Spiral diffusion of rotating self-propellers with stochastic perturbation

NASA Astrophysics Data System (ADS)

Nourhani, Amir; Ebbens, Stephen J.; Gibbs, John G.; Lammert, Paul E.

2016-09-01

Translationally diffusive behavior arising from the combination of orientational diffusion and powered motion at microscopic scales is a known phenomenon, but the peculiarities of the evolution of expected position conditioned on initial position and orientation have been neglected. A theory is given of the spiral motion of the mean trajectory depending upon propulsion speed, angular velocity, orientational diffusion, and rate of random chirality reversal. We demonstrate the experimental accessibility of this effect using both tadpole-like and Janus sphere dimer rotating motors. Sensitivity of the mean trajectory to the kinematic parameters suggest that it may be a useful way to determine those parameters.

Dependence of short and intermediate-range order on preparation in experimental and modeled pure a-Si

DOE PAGES

Holmstrom, Eero; Haberl, Bianca; Pakarinen, Olli H.; ...

2016-02-20

Variability in the short-to-intermediate range order of pure amorphous silicon prepared by different experimental and computational techniques is probed by measuring mass density, atomic coordination, bond-angle deviation, and dihedral angle deviation. It is found that there is significant variability in order parameters at these length scales in this archetypal covalently bonded, monoatomic system. This diversity strongly reflects preparation technique and thermal history in both experimental and simulated systems. Experiment and simulation do not fully quantitatively agree, partly due to differences in the way parameters are accessed. However, qualitative agreement in the trends is identified. Relaxed forms of amorphous silicon closelymore » resemble continuous random networks generated by a hybrid method of bond-switching Monte Carlo and molecular dynamics simulation. As-prepared ion implanted amorphous silicon can be adequately modeled using a structure generated from amorphization via ion bombardement using energetic recoils. Preparation methods which narrowly avoid crystallization such as experimental pressure-induced amorphization or simulated melt-quenching result in inhomogeneous structures that contain regions with significant variations in atomic ordering. Ad hoc simulated structures containing small (1 nm) diamond cubic crystal inclusions were found to possess relatively high bond-angle deviations and low dihedral angle deviations, a trend that could not be reconciled with any experimental material.« less

PRince: a web server for structural and physicochemical analysis of protein-RNA interface.

PubMed

Barik, Amita; Mishra, Abhishek; Bahadur, Ranjit Prasad

2012-07-01

We have developed a web server, PRince, which analyzes the structural features and physicochemical properties of the protein-RNA interface. Users need to submit a PDB file containing the atomic coordinates of both the protein and the RNA molecules in complex form (in '.pdb' format). They should also mention the chain identifiers of interacting protein and RNA molecules. The size of the protein-RNA interface is estimated by measuring the solvent accessible surface area buried in contact. For a given protein-RNA complex, PRince calculates structural, physicochemical and hydration properties of the interacting surfaces. All these parameters generated by the server are presented in a tabular format. The interacting surfaces can also be visualized with software plug-in like Jmol. In addition, the output files containing the list of the atomic coordinates of the interacting protein, RNA and interface water molecules can be downloaded. The parameters generated by PRince are novel, and users can correlate them with the experimentally determined biophysical and biochemical parameters for better understanding the specificity of the protein-RNA recognition process. This server will be continuously upgraded to include more parameters. PRince is publicly accessible and free for use. Available at http://www.facweb.iitkgp.ernet.in/~rbahadur/prince/home.html.

Long-distance measurement-device-independent multiparty quantum communication.

PubMed

Fu, Yao; Yin, Hua-Lei; Chen, Teng-Yun; Chen, Zeng-Bing

2015-03-06

The Greenberger-Horne-Zeilinger (GHZ) entanglement, originally introduced to uncover the extreme violation of local realism against quantum mechanics, is an important resource for multiparty quantum communication tasks. But the low intensity and fragility of the GHZ entanglement source in current conditions have made the practical applications of these multiparty tasks an experimental challenge. Here we propose a feasible scheme for practically distributing the postselected GHZ entanglement over a distance of more than 100 km for experimentally accessible parameter regimes. Combining the decoy-state and measurement-device-independent protocols for quantum key distribution, we anticipate that our proposal suggests an important avenue for practical multiparty quantum communication.

Remanent Magnetization: Signature of Many-Body Localization in Quantum Antiferromagnets

NASA Astrophysics Data System (ADS)

Ros, V.; Müller, M.

2017-06-01

We study the remanent magnetization in antiferromagnetic, many-body localized quantum spin chains, initialized in a fully magnetized state. Its long time limit is an order parameter for the localization transition, which is readily accessible by standard experimental probes in magnets. We analytically calculate its value in the strong-disorder regime exploiting the explicit construction of quasilocal conserved quantities of the localized phase. We discuss analogies in cold atomic systems.

Cognitive Radio Networks for Tactical Wireless Communications

DTIC Science & Technology

2014-12-01

exists. Instead, security is an evolving process, as we have seen in the context of WLANs and 2G / 3G networks. New system vulnerabilities continue to...in the network configuration and radio parameters take place due to mobility of platforms, and variation in other users of the RF environment. CRNs...dynamic spectrum access experimentally, and it represents the largest military Mobile Ad hoc Network (MANET) as of today. The WNaN demonstrator has been

Identification of adsorption sites in Cu-BTC by experimentation and molecular simulation.

PubMed

García-Pérez, Elena; Gascón, Jorge; Morales-Flórez, Víctor; Castillo, Juan Manuel; Kapteijn, Freek; Calero, Sofía

2009-02-03

The adsorption of several quadrupolar and nonpolar gases on the Metal Organic Framework Cu-BTC has been studied by combining experimental measurements and Monte Carlo simulations. Four main adsorption sites for this structure have been identified: site I close to the copper atoms, site I' in the bigger cavities, site II located in the small octahedral cages, and site III at the windows of the four open faces of the octahedral cage. Our simulations identify the octahedral cages (sites II and III) and the big cages (site I') as the preferred positions for adsorption, while site I, near the copper atoms, remains empty over the entire range of pressures analyzed due to its reduced accessibility. The occupation of the different sites for ethane and propane in Cu-BTC proceeds similarly as for methane, and shows small differences for O2 and N2 that can be attributed to the quadrupole moment of these molecules. Site II is filled predominantly for methane (the nonpolar molecule), whereas for N2, the occupation of II and I' can be considered almost equivalent. The molecular sitting for O2 shows an intermediate behavior between those observed for methane and for N2. The differences between simulated and experimental data at elevated temperatures for propane are tentatively attributed to a reversible change in the lattice parameters of Cu-BTC by dehydration and by temperature, blocking the accessibility to site III and reducing that to site I'. Adsorption parameters of the investigated molecules have been determined from the simulations.

NMRbot: Python scripts enable high-throughput data collection on current Bruker BioSpin NMR spectrometers.

PubMed

Clos, Lawrence J; Jofre, M Fransisca; Ellinger, James J; Westler, William M; Markley, John L

2013-06-01

To facilitate the high-throughput acquisition of nuclear magnetic resonance (NMR) experimental data on large sets of samples, we have developed a simple and straightforward automated methodology that capitalizes on recent advances in Bruker BioSpin NMR spectrometer hardware and software. Given the daunting challenge for non-NMR experts to collect quality spectra, our goal was to increase user accessibility, provide customized functionality, and improve the consistency and reliability of resultant data. This methodology, NMRbot, is encoded in a set of scripts written in the Python programming language accessible within the Bruker BioSpin TopSpin ™ software. NMRbot improves automated data acquisition and offers novel tools for use in optimizing experimental parameters on the fly. This automated procedure has been successfully implemented for investigations in metabolomics, small-molecule library profiling, and protein-ligand titrations on four Bruker BioSpin NMR spectrometers at the National Magnetic Resonance Facility at Madison. The investigators reported benefits from ease of setup, improved spectral quality, convenient customizations, and overall time savings.

Homeostatic enhancement of active mechanotransduction

NASA Astrophysics Data System (ADS)

Milewski, Andrew; O'Maoiléidigh, Dáibhid; Hudspeth, A. J.

2018-05-01

Our sense of hearing boasts exquisite sensitivity to periodic signals. Experiments and modeling imply, however, that the auditory system achieves this performance for only a narrow range of parameter values. As a result, small changes in these values could compromise the ability of the mechanosensory hair cells to detect stimuli. We propose that, rather than exerting tight control over parameters, the auditory system employs a homeostatic mechanism that ensures the robustness of its operation to variation in parameter values. Through analytical techniques and computer simulations we investigate whether a homeostatic mechanism renders the hair bundle's signal-detection ability more robust to alterations in experimentally accessible parameters. When homeostasis is enforced, the range of values for which the bundle's sensitivity exceeds a threshold can increase by more than an order of magnitude. The robustness of cochlear function based on somatic motility or hair bundle motility may be achieved by employing the approach we describe here.

Triple coupling and parameter resonance in quantum optomechanics with a single atom

NASA Astrophysics Data System (ADS)

Chang, Yue; Ian, H.; Sun, C. P.

2009-11-01

We study the energy level structure and quantum dynamics for a cavity optomechanical system assisted by a single atom. It is found that a triple coupling involving a photon, a phonon and an atom cannot be described only by the quasi-orbital angular momentum at frequency resonance, there also exists the phenomenon of parameter resonance, namely, when the system parameters are matched in some way, the evolution of the end mirror of the cavity is conditioned by the dressed states of the photon-atom subsystem. The quantum decoherence due to this conditional dynamics is studied in detail. In the quasi-classical limit of very large angular momentum, this system will behave like a standard cavity-QED system described by the Jaynes-Cummings (J-C) model when the angular momentum operators are transformed to bosonic operators of a single mode. We test this observation with an experimentally accessible parameter.

Video segmentation and camera motion characterization using compressed data

NASA Astrophysics Data System (ADS)

Milanese, Ruggero; Deguillaume, Frederic; Jacot-Descombes, Alain

1997-10-01

We address the problem of automatically extracting visual indexes from videos, in order to provide sophisticated access methods to the contents of a video server. We focus on tow tasks, namely the decomposition of a video clip into uniform segments, and the characterization of each shot by camera motion parameters. For the first task we use a Bayesian classification approach to detecting scene cuts by analyzing motion vectors. For the second task a least- squares fitting procedure determines the pan/tilt/zoom camera parameters. In order to guarantee the highest processing speed, all techniques process and analyze directly MPEG-1 motion vectors, without need for video decompression. Experimental results are reported for a database of news video clips.

