. Our study is a single-center prospective observational study conducted at the Stroke Unit of the University Medical Hospital of Trieste (January-December 2016). Patients treated with thrombolysis and nontreated patients underwent 3 aphasia assessments through our rapid screening test (at baseline, 24 hours, and 72 hours). The screening test assesses spontaneous speech, oral comprehension of words, reading aloud and comprehension of written words, oral comprehension of sentences, naming, repetition of words and a sentence, and writing words. The study included 40 patients: 18 patients treated with thrombolysis and 22 nontreated patients. Both groups improved over time. Among all language parameters, spontaneous speech was statistically significant between 24 and 72 hours (P value = .012), and between baseline and 72 hours (P value = .017). Our study demonstrates that patients treated with thrombolysis experience greater improvement in language than the nontreated patients. The difference between the 2 groups is increasingly evident over time. Moreover, spontaneous speech is the parameter marked by the greatest improvement. Copyright © 2018 National Stroke Association. Published by Elsevier Inc. All rights reserved.

Hexagonal boron nitride and water interaction parameters

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

Wu, Yanbin; Aluru, Narayana R., E-mail: aluru@illinois.edu; Wagner, Lucas K.

2016-04-28

The study of hexagonal boron nitride (hBN) in microfluidic and nanofluidic applications at the atomic level requires accurate force field parameters to describe the water-hBN interaction. In this work, we begin with benchmark quality first principles quantum Monte Carlo calculations on the interaction energy between water and hBN, which are used to validate random phase approximation (RPA) calculations. We then proceed with RPA to derive force field parameters, which are used to simulate water contact angle on bulk hBN, attaining a value within the experimental uncertainties. This paper demonstrates that end-to-end multiscale modeling, starting at detailed many-body quantum mechanics andmore » ending with macroscopic properties, with the approximations controlled along the way, is feasible for these systems.« less

Random Blume-Emery-Griffiths model on the Bethe lattice

NASA Astrophysics Data System (ADS)

Albayrak, Erhan

2015-12-01

The random phase transitions of the Blume-Emery-Griffiths (BEG) model for the spin-1 system are investigated on the Bethe lattice and the phase diagrams of the model are obtained. The biquadratic exchange interaction (K) is turned on, i.e. the BEG model, with probability p either attractively (K > 0) or repulsively (K < 0) and turned off, which leads to the BC model, with the probability (1 - p) throughout the Bethe lattice. By taking the bilinear exchange interaction parameter J as a scaling parameter, the effects of the competitions between the reduced crystal fields (D / J), reduced biquadratic exchange interaction parameter (K / J) and the reduced temperature (kT / J) for given values of the probability when the coordination number is q=4, i.e. on a square lattice, are studied in detail.

General two-species interacting Lotka-Volterra system: Population dynamics and wave propagation

NASA Astrophysics Data System (ADS)

Zhu, Haoqi; Wang, Mao-Xiang; Lai, Pik-Yin

2018-05-01

The population dynamics of two interacting species modeled by the Lotka-Volterra (LV) model with general parameters that can promote or suppress the other species is studied. It is found that the properties of the two species' isoclines determine the interaction of species, leading to six regimes in the phase diagram of interspecies interaction; i.e., there are six different interspecific relationships described by the LV model. Four regimes allow for nontrivial species coexistence, among which it is found that three of them are stable, namely, weak competition, mutualism, and predator-prey scenarios can lead to win-win coexistence situations. The Lyapunov function for general nontrivial two-species coexistence is also constructed. Furthermore, in the presence of spatial diffusion of the species, the dynamics can lead to steady wavefront propagation and can alter the population map. Propagating wavefront solutions in one dimension are investigated analytically and by numerical solutions. The steady wavefront speeds are obtained analytically via nonlinear dynamics analysis and verified by numerical solutions. In addition to the inter- and intraspecific interaction parameters, the intrinsic speed parameters of each species play a decisive role in species populations and wave properties. In some regimes, both species can copropagate with the same wave speeds in a finite range of parameters. Our results are further discussed in the light of possible biological relevance and ecological implications.

Piloted studies of Enhanced or Synthetic Vision display parameters

NASA Technical Reports Server (NTRS)

Harris, Randall L., Sr.; Parrish, Russell V.

1992-01-01

This paper summarizes the results of several studies conducted at Langley Research Center over the past few years. The purposes of these studies were to investigate parameters of pictorial displays and imaging sensors that affect pilot approach and landing performance. Pictorial displays have demonstrated exceptional tracking performance and improved the pilots' spatial awareness. Stereopsis cueing improved pilot flight performance and reduced pilot stress. Sensor image parameters such as increased field-of-view. faster image update rate, and aiding symbology improved flare initiation. Finer image resolution and magnification improved attitude control performance parameters.

ROCS: a Reproducibility Index and Confidence Score for Interaction Proteomics Studies

PubMed Central

2012-01-01

Background Affinity-Purification Mass-Spectrometry (AP-MS) provides a powerful means of identifying protein complexes and interactions. Several important challenges exist in interpreting the results of AP-MS experiments. First, the reproducibility of AP-MS experimental replicates can be low, due both to technical variability and the dynamic nature of protein interactions in the cell. Second, the identification of true protein-protein interactions in AP-MS experiments is subject to inaccuracy due to high false negative and false positive rates. Several experimental approaches can be used to mitigate these drawbacks, including the use of replicated and control experiments and relative quantification to sensitively distinguish true interacting proteins from false ones. Methods To address the issues of reproducibility and accuracy of protein-protein interactions, we introduce a two-step method, called ROCS, which makes use of Indicator Prey Proteins to select reproducible AP-MS experiments, and of Confidence Scores to select specific protein-protein interactions. The Indicator Prey Proteins account for measures of protein identifiability as well as protein reproducibility, effectively allowing removal of outlier experiments that contribute noise and affect downstream inferences. The filtered set of experiments is then used in the Protein-Protein Interaction (PPI) scoring step. Prey protein scoring is done by computing a Confidence Score, which accounts for the probability of occurrence of prey proteins in the bait experiments relative to the control experiment, where the significance cutoff parameter is estimated by simultaneously controlling false positives and false negatives against metrics of false discovery rate and biological coherence respectively. In summary, the ROCS method relies on automatic objective criterions for parameter estimation and error-controlled procedures. Results We illustrate the performance of our method by applying it to five previously published AP-MS experiments, each containing well characterized protein interactions, allowing for systematic benchmarking of ROCS. We show that our method may be used on its own to make accurate identification of specific, biologically relevant protein-protein interactions, or in combination with other AP-MS scoring methods to significantly improve inferences. Conclusions Our method addresses important issues encountered in AP-MS datasets, making ROCS a very promising tool for this purpose, either on its own or in conjunction with other methods. We anticipate that our methodology may be used more generally in proteomics studies and databases, where experimental reproducibility issues arise. The method is implemented in the R language, and is available as an R package called “ROCS”, freely available from the CRAN repository http://cran.r-project.org/. PMID:22682516