Study on the Carbonation Behavior of Cement Mortar by Electrochemical Impedance Spectroscopy

PubMed Central

Dong, Biqin; Qiu, Qiwen; Xiang, Jiaqi; Huang, Canjie; Xing, Feng; Han, Ningxu

2014-01-01

A new electrochemical model has been carefully established to explain the carbonation behavior of cement mortar, and the model has been validated by the experimental results. In fact, it is shown by this study that the electrochemical impedance behavior of mortars varies in the process of carbonation. With the cement/sand ratio reduced, the carbonation rate reveals more remarkable. The carbonation process can be quantitatively accessed by a parameter, which can be obtained by means of the electrochemical impedance spectroscopy (EIS)-based electrochemical model. It has been found that the parameter is a function of carbonation depth and of carbonation time. Thereby, prediction of carbonation depth can be achieved. PMID:28788452

Study on the Carbonation Behavior of Cement Mortar by Electrochemical Impedance Spectroscopy.

PubMed

Dong, Biqin; Qiu, Qiwen; Xiang, Jiaqi; Huang, Canjie; Xing, Feng; Han, Ningxu

2014-01-03

A new electrochemical model has been carefully established to explain the carbonation behavior of cement mortar, and the model has been validated by the experimental results. In fact, it is shown by this study that the electrochemical impedance behavior of mortars varies in the process of carbonation. With the cement/sand ratio reduced, the carbonation rate reveals more remarkable. The carbonation process can be quantitatively accessed by a parameter, which can be obtained by means of the electrochemical impedance spectroscopy (EIS)-based electrochemical model. It has been found that the parameter is a function of carbonation depth and of carbonation time. Thereby, prediction of carbonation depth can be achieved.

Acoustically Driven Fluid and Particle Motion in Confined and Leaky Systems

NASA Astrophysics Data System (ADS)

Barnkob, Rune; Nama, Nitesh; Ren, Liqiang; Huang, Tony Jun; Costanzo, Francesco; Kähler, Christian J.

2018-01-01

The acoustic motion of fluids and particles in confined and acoustically leaky systems is receiving increasing attention for its use in medicine and biotechnology. A number of contradicting physical and numerical models currently exist, but their validity is uncertain due to the unavailability of hard-to-access experimental data for validation. We provide experimental benchmarking data by measuring 3D particle trajectories and demonstrate that the particle trajectories can be described numerically without any fitting parameter by a reduced-fluid model with leaky impedance-wall conditions. The results reveal the hitherto unknown existence of a pseudo-standing wave that drives the acoustic streaming as well as the acoustic radiation force on suspended particles.

Water accessibility in a membrane-inserting peptide comparing Overhauser DNP and pulse EPR methods

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

Segawa, Takuya F., E-mail: takuya.segawa@alumni.ethz.ch; Doppelbauer, Maximilian; Garbuio, Luca

2016-05-21

Water accessibility is a key parameter for the understanding of the structure of biomolecules, especially membrane proteins. Several experimental techniques based on the combination of electron paramagnetic resonance (EPR) spectroscopy with site-directed spin labeling are currently available. Among those, we compare relaxation time measurements and electron spin echo envelope modulation (ESEEM) experiments using pulse EPR with Overhauser dynamic nuclear polarization (DNP) at X-band frequency and a magnetic field of 0.33 T. Overhauser DNP transfers the electron spin polarization to nuclear spins via cross-relaxation. The change in the intensity of the {sup 1}H NMR spectrum of H{sub 2}O at a Larmormore » frequency of 14 MHz under a continuous-wave microwave irradiation of the nitroxide spin label contains information on the water accessibility of the labeled site. As a model system for a membrane protein, we use the hydrophobic α-helical peptide WALP23 in unilamellar liposomes of DOPC. Water accessibility measurements with all techniques are conducted for eight peptides with different spin label positions and low radical concentrations (10–20 μM). Consistently in all experiments, the water accessibility appears to be very low, even for labels positioned near the end of the helix. The best profile is obtained by Overhauser DNP, which is the only technique that succeeds in discriminating neighboring positions in WALP23. Since the concentration of the spin-labeled peptides varied, we normalized the DNP parameter ϵ, being the relative change of the NMR intensity, by the electron spin concentration, which was determined from a continuous-wave EPR spectrum.« less

Water accessibility in a membrane-inserting peptide comparing Overhauser DNP and pulse EPR methods.

PubMed

Segawa, Takuya F; Doppelbauer, Maximilian; Garbuio, Luca; Doll, Andrin; Polyhach, Yevhen O; Jeschke, Gunnar

2016-05-21

Water accessibility is a key parameter for the understanding of the structure of biomolecules, especially membrane proteins. Several experimental techniques based on the combination of electron paramagnetic resonance (EPR) spectroscopy with site-directed spin labeling are currently available. Among those, we compare relaxation time measurements and electron spin echo envelope modulation (ESEEM) experiments using pulse EPR with Overhauser dynamic nuclear polarization (DNP) at X-band frequency and a magnetic field of 0.33 T. Overhauser DNP transfers the electron spin polarization to nuclear spins via cross-relaxation. The change in the intensity of the (1)H NMR spectrum of H2O at a Larmor frequency of 14 MHz under a continuous-wave microwave irradiation of the nitroxide spin label contains information on the water accessibility of the labeled site. As a model system for a membrane protein, we use the hydrophobic α-helical peptide WALP23 in unilamellar liposomes of DOPC. Water accessibility measurements with all techniques are conducted for eight peptides with different spin label positions and low radical concentrations (10-20 μM). Consistently in all experiments, the water accessibility appears to be very low, even for labels positioned near the end of the helix. The best profile is obtained by Overhauser DNP, which is the only technique that succeeds in discriminating neighboring positions in WALP23. Since the concentration of the spin-labeled peptides varied, we normalized the DNP parameter ϵ, being the relative change of the NMR intensity, by the electron spin concentration, which was determined from a continuous-wave EPR spectrum.

Experimental quantum simulations of many-body physics with trapped ions.

PubMed

Schneider, Ch; Porras, Diego; Schaetz, Tobias

2012-02-01

Direct experimental access to some of the most intriguing quantum phenomena is not granted due to the lack of precise control of the relevant parameters in their naturally intricate environment. Their simulation on conventional computers is impossible, since quantum behaviour arising with superposition states or entanglement is not efficiently translatable into the classical language. However, one could gain deeper insight into complex quantum dynamics by experimentally simulating the quantum behaviour of interest in another quantum system, where the relevant parameters and interactions can be controlled and robust effects detected sufficiently well. Systems of trapped ions provide unique control of both the internal (electronic) and external (motional) degrees of freedom. The mutual Coulomb interaction between the ions allows for large interaction strengths at comparatively large mutual ion distances enabling individual control and readout. Systems of trapped ions therefore exhibit a prominent system in several physical disciplines, for example, quantum information processing or metrology. Here, we will give an overview of different trapping techniques of ions as well as implementations for coherent manipulation of their quantum states and discuss the related theoretical basics. We then report on the experimental and theoretical progress in simulating quantum many-body physics with trapped ions and present current approaches for scaling up to more ions and more-dimensional systems.

dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions

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

Liu, Ling; Xiong, Yi; Gao, Hongyun

Protein–nucleic acid interactions play essential roles in various biological activities such as gene regulation, transcription, DNA repair and DNA packaging. Understanding the effects of amino acid substitutions on protein–nucleic acid binding affinities can help elucidate the molecular mechanism of protein–nucleic acid recognition. Until now, no comprehensive and updated database of quantitative binding data on alanine mutagenic effects for protein–nucleic acid interactions is publicly accessible. Thus, we developed a new database of Alanine Mutagenic Effects for Protein-Nucleic Acid Interactions (dbAMEPNI). dbAMEPNI is a manually curated, literature-derived database, comprising over 577 alanine mutagenic data with experimentally determined binding affinities for protein–nucleic acidmore » complexes. Here, it contains several important parameters, such as dissociation constant (Kd), Gibbs free energy change (ΔΔG), experimental conditions and structural parameters of mutant residues. In addition, the database provides an extended dataset of 282 single alanine mutations with only qualitative data (or descriptive effects) of thermodynamic information.« less

dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions

DOE PAGES

Liu, Ling; Xiong, Yi; Gao, Hongyun; ...

2018-04-02

Protein–nucleic acid interactions play essential roles in various biological activities such as gene regulation, transcription, DNA repair and DNA packaging. Understanding the effects of amino acid substitutions on protein–nucleic acid binding affinities can help elucidate the molecular mechanism of protein–nucleic acid recognition. Until now, no comprehensive and updated database of quantitative binding data on alanine mutagenic effects for protein–nucleic acid interactions is publicly accessible. Thus, we developed a new database of Alanine Mutagenic Effects for Protein-Nucleic Acid Interactions (dbAMEPNI). dbAMEPNI is a manually curated, literature-derived database, comprising over 577 alanine mutagenic data with experimentally determined binding affinities for protein–nucleic acidmore » complexes. Here, it contains several important parameters, such as dissociation constant (Kd), Gibbs free energy change (ΔΔG), experimental conditions and structural parameters of mutant residues. In addition, the database provides an extended dataset of 282 single alanine mutations with only qualitative data (or descriptive effects) of thermodynamic information.« less

High-temperature annealing of graphite: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Petersen, Andrew; Gillette, Victor

2018-05-01

A modified AIREBO potential was developed to simulate the effects of thermal annealing on the structure and physical properties of damaged graphite. AIREBO parameter modifications were made to reproduce Density Functional Theory interstitial results. These changes to the potential resulted in high-temperature annealing of the model, as measured by stored-energy reduction. These results show some resemblance to experimental high-temperature annealing results, and show promise that annealing effects in graphite are accessible with molecular dynamics and reactive potentials.

Storage and retrieval of quantum information with a hybrid optomechanics-spin system

NASA Astrophysics Data System (ADS)

Feng, Zhi-Bo; Zhang, Jian-Qi; Yang, Wan-Li; Feng, Mang

2016-08-01

We explore an efficient scheme for transferring the quantum state between an optomechanical cavity and an electron spin of diamond nitrogen-vacancy center. Assisted by a mechanical resonator, quantum information can be controllably stored (retrieved) into (from) the electron spin by adjusting the external field-induced detuning or coupling. Our scheme connects effectively the cavity photon and the electron spin and transfers quantum states between two regimes with large frequency difference. The experimental feasibility of our protocol is justified with accessible laboratory parameters.

Structure, dynamics and bifurcations of discrete solitons in trapped ion crystals

NASA Astrophysics Data System (ADS)

Landa, H.; Reznik, B.; Brox, J.; Mielenz, M.; Schaetz, T.

2013-09-01

We study discrete solitons (kinks) accessible in the state-of-the-art trapped ion experiments, considering zigzag crystals and quasi-three-dimensional configurations, both theoretically and experimentally. We first extend the theoretical understanding of different phenomena predicted and recently experimentally observed in the structure and dynamics of these topological excitations. Employing tools from topological degree theory, we analyze bifurcations of crystal configurations in dependence on the trapping parameters, and investigate the formation of kink configurations and the transformations of kinks between different structures. This allows us to accurately define and calculate the effective potential experienced by solitons within the Wigner crystal, and study how this (so-called Peierls-Nabarro) potential gets modified to a non-periodic globally trapping potential in certain parameter regimes. The kinks' rest mass (energy) and spectrum of modes are computed and the dynamics of linear and nonlinear kink oscillations are analyzed. We also present novel, experimentally observed, configurations of kinks incorporating a large-mass defect realized by an embedded molecular ion, and of pairs of interacting kinks stable for long times, offering the perspective for exploring and exploiting complex collective nonlinear excitations, controllable on the quantum level.

High Performance Input/Output for Parallel Computer Systems

NASA Technical Reports Server (NTRS)

Ligon, W. B.

1996-01-01

The goal of our project is to study the I/O characteristics of parallel applications used in Earth Science data processing systems such as Regional Data Centers (RDCs) or EOSDIS. Our approach is to study the runtime behavior of typical programs and the effect of key parameters of the I/O subsystem both under simulation and with direct experimentation on parallel systems. Our three year activity has focused on two items: developing a test bed that facilitates experimentation with parallel I/O, and studying representative programs from the Earth science data processing application domain. The Parallel Virtual File System (PVFS) has been developed for use on a number of platforms including the Tiger Parallel Architecture Workbench (TPAW) simulator, The Intel Paragon, a cluster of DEC Alpha workstations, and the Beowulf system (at CESDIS). PVFS provides considerable flexibility in configuring I/O in a UNIX- like environment. Access to key performance parameters facilitates experimentation. We have studied several key applications fiom levels 1,2 and 3 of the typical RDC processing scenario including instrument calibration and navigation, image classification, and numerical modeling codes. We have also considered large-scale scientific database codes used to organize image data.

Experimental design to understand the interaction of stellar radiation with molecular clouds

NASA Astrophysics Data System (ADS)

VanDervort, Robert; Davis, Josh; Trantham, Matt; Klein, Sallee; Frank, Yechiel; Raicher, Erez; Fraenkel, Moshe; Shvarts, Dov; Keiter, Paul; Drake, R. Paul

2017-06-01

Enhanced star formation triggered by local O and B type stars is an astrophysical problem of interest. O and B type stars are massive, hot stars that emit an enormous amount of radiation. This radiation acts to either compress or blow apart clumps of gas in the interstellar media. For example, in the optically thick limit, when the x-ray radiation in the gas clump has a short mean free path length the x-ray radiation is absorbed near the clump edge and compresses the clump. In the optically thin limit, when the mean free path is long, the radiation is absorbed throughout acting to heat the clump. This heating explodes the gas clump. Careful selection of parameters, such as foam density or source temperature, allow the experimental platform to access different hydrodynamic regimes. The stellar radiation source is mimicked by a laser irradiated thin gold foil. This will provide a source of thermal x-rays (around ~100 eV). The gas clump is mimicked by a low-density foam around 0.150 g/cc. Simulations were done using radiation hydrodynamics codes to tune the experimental parameters. The experiment will be carried out at the Omega laser facility on OMEGA 60.

Valorization of genetic variability for the qualitative improvement of autochthonous grape cultivars of Cirò's terroir through the self-fertilization.

PubMed

Meneghetti, Stefano; Gaiotti, Federica; Giust, Mirella; Belfiore, Nicola; Tomasi, Diego

2015-03-01

This study uses PCR-derived marker systems to investigate the genetic differences of 22 grapevine accessions obtained through a self-fertilization program using Gaglioppo and Magliocco dolce. The aim of the study was to improve some qualitative parameters, while preserving the adaptive characteristics of these two cultivars to the adverse environmental conditions of the Calabria region (southern Italy). These two Calabrian grapevines have been cultivated within a restricted area and have been placed under a strong anthropic pressure which has limited their phenotypical variability with no selection of higher performant biotypes. Therefore, to have accessions with improved qualitative traits, a program of genetic improvement based on the self-fertilization of Gaglioppo and Magliocco dolce cultivars was performed in 1998, producing 3,122 accessions. Selection cycles were performed in 14 years. A first selection cycle (1998-2000), based on visual inspection of vegetative traits, selected 1,320 accessions, planted in an experimental vineyard in 2000. A second selection cycle (2000-2008), based on phenotypic traits, sanitary aspects, and chemical composition of the grapes, selected 42 accessions, planted in a new experimental vineyard in 2008. A final selection cycle (2008-2012), produced 22 accessions (virus free), with the best agronomic, sanitary, and qualitative aspects: two accessions obtained from Gaglioppo have been selected by color characteristics (i.e., anthocyanin total content and stability); 20 genotypes obtained from Magliocco dolce had a better macro-composition of the grape (i.e., good sugar content with a balanced acidity). SSR analyses were performed to check the self-fertilization process. The study of genetic differences between accessions was performed by AFLPs, SAMPLs, and M-AFLPs. The application of the above-mentioned techniques allowed both to discriminate molecularly the 22 accessions grouped these accessions according to their genetic similarity. The self-fertilization approach has enabled improvement in the quality of the grapes, while preserving the high degree of adaptation to the environment of these two native Calabrian cultivars in southern Italy.

Dual-band plasmonic resonator based on Jerusalem cross-shaped nanoapertures

NASA Astrophysics Data System (ADS)

Cetin, Arif E.; Kaya, Sabri; Mertiri, Alket; Aslan, Ekin; Erramilli, Shyamsunder; Altug, Hatice; Turkmen, Mustafa

2015-06-01

In this paper, we both experimentally and numerically introduce a dual-resonant metamaterial based on subwavelength Jerusalem cross-shaped apertures. We numerically investigate the physical origin of the dual-resonant behavior, originating from the constituting aperture elements, through finite difference time domain calculations. Our numerical calculations show that at the dual-resonances, the aperture system supports large and easily accessible local electromagnetic fields. In order to experimentally realize the aperture system, we utilize a high-precision and lift-off free fabrication method based on electron-beam lithography. We also introduce a fine-tuning mechanism for controlling the dual-resonant spectral response through geometrical device parameters. Finally, we show the aperture system's highly advantageous far- and near-field characteristics through numerical calculations on refractive index sensitivity. The quantitative analyses on the availability of the local fields supported by the aperture system are employed to explain the grounds behind the sensitivity of each spectral feature within the dual-resonant behavior. Possessing dual-resonances with large and accessible electromagnetic fields, Jerusalem cross-shaped apertures can be highly advantageous for wide range of applications demanding multiple spectral features with strong nearfield characteristics.

A CDMA system implementation with dimming control for visible light communication

NASA Astrophysics Data System (ADS)

Chen, Danyang; Wang, Jianping; Jin, Jianli; Lu, Huimin; Feng, Lifang

2018-04-01

Visible light communication (VLC), using solid-state lightings to transmit information, has become a complement technology to wireless radio communication. As a realistic multiple access scheme for VLC system, code division multiple access (CDMA) has attracted more and more attentions in recent years. In this paper, we address and implement an improved CDMA scheme for VLC system. The simulation results reveal that the improved CDMA scheme not only supports multi-users' transmission but also maintains dimming value at about 50% and enhances the system efficiency. It can also realize the flexible dimming control by adjusting some parameters of system structure, which rarely affects the system BER performance. A real-time experimental VLC system with improved CDMA scheme is performed based on field programmable gate array (FPGA), reaching a good BER performance.

Numerical Investigation of the Performance of a Supersonic Combustion Chamber and Comparison with Experiments

NASA Astrophysics Data System (ADS)

Banica, M. C.; Chun, J.; Scheuermann, T.; Weigand, B.; Wolfersdorf, J. v.

2009-01-01

Scramjet powered vehicles can decrease costs for access to space but substantial obstacles still exist in their realization. For example, experiments in the relevant Mach number regime are difficult to perform and flight testing is expensive. Therefore, numerical methods are often employed for system layout but they require validation against experimental data. Here, we validate the commercial code CFD++ against experimental results for hydrogen combustion in the supersonic combustion facility of the Institute of Aerospace Thermodynamics (ITLR) at the Universität Stuttgart. Fuel is injected through a lobed a strut injector, which provides rapid mixing. Our numerical data shows reasonable agreement with experiments. We further investigate effects of varying equivalence ratios on several important performance parameters.

Effective simulations of gas diffusion through kinetically accessible tunnels in multisubunit proteins: O2 pathways and escape routes in T-state deoxyhemoglobin.

PubMed

Shadrina, Maria S; English, Ann M; Peslherbe, Gilles H

2012-07-11

The diffusion of small gases to special binding sites within polypeptide matrices pivotally defines the biochemical specificity and reactivity of proteins. We investigate here explicit O(2) diffusion in adult human hemoglobin (HbA) as a case study employing the recently developed temperature-controlled locally enhanced sampling (TLES) method and vary the parameters to greatly increase the simulation efficiency. The method is carefully validated against standard molecular dynamics (MD) simulations and available experimental structural and kinetic data on ligand diffusion in T-state deoxyHbA. The methodology provides a viable alternative approach to traditional MD simulations and/or potential of mean force calculations for: (i) characterizing kinetically accessible diffusion tunnels and escape routes for light ligands in porous proteins; (ii) very large systems when realistic simulations require the inclusion of multiple subunits of a protein; and (iii) proteins that access short-lived conformations relative to the simulation time. In the case of T-state deoxyHbA, we find distinct ligand diffusion tunnels consistent with the experimentally observed disparate Xe cavities in the α- and β-subunits. We identify two distal barriers including the distal histidine (E7) that control access to the heme. The multiple escape routes uncovered by our simulations call for a review of the current popular hypothesis on ligand escape from hemoglobin. Larger deviations from the crystal structure during simulated diffusion in isolated α- and β-subunits highlight the dampening effects of subunit interactions and the importance of including all subunits of multisubunit proteins to map realistic kinetically accessible diffusion tunnels and escape routes.

Activity-dependent self-regulation of viscous length scales in biological systems

NASA Astrophysics Data System (ADS)

Nandi, Saroj Kumar

2018-05-01

The cellular cortex, which is a highly viscous thin cytoplasmic layer just below the cell membrane, controls the cell's mechanical properties, which can be characterized by a hydrodynamic length scale ℓ . Cells actively regulate ℓ via the activity of force-generating molecules, such as myosin II. Here we develop a general theory for such systems through a coarse-grained hydrodynamic approach including activity in the static description of the system providing an experimentally accessible parameter and elucidate the detailed mechanism of how a living system can actively self-regulate its hydrodynamic length scale, controlling the rigidity of the system. Remarkably, we find that ℓ , as a function of activity, behaves universally and roughly inversely proportional to the activity of the system. Our theory rationalizes a number of experimental findings on diverse systems, and comparison of our theory with existing experimental data shows good agreement.

Exploring natural variation of photosynthetic, primary metabolism and growth parameters in a large panel of Capsicum chinense accessions.

PubMed

Rosado-Souza, Laise; Scossa, Federico; Chaves, Izabel S; Kleessen, Sabrina; Salvador, Luiz F D; Milagre, Jocimar C; Finger, Fernando; Bhering, Leonardo L; Sulpice, Ronan; Araújo, Wagner L; Nikoloski, Zoran; Fernie, Alisdair R; Nunes-Nesi, Adriano

2015-09-01

Collectively, the results presented improve upon the utility of an important genetic resource and attest to a complex genetic basis for differences in both leaf metabolism and fruit morphology between natural populations. Diversity of accessions within the same species provides an alternative method to identify physiological and metabolic traits that have large effects on growth regulation, biomass and fruit production. Here, we investigated physiological and metabolic traits as well as parameters related to plant growth and fruit production of 49 phenotypically diverse pepper accessions of Capsicum chinense grown ex situ under controlled conditions. Although single-trait analysis identified up to seven distinct groups of accessions, working with the whole data set by multivariate analyses allowed the separation of the 49 accessions in three clusters. Using all 23 measured parameters and data from the geographic origin for these accessions, positive correlations between the combined phenotypes and geographic origin were observed, supporting a robust pattern of isolation-by-distance. In addition, we found that fruit set was positively correlated with photosynthesis-related parameters, which, however, do not explain alone the differences in accession susceptibility to fruit abortion. Our results demonstrated that, although the accessions belong to the same species, they exhibit considerable natural intraspecific variation with respect to physiological and metabolic parameters, presenting diverse adaptation mechanisms and being a highly interesting source of information for plant breeders. This study also represents the first study combining photosynthetic, primary metabolism and growth parameters for Capsicum to date.

Adaptive Phase Delay Generator

NASA Technical Reports Server (NTRS)

Greer, Lawrence

2013-01-01

There are several experimental setups involving rotating machinery that require some form of synchronization. The adaptive phase delay generator (APDG) the Bencic-1000 is a flexible instrument that allows the user to generate pulses synchronized to the rising edge of a tachometer signal from any piece of rotating machinery. These synchronized pulses can vary by the delay angle, pulse width, number of pulses per period, number of skipped pulses, and total number of pulses. Due to the design of the pulse generator, any and all of these parameters can be changed independently, yielding an unparalleled level of versatility. There are two user interfaces to the APDG. The first is a LabVIEW program that has the advantage of displaying all of the pulse parameters and input signal data within one neatly organized window on the PC monitor. Furthermore, the LabVIEW interface plots the rpm of the two input signal channels in real time. The second user interface is a handheld portable device that goes anywhere a computer is not accessible. It consists of a liquid-crystal display and keypad, which enable the user to control the unit by scrolling through a host of command menus and parameter listings. The APDG combines all of the desired synchronization control into one unit. The experimenter can adjust the delay, pulse width, pulse count, number of skipped pulses, and produce a specified number of pulses per revolution. Each of these parameters can be changed independently, providing an unparalleled level of versatility when synchronizing hardware to a host of rotating machinery. The APDG allows experimenters to set up quickly and generate a host of synchronizing configurations using a simple user interface, which hopefully leads to faster results.

Lanthanide and transition metal complexes of bioactive coumarins: molecular modeling and spectroscopic studies.

PubMed

Georgieva, I; Mihaylov, Tz; Trendafilova, N

2014-06-01

The present paper summarizes theoretical and spectroscopic investigations on a series of active coumarins and their lanthanide and transition metal complexes with application in medicine and pharmacy. Molecular modeling as well as IR, Raman, NMR and electronic spectral simulations at different levels of theory were performed to obtain important molecular descriptors: total energy, formation energy, binding energy, stability, conformations, structural parameters, electron density distribution, molecular electrostatic potential, Fukui functions, atomic charges, and reactive indexes. The computations are performed both in gas phase and in solution with consideration of the solvent effect on the molecular structural and energetic parameters. The investigations have shown that the advanced computational methods are reliable for prediction of the metal-coumarin binding mode, electron density distribution, thermodynamic properties as well as the strength and nature of the metal-coumarin interaction (not experimentally accessible) and correctly interpret the experimental spectroscopic data. Known results from biological tests for cytotoxic, antimicrobial, anti-fungal, spasmolytic and anti-HIV activities on the studied metal complexes are reported and discussed. Copyright © 2014 Elsevier Inc. All rights reserved.

Nuclear magnetic resonance signal dynamics of liquids in the presence of distant dipolar fields, revisited

PubMed Central

Barros, Wilson; Gochberg, Daniel F.; Gore, John C.

2009-01-01

The description of the nuclear magnetic resonance magnetization dynamics in the presence of long-range dipolar interactions, which is based upon approximate solutions of Bloch–Torrey equations including the effect of a distant dipolar field, has been revisited. New experiments show that approximate analytic solutions have a broader regime of validity as well as dependencies on pulse-sequence parameters that seem to have been overlooked. In order to explain these experimental results, we developed a new method consisting of calculating the magnetization via an iterative formalism where both diffusion and distant dipolar field contributions are treated as integral operators incorporated into the Bloch–Torrey equations. The solution can be organized as a perturbative series, whereby access to higher order terms allows one to set better boundaries on validity regimes for analytic first-order approximations. Finally, the method legitimizes the use of simple analytic first-order approximations under less demanding experimental conditions, it predicts new pulse-sequence parameter dependencies for the range of validity, and clarifies weak points in previous calculations. PMID:19425789

Strong-field ionization with twisted laser pulses

NASA Astrophysics Data System (ADS)

Paufler, Willi; Böning, Birger; Fritzsche, Stephan

2018-04-01

We apply quantum trajectory Monte Carlo computations in order to model strong-field ionization of atoms by twisted Bessel pulses and calculate photoelectron momentum distributions (PEMD). Since Bessel beams can be considered as an infinite superposition of circularly polarized plane waves with the same helicity, whose wave vectors lie on a cone, we compared the PEMD of such Bessel pulses to those of a circularly polarized pulse. We focus on the momentum distributions in propagation direction of the pulse and show how these momentum distributions are affected by experimental accessible parameters, such as the opening angle of the beam or the impact parameter of the atom with regard to the beam axis. In particular, we show that we can find higher momenta of the photoelectrons, if the opening angle is increased.

Transesophageal NOTES--a critical analysis of relevant problems.

PubMed

Grund, Karl E; Lehmann, Thorsten G

2010-10-01

The transesophageal access route has not become a principal topic in the discussion about NOTES up to now. Analyzing the problems in this new field of surgery, however, the transesophageal route shows high relevance. Here, all possibilities, limitations, and problems of NOTES become obvious. This paper contains a critical analysis of the literature published to date (nine full papers, five abstracts). Nearly all publications represent experimental studies in living pigs. In most cases a submucosal tunnel technique is performed as access route to mediastinum, pleural cavity, and heart. Interventions and operations include simple mediastinoscopies as well as epicardial operations after exposition of the heart. For access and manipulation, conventional flexible endoscopes and instruments are used. Clips, T-bars, or a combination of both achieve the closure. Some studies rely on spontaneous closure of the incision without any suturing or approximation. In such experimental settings, the following results are presented: Access is achieved in 90% of cases, the aim of the operation is met in 92%, technical success in closure is achieved in 90%, healing of incision assessed as good in two of five studies, satisfactory in three of five studies. Mortality, ranging from 6 to 25%, and complication rates were (surprisingly) high. It has to be stressed that analyzing these papers published to date, no adequate attention is paid to basic facts and problems of general and thoracic surgery (e.g. different forms, prevention, diagnosis and therapy of pneumothorax or differentiated forms of ventilation). Relevant differences in the anatomy and physiology of the esophagus and mediastinum between humans and pigs should additionally be taken into account to choose optimal experimental parameters when transferring results to human settings. Moreover, requirements regarding sterility and hygiene in a structure like the mediastinum, which is at high risk from the point of view of infection biology, have not yet been respected. These factors should be taken into account in further studies--as well as clinically relevant disease patterns in humans--to be able to realize possible advantages of this NOTES access in a clinical setting.

Semileptonic decays of Λ _c baryons in the relativistic quark model

NASA Astrophysics Data System (ADS)

Faustov, R. N.; Galkin, V. O.

2016-11-01

Motivated by recent experimental progress in studying weak decays of the Λ _c baryon we investigate its semileptonic decays in the framework of the relativistic quark model based on the quasipotential approach with the QCD-motivated potential. The form factors of the Λ _c→ Λ lν _l and Λ _c→ nlν _l decays are calculated in the whole accessible kinematical region without extrapolations and additional model assumptions. Relativistic effects are systematically taken into account including transformations of baryon wave functions from the rest to moving reference frame and contributions of the intermediate negative-energy states. Baryon wave functions found in the previous mass spectrum calculations are used for the numerical evaluation. Comprehensive predictions for decay rates, asymmetries and polarization parameters are given. They agree well with available experimental data.

All-optical signatures of strong-field QED in the vacuum emission picture

NASA Astrophysics Data System (ADS)

Gies, Holger; Karbstein, Felix; Kohlfürst, Christian

2018-02-01

We study all-optical signatures of the effective nonlinear couplings among electromagnetic fields in the quantum vacuum, using the collision of two focused high-intensity laser pulses as an example. The experimental signatures of quantum vacuum nonlinearities are encoded in signal photons, whose kinematic and polarization properties differ from the photons constituting the macroscopic laser fields. We implement an efficient numerical algorithm allowing for the theoretical investigation of such signatures in realistic field configurations accessible in experiment. This algorithm is based on a vacuum emission scheme and can readily be adapted to the collision of more laser beams or further involved field configurations. We solve the case of two colliding pulses in full 3 +1 -dimensional spacetime and identify experimental geometries and parameter regimes with improved signal-to-noise ratios.

BIOPACK: the ground controlled late access biological research facility.

PubMed

van Loon, Jack J W A

2004-03-01

Future Space Shuttle flights shall be characterized by activities necessary to further build the International Space Station, ISS. During these missions limited resources are available to conduct biological experiments in space. The Shuttles' Middeck is a very suitable place to conduct science during the ISS assembly missions or dedicated science missions. The BIOPACK, which flew its first mission during the STS-107, provides a versatile Middeck Locker based research tool for gravitational biology studies. The core facility occupies the space of only two Middeck Lockers. Experiment temperatures are controlled for bacteria, plant, invertebrate and mammalian cultures. Gravity levels and profiles can be set ranging from 0 to 2.0 x g on three independent centrifuges. This provides the experimenter with a 1.0 x g on-board reference and intermediate hypogravity and hypergravity data points to investigate e.g. threshold levels in biological responses. Temperature sensitive items can be stored in the facilities' -10 degrees C and +4 degrees C stowage areas. During STS-107 the facility also included a small glovebox (GBX) and passive temperature controlled units (PTCU). The GBX provides the experimenter with two extra levels of containment for safe sample handling. This biological research facility is a late access (L-10 hrs) laboratory, which, when reaching orbit, could automatically be starting up reducing important experiment lag-time and valuable crew time. The system is completely telecommanded when needed. During flight system parameters like temperatures, centrifuge speeds, experiment commanding or sensor readouts can be monitored and changed when needed. Although ISS provides a wide range of research facilities there is still need for an STS-based late access facility such as the BIOPACK providing experimenters with a very versatile research cabinet for biological experiments under microgravity and in-flight control conditions.

Building Models in the Classroom: Taking Advantage of Sophisticated Geomorphic Numerical Tools Using a Simple Graphical User Interface

NASA Astrophysics Data System (ADS)

Roy, S. G.; Koons, P. O.; Gerbi, C. C.; Capps, D. K.; Tucker, G. E.; Rogers, Z. A.

2014-12-01

Sophisticated numerical tools exist for modeling geomorphic processes and linking them to tectonic and climatic systems, but they are often seen as inaccessible for users with an exploratory level of interest. We have improved the accessibility of landscape evolution models by producing a simple graphics user interface (GUI) that takes advantage of the Channel-Hillslope Integrated Landscape Development (CHILD) model. Model access is flexible: the user can edit values for basic geomorphic, tectonic, and climate parameters, or obtain greater control by defining the spatiotemporal distributions of those parameters. Users can make educated predictions by choosing their own parametric values for the governing equations and interpreting the results immediately through model graphics. This method of modeling allows users to iteratively build their understanding through experimentation. Use of this GUI is intended for inquiry and discovery-based learning activities. We discuss a number of examples of how the GUI can be used at the upper high school, introductory university, and advanced university level. Effective teaching modules initially focus on an inquiry-based example guided by the instructor. As students become familiar with the GUI and the CHILD model, the class can shift to more student-centered exploration and experimentation. To make model interpretations more robust, digital elevation models can be imported and direct comparisons can be made between CHILD model results and natural topography. The GUI is available online through the University of Maine's Earth and Climate Sciences website, through the Community Surface Dynamics Modeling System (CSDMS) model repository, or by contacting the corresponding author.

Distribution of lead in selected organs and its effect on reproduction parameters of pheasants (Phasianus colchicus) after an experimental per oral administration.

PubMed

Gasparik, Jozef; Venglarcik, Jozef; Slamecka, Jaroslav; Kropil, Rudolf; Smehyl, Peter; Kopecky, Jan

2012-01-01

Lead poisoning has been reported in almost every country on earth. In this study the effect of experimental lead pellet intake (2-6 pellets per week [groups B2, B4, B6] and ad libitum [BAD] accessibility for 10 weeks) on its distribution in liver, kidney, pectoral muscle, ovary, eggs and the effect of selected reproductive parameters (egg weight, fertilization, hatchability) was analyzed in breeding pheasants. Lead pellets were force fed to the digestive tract (struma, ingluvies) and the ingestion was controlled. Concentration of lead was detected using the atomic absorption spectrophotometry. Analysis of the lead concentration in liver showed a significantly higher concentration in all group after the lead pellets intake. The increase of the lead concentration was dose-dependent and the concentration detected in group BAD was similar as in group B2. Very similar tendencies were detected for the lead concentration in kidney. The accumulation of lead in pectoral muscle was lower, in comparison with liver and kidney. Compared to lead concentration detected in ovary of the control group a significant increase was detected in all experimental groups, reaching the maximum in the group B6. Similar significant increase of lead concentration was detected in eggs. The average weight of eggs was 32.01 ± 2.71 g in the control group and lower in all experimental groups, but this decrease was significant only in the group B6. The fertilization rate was the highest in the control group and a dose-dependent decrease was detected with the lowest value in the group B6. For egg hatching ratio a significant decrease was detected in groups B4 and B6. Results of this study clearly describe accumulation of lead in the body and a its negative effect on the reproductive parameters. In the ad libitum experimental group the most similar results were found as in group B2, suggesting a rate of "natural" lead pellet intake.

Extended solvent-contact model approach to blind SAMPL5 prediction challenge for the distribution coefficients of drug-like molecules

NASA Astrophysics Data System (ADS)

Chung, Kee-Choo; Park, Hwangseo

2016-11-01

The performance of the extended solvent-contact model has been addressed in the SAMPL5 blind prediction challenge for distribution coefficient (LogD) of drug-like molecules with respect to the cyclohexane/water partitioning system. All the atomic parameters defined for 41 atom types in the solvation free energy function were optimized by operating a standard genetic algorithm with respect to water and cyclohexane solvents. In the parameterizations for cyclohexane, the experimental solvation free energy (Δ G sol ) data of 15 molecules for 1-octanol were combined with those of 77 molecules for cyclohexane to construct a training set because Δ G sol values of the former were unavailable for cyclohexane in publicly accessible databases. Using this hybrid training set, we established the LogD prediction model with the correlation coefficient ( R), average error (AE), and root mean square error (RMSE) of 0.55, 1.53, and 3.03, respectively, for the comparison of experimental and computational results for 53 SAMPL5 molecules. The modest accuracy in LogD prediction could be attributed to the incomplete optimization of atomic solvation parameters for cyclohexane. With respect to 31 SAMPL5 molecules containing the atom types for which experimental reference data for Δ G sol were available for both water and cyclohexane, the accuracy in LogD prediction increased remarkably with the R, AE, and RMSE values of 0.82, 0.89, and 1.60, respectively. This significant enhancement in performance stemmed from the better optimization of atomic solvation parameters by limiting the element of training set to the molecules with experimental Δ G sol data for cyclohexane. Due to the simplicity in model building and to low computational cost for parameterizations, the extended solvent-contact model is anticipated to serve as a valuable computational tool for LogD prediction upon the enrichment of experimental Δ G sol data for organic solvents.

MatProps: Material Properties Database and Associated Access Library

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

Durrenberger, J K; Becker, R C; Goto, D M

2007-08-13

Coefficients for analytic constitutive and equation of state models (EOS), which are used by many hydro codes at LLNL, are currently stored in a legacy material database (Steinberg, UCRL-MA-106349). Parameters for numerous materials are available through this database, and include Steinberg-Guinan and Steinberg-Lund constitutive models for metals, JWL equations of state for high explosives, and Mie-Gruniesen equations of state for metals. These constitutive models are used in most of the simulations done by ASC codes today at Livermore. Analytic EOSs are also still used, but have been superseded in many cases by tabular representations in LEOS (http://leos.llnl.gov). Numerous advanced constitutivemore » models have been developed and implemented into ASC codes over the past 20 years. These newer models have more physics and better representations of material strength properties than their predecessors, and therefore more model coefficients. However, a material database of these coefficients is not readily available. Therefore incorporating these coefficients with those of the legacy models into a portable database that could be shared amongst codes would be most welcome. The goal of this paper is to describe the MatProp effort at LLNL to create such a database and associated access library that could be used by codes throughout the DOE complex and beyond. We have written an initial version of the MatProp database and access library and our DOE/ASC code ALE3D (Nichols et. al., UCRL-MA-152204) is able to import information from the database. The database, a link to which exists on the Sourceforge server at LLNL, contains coefficients for many materials and models (see Appendix), and includes material parameters in the following categories--flow stress, shear modulus, strength, damage, and equation of state. Future versions of the Matprop database and access library will include the ability to read and write material descriptions that can be exchanged between codes. It will also include an ability to do unit changes, i.e. have the library return parameters in user-specified unit systems. In addition to these, additional material categories can be added (e.g., phase change kinetics, etc.). The Matprop database and access library is part of a larger set of tools used at LLNL for assessing material model behavior. One of these is MSlib, a shared constitutive material model library. Another is the Material Strength Database (MSD), which allows users to compare parameter fits for specific constitutive models to available experimental data. Together with Matprop, these tools create a suite of capabilities that provide state-of-the-art models and parameters for those models to integrated simulation codes. This document is broken into several appendices. Appendix A contains a code example to retrieve several material coefficients. Appendix B contains the API for the Matprop data access library. Appendix C contains a list of the material names and model types currently available in the Matprop database. Appendix D contains a list of the parameter names for the currently recognized model types. Appendix E contains a full xml description of the material Tantalum.« less

Modeling and experimental design for metabolic flux analysis of lysine-producing Corynebacteria by mass spectrometry.

PubMed

Wittmann, C; Heinzle, E

2001-04-01

Experimental design of (13)C-tracer studies for metabolic flux analysis with mass spectrometric determination of labeling patterns was performed for the central metabolism of Corynebacterium glutamicum comprising various flux scenarios. Ratio measurement of mass isotopomer pools of Corynebacterium products lysine, alanine, and trehalose is sufficient to quantify the flux partitioning ratios (i) between glycolysis and pentose phosphate pathways (Phi(PPP)), (ii) between the split pathways in the lysine biosynthesis (Phi(DH)), (iii) at the pyruvate node (Phi(PC)), and reversibilities of (iv) glucose 6-phosphate isomerase (zeta(PGI)), (v) at the pyruvate node (zeta(PC/PEPCK)), and (vi) of transaldolase and transketolases in the PPP. Weighted sensitivities for flux parameters were derived from partial derivatives to quantitatively evaluate experimental approaches and predict precision for estimated flux parameters. Deviation of intensity ratios from ideal values of 1 was used as weighting function. Weighted flux sensitivities can be used to identify optimal type and degree of tracer labeling or potential intensity ratios to be measured. Experimental design for lysine-producing strain C. glutamicum MH 20-22B (Marx et al., Biotechnol. Bioeng. 49, 111-129, 1996) and various potential mutants with different alterations in the flux pattern showed that specific tracer labelings are optimal to quantify a certain flux parameter uninfluenced by the overall flux situation. Identified substrates of choice are [1-(13)C]glucose for the estimation of Phi(PPP) and zeta(PGI) and a 1 : 1 mixture of [U-(12)C/U-(13)C]glucose for the determination of zeta(PC/PEPCK). Phi(PC) can be quantified by feeding [4-(13)C]glucose or [U-(12)C/U-(13)C]glucose (1 : 1), whereas Phi(DH) is accessible via [4-(13)C]glucose. The sensitivity for the quantification of a certain flux parameter can be influenced by superposition through other flux parameters in the network, but substrate and measured mass isotopomers of choice remain the same. In special cases, reduced labeling degree of the tracer substrate can increase the precision of flux analysis. Enhanced precision and flux information can be achieved via multiply labeled substrates. The presented approach can be applied for effective experimental design of (13)C tracer studies for metabolic flux analysis. Intensity ratios of other products such as glutamate, valine, phenylalanine, and riboflavin also sensitively reflect flux parameters, which underlines the great potential of mass spectrometry for flux analysis. Copyright 2001 Academic Press.

Nubia's mother: being pregnant in the time of experimental vaccines and therapeutics for Ebola.

PubMed

Caluwaerts, Séverine

2017-12-14

During the 2014-2016 Ebola epidemic, Médecins Sans Frontières (MSF) treated Ebola-positive pregnant women in its Ebola Treatment Centers (ETCs). For pregnant women with confirmed Ebola virus disease, inclusion in clinical vaccine/drug/therapeutic trials was complicated. Despite their extremely high Ebola-related mortality in previous epidemics (89-93%) and a neonatal mortality of 100%, theoretical concerns about safety of vaccines and therapeutics in pregnancy were invoked, limiting pregnant women's access to an experimental live attenuated vaccine and brincidofovir, an experimental antiviral. Favipiravir, another experimental antiviral, was made available to pregnant women only after extensive negotiations and under a 'Monitored Emergency Use of Unregistered and Experimental Interventions' (MEURI) protocol. This paper describes the case of a pregnant woman who presented to the ETCs near the end of the Ebola epidemic in Guinea. The pregnant patient was admitted with confirmed Ebola disease. She was previously denied access to potentially protective vaccination due to pregnancy, and access to experimental ZMapp was only possible through a randomized clinical trial (presenting a 50% chance of not receiving ZMapp). She received favipiravir, but died of Ebola-related complications. The infant, born in the ETC, tested positive for Ebola at birth. The infant received ZMapp (under MEURI access outside of the clinical trial), an experimental drug GS5734, and a buffy coat of an Ebola survivor, and survived. Though the infant did have access to experimental therapeutics within 24 h of birth, access to other experimental compounds for her mother was denied, raising serious ethical concerns.

A Microfluidics and Agent-Based Modeling Framework for Investigating Spatial Organization in Bacterial Colonies: The Case of Pseudomonas Aeruginosa and H1-Type VI Secretion Interactions.

PubMed

Wilmoth, Jared L; Doak, Peter W; Timm, Andrea; Halsted, Michelle; Anderson, John D; Ginovart, Marta; Prats, Clara; Portell, Xavier; Retterer, Scott T; Fuentes-Cabrera, Miguel

2018-01-01

The factors leading to changes in the organization of microbial assemblages at fine spatial scales are not well characterized or understood. However, they are expected to guide the succession of community development and function toward specific outcomes that could impact human health and the environment. In this study, we put forward a combined experimental and agent-based modeling framework and use it to interpret unique spatial organization patterns of H1-Type VI secretion system (T6SS) mutants of P . aeruginosa under spatial confinement. We find that key parameters, such as T6SS-mediated cell contact and lysis, spatial localization, relative species abundance, cell density and local concentrations of growth substrates and metabolites are influenced by spatial confinement. The model, written in the accessible programming language NetLogo, can be adapted to a variety of biological systems of interest and used to simulate experiments across a broad parameter space. It was implemented and run in a high-throughput mode by deploying it across multiple CPUs, with each simulation representing an individual well within a high-throughput microwell array experimental platform. The microfluidics and agent-based modeling framework we present in this paper provides an effective means by which to connect experimental studies in microbiology to model development. The work demonstrates progress in coupling experimental results to simulation while also highlighting potential sources of discrepancies between real-world experiments and idealized models.

A Microfluidics and Agent-Based Modeling Framework for Investigating Spatial Organization in Bacterial Colonies: The Case of Pseudomonas Aeruginosa and H1-Type VI Secretion Interactions

PubMed Central

Wilmoth, Jared L.; Doak, Peter W.; Timm, Andrea; Halsted, Michelle; Anderson, John D.; Ginovart, Marta; Prats, Clara; Portell, Xavier; Retterer, Scott T.; Fuentes-Cabrera, Miguel

2018-01-01

The factors leading to changes in the organization of microbial assemblages at fine spatial scales are not well characterized or understood. However, they are expected to guide the succession of community development and function toward specific outcomes that could impact human health and the environment. In this study, we put forward a combined experimental and agent-based modeling framework and use it to interpret unique spatial organization patterns of H1-Type VI secretion system (T6SS) mutants of P. aeruginosa under spatial confinement. We find that key parameters, such as T6SS-mediated cell contact and lysis, spatial localization, relative species abundance, cell density and local concentrations of growth substrates and metabolites are influenced by spatial confinement. The model, written in the accessible programming language NetLogo, can be adapted to a variety of biological systems of interest and used to simulate experiments across a broad parameter space. It was implemented and run in a high-throughput mode by deploying it across multiple CPUs, with each simulation representing an individual well within a high-throughput microwell array experimental platform. The microfluidics and agent-based modeling framework we present in this paper provides an effective means by which to connect experimental studies in microbiology to model development. The work demonstrates progress in coupling experimental results to simulation while also highlighting potential sources of discrepancies between real-world experiments and idealized models. PMID:29467721

Terminal illness and access to Phase 1 experimental agents, surgeries and devices: reviewing the ethical arguments.

PubMed

Schüklenk, Udo; Lowry, Christopher

2009-01-01

The advent of AIDS brought about a group of patients unwilling to accept crucial aspects of the methodological standards for clinical research investigating Phase 1 drugs, surgeries or devices. Their arguments against placebo controls in trials, which depended--at the time--on the terminal status of patient volunteers led to a renewed discussion of the ethics of denying patients with catastrophic illnesses access to last-chance experimental drugs, surgeries or devices. Existing ethics and health policy literature on the topic of access to experimental drugs. The positions of those arguing for or against free access to experimental drugs for terminally ill patients are irreconcilable. At stake are questions about the kinds of personal sacrifices society can reasonably expect patients in clinical trials to make to ensure statistically predictive results. These would benefit by necessity a much larger number of current and future patients--the conflict is about individual versus public interests. It is also about the question of whether or not the state can legitimately prevent patients with terminal illnesses from unfettered access to experimental drugs, surgeries or devices in order to motivate them to participate in clinical trials. We review the ethical arguments for and against the provision of access to Phase 1 agents for terminally ill patients. Finding a compromise between providing free or no access to Phase 1 drugs for terminally ill patients. We ought to investigate means to increase access to experimental drugs for terminally ill patients without sacrificing necessary clinical trials' sounds scientific methods.

Going "social" to access experimental and potentially life-saving treatment: an assessment of the policy and online patient advocacy environment for expanded access.

PubMed

Mackey, Tim K; Schoenfeld, Virginia J

2016-02-02

Social media is fundamentally altering how we access health information and make decisions about medical treatment, including for terminally ill patients. This specifically includes the growing phenomenon of patients who use online petitions and social media campaigns in an attempt to gain access to experimental drugs through expanded access pathways. Importantly, controversy surrounding expanded access and "compassionate use" involves several disparate stakeholders, including patients, manufacturers, policymakers, and regulatory agencies-all with competing interests and priorities, leading to confusion, frustration, and ultimately advocacy. In order to explore this issue in detail, this correspondence article first conducts a literature review to describe how the expanded access policy and regulatory environment in the United States has evolved over time and how it currently impacts access to experimental drugs. We then conducted structured web searches to identify patient use of online petitions and social media campaigns aimed at compelling access to experimental drugs. This was carried out in order to characterize the types of communication strategies utilized, the diseases and drugs subject to expanded access petitions, and the prevalent themes associated with this form of "digital" patient advocacy. We find that patients and their families experience mixed results, but still gravitate towards the use of online campaigns out of desperation, lack of reliable information about treatment access options, and in direct response to limitations of the current fragmented structure of expanded access regulation and policy currently in place. In response, we discuss potential policy reforms to improve expanded access processes, including advocating greater transparency for expanded access programs, exploring use of targeted economic incentives for manufacturers, and developing systems to facilitate patient information about existing treatment options. This includes leveraging recent legislative attention to reform expanded access through the CURE Act Provisions contained in the proposed U.S. 21st Century Cures Act. While expanded access may not be the best option for the majority of individuals, terminally ill patients and their families nevertheless deserve better processes, policies, and availability to potentially life-changing information, before they decide to pursue an online campaign in the desperate hope of gaining access to experimental drugs.

Structural kinetic modeling of metabolic networks.

PubMed

Steuer, Ralf; Gross, Thilo; Selbig, Joachim; Blasius, Bernd

2006-08-08

To develop and investigate detailed mathematical models of metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, kinetic modeling is still often severely hampered by inadequate knowledge of the enzyme-kinetic rate laws and their associated parameter values. Here we propose a method that aims to give a quantitative account of the dynamical capabilities of a metabolic system, without requiring any explicit information about the functional form of the rate equations. Our approach is based on constructing a local linear model at each point in parameter space, such that each element of the model is either directly experimentally accessible or amenable to a straightforward biochemical interpretation. This ensemble of local linear models, encompassing all possible explicit kinetic models, then allows for a statistical exploration of the comprehensive parameter space. The method is exemplified on two paradigmatic metabolic systems: the glycolytic pathway of yeast and a realistic-scale representation of the photosynthetic Calvin cycle.

A global fit of the MSSM with GAMBIT

NASA Astrophysics Data System (ADS)

Athron, Peter; Balázs, Csaba; Bringmann, Torsten; Buckley, Andy; Chrząszcz, Marcin; Conrad, Jan; Cornell, Jonathan M.; Dal, Lars A.; Edsjö, Joakim; Farmer, Ben; Jackson, Paul; Krislock, Abram; Kvellestad, Anders; Mahmoudi, Farvah; Martinez, Gregory D.; Putze, Antje; Raklev, Are; Rogan, Christopher; Saavedra, Aldo; Savage, Christopher; Scott, Pat; Serra, Nicola; Weniger, Christoph; White, Martin

2017-12-01

We study the seven-dimensional Minimal Supersymmetric Standard Model (MSSM7) with the new GAMBIT software framework, with all parameters defined at the weak scale. Our analysis significantly extends previous weak-scale, phenomenological MSSM fits, by adding more and newer experimental analyses, improving the accuracy and detail of theoretical predictions, including dominant uncertainties from the Standard Model, the Galactic dark matter halo and the quark content of the nucleon, and employing novel and highly-efficient statistical sampling methods to scan the parameter space. We find regions of the MSSM7 that exhibit co-annihilation of neutralinos with charginos, stops and sbottoms, as well as models that undergo resonant annihilation via both light and heavy Higgs funnels. We find high-likelihood models with light charginos, stops and sbottoms that have the potential to be within the future reach of the LHC. Large parts of our preferred parameter regions will also be accessible to the next generation of direct and indirect dark matter searches, making prospects for discovery in the near future rather good.

Kondo length in bosonic lattices

NASA Astrophysics Data System (ADS)

Giuliano, Domenico; Sodano, Pasquale; Trombettoni, Andrea

2017-09-01

Motivated by the fact that the low-energy properties of the Kondo model can be effectively simulated in spin chains, we study the realization of the effect with bond impurities in ultracold bosonic lattices at half filling. After presenting a discussion of the effective theory and of the mapping of the bosonic chain onto a lattice spin Hamiltonian, we provide estimates for the Kondo length as a function of the parameters of the bosonic model. We point out that the Kondo length can be extracted from the integrated real-space correlation functions, which are experimentally accessible quantities in experiments with cold atoms.

Dark-soliton dynamics in Bose-Einstein condensates at finite temperature

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

Jackson, B.; Proukakis, N. P.; Barenghi, C. F.

2007-05-15

The dynamics of a dark soliton in an elongated Bose-Einstein condensate is studied at finite temperatures. In addition to accurately reproducing all stages of the decay of the soliton observed in the experiment of Burger et al. [Phys. Rev. Lett. 83, 5198 (1999)], our numerical simulations reveal the existence of an experimentally accessible parameter regime for which phase-imprinted dark solitons can execute at least one full axial oscillation prior to their decay. The dependence of the decay time scale on temperature and initial soliton depth is analyzed and the role of interatomic collisions quantified.

Entanglement manipulation via Coulomb interaction in an optomechanical cavity assisted by two-level cold atoms

NASA Astrophysics Data System (ADS)

Wang, Jing; Tian, Xue-Dong; Liu, Yi-Mou; Cui, Cui-Li; Wu, Jin-Hui

2018-06-01

We investigate the stationary entanglement properties in a hybrid system consisting of an optical cavity, a mechanical resonator, a charged object, and an atomic ensemble. Numerical results show that this hybrid system exhibits three kinds of controllable bipartite entanglements in an experimentally accessible parameter regime with the help of the charged object. More importantly, it is viable to enhance on demand each bipartite entanglement at the expense of reducing others by modulating the Coulomb coupling strength. Last but not least, these bipartite entanglements seem more robust against on the environmental temperature for the positive Coulomb interaction.

Benefits of detailed models of muscle activation and mechanics

NASA Technical Reports Server (NTRS)

Lehman, S. L.; Stark, L.

1981-01-01

Recent biophysical and physiological studies identified some of the detailed mechanisms involved in excitation-contraction coupling, muscle contraction, and deactivation. Mathematical models incorporating these mechanisms allow independent estimates of key parameters, direct interplay between basic muscle research and the study of motor control, and realistic model behaviors, some of which are not accessible to previous, simpler, models. The existence of previously unmodeled behaviors has important implications for strategies of motor control and identification of neural signals. New developments in the analysis of differential equations make the more detailed models feasible for simulation in realistic experimental situations.

Laser singular Theta-pinch

NASA Astrophysics Data System (ADS)

Okulov, A. Yu.

2010-10-01

The interaction of the two counter-propagating ultrashort laser pulses with singular wavefronts in the thin slice of the underdense plasma is considered. It is shown that ion-acoustic wave is excited via Brillouin three-wave resonance by corkscrew interference pattern of paraxial singular laser beams. The orbital angular momentum carried by light is transferred to plasma ion-acoustic vortex. The rotation of the density perturbations of electron fluid is the cause of helical current which produces the kilogauss axial quasi-static magnetic field. The exact analytical configurations are presented for an ion-acoustic current field and magnetic induction. The range of experimentally accessible parameters is evaluated.

Nonleaky Population Transfer in a Transmon Qutrit via Largely-Detuned Drivings

NASA Astrophysics Data System (ADS)

Yan, Run-Ying; Feng, Zhi-Bo

2018-06-01

We propose an efficient scheme to implement nonleaky population transfer in a transmon qutrit via largely-detuned drivings. Due to weak level anharmonicity of the transmon system, the remarkable quantum leakages need to be considered in quantum coherent operations. Under the conditions of two-photon resonance and large detunings, the robust population transfer within a qutrit can be implemented via the technique of stimulated Raman adiabatic passage. Based on the accessible parameters, the feasible approach can remove the leakage error effectively, and then provides a potential approach for enhancing the transfer fidelity with transmon-regime artificial atoms experimentally.

Plasma versus Drude Modeling of the Casimir Force: Beyond the Proximity Force Approximation

NASA Astrophysics Data System (ADS)

Hartmann, Michael; Ingold, Gert-Ludwig; Neto, Paulo A. Maia

2017-07-01

We calculate the Casimir force and its gradient between a spherical and a planar gold surface. Significant numerical improvements allow us to extend the range of accessible parameters into the experimental regime. We compare our numerically exact results with those obtained within the proximity force approximation (PFA) employed in the analysis of all Casimir force experiments reported in the literature so far. Special attention is paid to the difference between the Drude model and the dissipationless plasma model at zero frequency. It is found that the correction to PFA is too small to explain the discrepancy between the experimental data and the PFA result based on the Drude model. However, it turns out that for the plasma model, the corrections to PFA lie well outside the experimental bound obtained by probing the variation of the force gradient with the sphere radius [D. E. Krause et al., Phys. Rev. Lett. 98, 050403 (2007), 10.1103/PhysRevLett.98.050403]. The corresponding corrections based on the Drude model are significantly smaller but still in violation of the experimental bound for small distances between plane and sphere.

Dynamical Detection of Topological Phase Transitions in Short-Lived Atomic Systems.

PubMed

Setiawan, F; Sengupta, K; Spielman, I B; Sau, Jay D

2015-11-06

We demonstrate that dynamical probes provide direct means of detecting the topological phase transition (TPT) between conventional and topological phases, which would otherwise be difficult to access because of loss or heating processes. We propose to avoid such heating by rapidly quenching in and out of the short-lived topological phase across the transition that supports gapless excitations. Following the quench, the distribution of excitations in the final conventional phase carries signatures of the TPT. We apply this strategy to study the TPT into a Majorana-carrying topological phase predicted in one-dimensional spin-orbit-coupled Fermi gases with attractive interactions. The resulting spin-resolved momentum distribution, computed by self-consistently solving the time-dependent Bogoliubov-de Gennes equations, exhibits Kibble-Zurek scaling and Stückelberg oscillations characteristic of the TPT. We discuss parameter regimes where the TPT is experimentally accessible.

Dynamical Detection of Topological Phase Transitions in Short-Lived Atomic Systems

NASA Astrophysics Data System (ADS)

Setiawan, F.; Sengupta, K.; Spielman, I. B.; Sau, Jay D.

2015-11-01

We demonstrate that dynamical probes provide direct means of detecting the topological phase transition (TPT) between conventional and topological phases, which would otherwise be difficult to access because of loss or heating processes. We propose to avoid such heating by rapidly quenching in and out of the short-lived topological phase across the transition that supports gapless excitations. Following the quench, the distribution of excitations in the final conventional phase carries signatures of the TPT. We apply this strategy to study the TPT into a Majorana-carrying topological phase predicted in one-dimensional spin-orbit-coupled Fermi gases with attractive interactions. The resulting spin-resolved momentum distribution, computed by self-consistently solving the time-dependent Bogoliubov-de Gennes equations, exhibits Kibble-Zurek scaling and Stückelberg oscillations characteristic of the TPT. We discuss parameter regimes where the TPT is experimentally accessible.

Cellular-enabled water quality measurements

NASA Astrophysics Data System (ADS)

Zhao, Y.; Kerkez, B.

2013-12-01

While the past decade has seen significant improvements in our ability to measure nutrients and other water quality parameters, the use of these sensors has yet to gain traction due to their costprohibitive nature and deployment expertise required on the part of researchers. Furthermore, an extra burden is incurred when real-time data access becomes an experimental requirement. We present an open-source hardware design to facilitate the real-time, low-cost, and robust measurements of water quality across large urbanized areas. Our hardware platform interfaces an embedded, vastly configurable, high-precision, ultra-low power measurement system, with a low-power cellular module. Each sensor station is configured with an IP address, permitting reliable streaming of sensor data to off-site locations as measurements are made. We discuss the role of high-quality hardware components during extreme event scenarios, and present preliminary performance metrics that validate the ability of the platform to provide streaming access to sensor measurements.

Performance Optimization of Marine Science and Numerical Modeling on HPC Cluster

PubMed Central

Yang, Dongdong; Yang, Hailong; Wang, Luming; Zhou, Yucong; Zhang, Zhiyuan; Wang, Rui; Liu, Yi

2017-01-01

Marine science and numerical modeling (MASNUM) is widely used in forecasting ocean wave movement, through simulating the variation tendency of the ocean wave. Although efforts have been devoted to improve the performance of MASNUM from various aspects by existing work, there is still large space unexplored for further performance improvement. In this paper, we aim at improving the performance of propagation solver and data access during the simulation, in addition to the efficiency of output I/O and load balance. Our optimizations include several effective techniques such as the algorithm redesign, load distribution optimization, parallel I/O and data access optimization. The experimental results demonstrate that our approach achieves higher performance compared to the state-of-the-art work, about 3.5x speedup without degrading the prediction accuracy. In addition, the parameter sensitivity analysis shows our optimizations are effective under various topography resolutions and output frequencies. PMID:28045972

Accurate modeling of defects in graphene transport calculations

NASA Astrophysics Data System (ADS)

Linhart, Lukas; Burgdörfer, Joachim; Libisch, Florian

2018-01-01

We present an approach for embedding defect structures modeled by density functional theory into large-scale tight-binding simulations. We extract local tight-binding parameters for the vicinity of the defect site using Wannier functions. In the transition region between the bulk lattice and the defect the tight-binding parameters are continuously adjusted to approach the bulk limit far away from the defect. This embedding approach allows for an accurate high-level treatment of the defect orbitals using as many as ten nearest neighbors while keeping a small number of nearest neighbors in the bulk to render the overall computational cost reasonable. As an example of our approach, we consider an extended graphene lattice decorated with Stone-Wales defects, flower defects, double vacancies, or silicon substitutes. We predict distinct scattering patterns mirroring the defect symmetries and magnitude that should be experimentally accessible.

Promoter architecture dictates cell-to-cell variability in gene expression.

PubMed

Jones, Daniel L; Brewster, Robert C; Phillips, Rob

2014-12-19

Variability in gene expression among genetically identical cells has emerged as a central preoccupation in the study of gene regulation; however, a divide exists between the predictions of molecular models of prokaryotic transcriptional regulation and genome-wide experimental studies suggesting that this variability is indifferent to the underlying regulatory architecture. We constructed a set of promoters in Escherichia coli in which promoter strength, transcription factor binding strength, and transcription factor copy numbers are systematically varied, and used messenger RNA (mRNA) fluorescence in situ hybridization to observe how these changes affected variability in gene expression. Our parameter-free models predicted the observed variability; hence, the molecular details of transcription dictate variability in mRNA expression, and transcriptional noise is specifically tunable and thus represents an evolutionarily accessible phenotypic parameter. Copyright © 2014, American Association for the Advancement of Science.

Scalable randomized benchmarking of non-Clifford gates

NASA Astrophysics Data System (ADS)

Cross, Andrew; Magesan, Easwar; Bishop, Lev; Smolin, John; Gambetta, Jay

Randomized benchmarking is a widely used experimental technique to characterize the average error of quantum operations. Benchmarking procedures that scale to enable characterization of n-qubit circuits rely on efficient procedures for manipulating those circuits and, as such, have been limited to subgroups of the Clifford group. However, universal quantum computers require additional, non-Clifford gates to approximate arbitrary unitary transformations. We define a scalable randomized benchmarking procedure over n-qubit unitary matrices that correspond to protected non-Clifford gates for a class of stabilizer codes. We present efficient methods for representing and composing group elements, sampling them uniformly, and synthesizing corresponding poly (n) -sized circuits. The procedure provides experimental access to two independent parameters that together characterize the average gate fidelity of a group element. We acknowledge support from ARO under Contract W911NF-14-1-0124.

Quantum fluctuations in anisotropic triangular lattices with ferromagnetic and antiferromagnetic exchange

NASA Astrophysics Data System (ADS)

Schmidt, Burkhard; Thalmeier, Peter

2014-05-01

The Heisenberg model on a triangular lattice is a prime example of a geometrically frustrated spin system. However most experimentally accessible compounds have spatially anisotropic exchange interactions. As a function of this anisotropy, ground states with different magnetic properties can be realized. Motivated by recent experimental findings on Cs2CuCl4-xBrx, we discuss the full phase diagram of the anisotropic model with two exchange constants J1 and J2, including possible ferromagnetic exchange. Furthermore a comparison with the related square lattice model is carried out. We discuss the zero-temperature phase diagram, ordering vector, ground-state energy, and ordered moment on a classical level and investigate the effect of quantum fluctuations within the framework of spin-wave theory. The field dependence of the ordered moment is shown to be nonmonotonic with field and control parameter.

The interaction of intense subpicosecond laser pulses with underdense plasmas

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

Coverdale, Christine Ann

1995-05-11

Laser-plasma interactions have been of interest for many years not only from a basic physics standpoint, but also for their relevance to numerous applications. Advances in laser technology in recent years have resulted in compact laser systems capable of generating (psec), 10 16 W/cm 2 laser pulses. These lasers have provided a new regime in which to study laser-plasma interactions, a regime characterized by L plasma ≥ 2L Rayleigh > cτ. The goal of this dissertation is to experimentally characterize the interaction of a short pulse, high intensity laser with an underdense plasma (n o ≤ 0.05n cr). Specifically, themore » parametric instability known as stimulated Raman scatter (SRS) is investigated to determine its behavior when driven by a short, intense laser pulse. Both the forward Raman scatter instability and backscattered Raman instability are studied. The coupled partial differential equations which describe the growth of SRS are reviewed and solved for typical experimental laser and plasma parameters. This solution shows the growth of the waves (electron plasma and scattered light) generated via stimulated Raman scatter. The dispersion relation is also derived and solved for experimentally accessible parameters. The solution of the dispersion relation is used to predict where (in k-space) and at what frequency (in ω-space) the instability will grow. Both the nonrelativistic and relativistic regimes of the instability are considered.« less

A gyrokinetic perspective on the JET-ILW pedestal

NASA Astrophysics Data System (ADS)

Hatch, D. R.; Kotschenreuther, M.; Mahajan, S.; Valanju, P.; Liu, X.

2017-03-01

JET has been unable to recover historical confinement levels when operating with an ITER-like wall (ILW) due largely to the inaccessibility of high pedestal temperatures. Finding a path to overcome this challenge is of utmost importance for both a prospective JET DT campaign and for future ITER operation. Gyrokinetic simulations (using the Gene code) quantitatively capture experimental transport levels for a representative experimental discharge and qualitatively recover the major experimental trends. Microtearing turbulence is a major transport mechanisms for the low-temperature pedestals characteristic of unseeded JET-ILW discharges. At higher temperatures and/or lower {ρ\\ast} , we identify electrostatic ITG transport of a type that is strongly shear-suppressed on smaller machines. Consistent with observations, this transport mechanism is strongly reduced by the presence of a low-Z impurity (e.g. carbon or nitrogen at the level of {{Z}\\text{eff}}∼ 2 ), recovering the accessibility of high pedestal temperatures. Notably, simulations based on dimensionless {ρ\\ast} scans recover historical scaling behavior except in the unique JET-ILW parameter regime where ITG turbulence becomes important. Our simulations also elucidate the observed degradation of confinement caused by gas puffing, emphasizing the important role of the density pedestal structure. This study maps out important regions of parameter space, providing insights that may point to optimal physical regimes that can enable the recovery of high pedestal temperatures on JET.

Imaging on a Shoestring: Cost-Effective Technologies for Probing Vadose Zone Transport Processes

NASA Astrophysics Data System (ADS)

Corkhill, C.; Bridge, J. W.; Barns, G.; Fraser, R.; Romero-Gonzalez, M.; Wilson, R.; Banwart, S.

2010-12-01

Key barriers to the widespread uptake of imaging technology for high spatial resolution monitoring of porous media systems are cost and accessibility. X-ray tomography, magnetic resonance imaging (MRI), gamma and neutron radiography require highly specialised equipment, controlled laboratory environments and/or access to large synchrotron facilities. Here we present results from visible light, fluorescence and autoradiographic imaging techniques developed at low cost and applied in standard analytical laboratories, adapted where necessary at minimal capital expense. UV-visible time lapse fluorescence imaging (UV-vis TLFI) in a transparent thin bed chamber enabled microspheres labelled with fluorescent dye and a conservative fluorophore solute (disodium fluorescein) to be measured simultaneously in saturated, partially-saturated and actively draining quartz sand to elucidate empirical values for colloid transport and deposition parameters distributed throughout the flow field, independently of theoretical approximations. Key results include the first experimental quantification of the effects of ionic strength and air-water interfacial area on colloid deposition above a capillary fringe, and the first direct observations of particle mobilisation and redeposition by moving saturation gradients during drainage. UV-vis imaging was also used to study biodegradation and reactive transport in a variety of saturated conditions, applying fluorescence as a probe for oxygen and nitrate concentration gradients, pH, solute transport parameters, reduction of uranium, and mapping of two-dimensional flow fields around a model dipole flow borehole system to validate numerical models. Costs are low: LED excitation sources (< US 50), flow chambers (US 200) and detectors (although a complete scientific-grade CCD set-up costs around US$ 8000, robust datasets can be obtained using a commercial digital SLR camera) mean that set-ups can be flexible to meet changing experimental requirements. The critical limitations of UV-vis fluorescence imaging are the need for reliable fluorescent probes suited to the experimental objective, and the reliance on thin-bed (2D) transparent porous media. Autoradiographic techniques address some of these limitations permit imaging of key biogeochemical processes in opaque media using radioactive probes, without the need for specialised radiation sources. We present initial calibration data for the use of autoradiography to monitor transport parameters for radionuclides (99-technetium), and a novel application of a radioactive salt tracer as a probe for pore water content, in model porous media systems.

Pd (II) complexes of bidentate chalcone ligands: Synthesis, spectral, thermal, antitumor, antioxidant, antimicrobial, DFT and SAR studies

NASA Astrophysics Data System (ADS)

Gaber, Mohamed; Awad, Mohamed K.; Atlam, Faten M.

2018-05-01

The ligation behavior of two chalcone ligands namely, (E)-3-(4-chlorophenyl)-1-(pyridin-2-yl)prop-2-en-1-one (L1) and (E)-3-(4-methoxyphenyl)-1-(pyridin-2-yl)prop-2-en-1-one (L2), towards the Pd(II) ion is determined. The structures of the complexes are elucidated by elemental analysis, spectral methods (IR, electronic and NMR spectra) as well as the conductance measurements and thermal analysis. The metal complexes exhibit a square planar geometrical arrangement. The kinetic and thermodynamic parameters for some selected decomposition steps have been calculated. The antimicrobial, antioxidant and anticancer activities of the chalcones and their Pd(II) complexes have been evaluated. Molecular orbital computations are performed using DFT at B3LYP level with 6-31 + G(d) and LANL2DZ basis sets to access reliable results to the experimental values. The calculations are performed to obtain the optimized molecular geometry, charge density distribution, extent of distortion from regular geometry. Thermodynamic parameters for the investigated compounds are also studied. The calculations confirm that the investigated complexes have square planner geometry, which is in a good agreement with the experimental observation.

Dirac Cellular Automaton from Split-step Quantum Walk

PubMed Central

Mallick, Arindam; Chandrashekar, C. M.

2016-01-01

Simulations of one quantum system by an other has an implication in realization of quantum machine that can imitate any quantum system and solve problems that are not accessible to classical computers. One of the approach to engineer quantum simulations is to discretize the space-time degree of freedom in quantum dynamics and define the quantum cellular automata (QCA), a local unitary update rule on a lattice. Different models of QCA are constructed using set of conditions which are not unique and are not always in implementable configuration on any other system. Dirac Cellular Automata (DCA) is one such model constructed for Dirac Hamiltonian (DH) in free quantum field theory. Here, starting from a split-step discrete-time quantum walk (QW) which is uniquely defined for experimental implementation, we recover the DCA along with all the fine oscillations in position space and bridge the missing connection between DH-DCA-QW. We will present the contribution of the parameters resulting in the fine oscillations on the Zitterbewegung frequency and entanglement. The tuneability of the evolution parameters demonstrated in experimental implementation of QW will establish it as an efficient tool to design quantum simulator and approach quantum field theory from principles of quantum information theory. PMID:27184159

Fragmentation modeling of a resin bonded sand

NASA Astrophysics Data System (ADS)

Hilth, William; Ryckelynck, David

2017-06-01

Cemented sands exhibit a complex mechanical behavior that can lead to sophisticated models, with numerous parameters without real physical meaning. However, using a rather simple generalized critical state bonded soil model has proven to be a relevant compromise between an easy calibration and good results. The constitutive model formulation considers a non-associated elasto-plastic formulation within the critical state framework. The calibration procedure, using standard laboratory tests, is complemented by the study of an uniaxial compression test observed by tomography. Using finite elements simulations, this test is simulated considering a non-homogeneous 3D media. The tomography of compression sample gives access to 3D displacement fields by using image correlation techniques. Unfortunately these fields have missing experimental data because of the low resolution of correlations for low displacement magnitudes. We propose a recovery method that reconstructs 3D full displacement fields and 2D boundary displacement fields. These fields are mandatory for the calibration of the constitutive parameters by using 3D finite element simulations. The proposed recovery technique is based on a singular value decomposition of available experimental data. This calibration protocol enables an accurate prediction of the fragmentation of the specimen.

General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations

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

Liu, Qing; Shi, Chaowei; Yu, Lu

Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of {sup 15}N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S{sup 2}) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in amore » defined hydrated box at neutral pH were conducted and the general order parameters (S{sup 2}) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S{sup 2} values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S{sup 2} parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S{sup 2} calculated from the experimental NMR relaxation measurements, in a site-specific manner. - Highlights: • Correlation analysis between NMR relaxation measurements and MD simulations. • General order parameter (S{sup 2}) as common reference between the two methods. • Different protein dynamics with different Histidine charge states in neutral pH. • Different protein dynamics with different water models.« less

Looking for the WIMP next door

NASA Astrophysics Data System (ADS)

Evans, Jared A.; Gori, Stefania; Shelton, Jessie

2018-02-01

We comprehensively study experimental constraints and prospects for a class of minimal hidden sector dark matter (DM) models, highlighting how the cosmological history of these models informs the experimental signals. We study simple `secluded' models, where the DM freezes out into unstable dark mediator states, and consider the minimal cosmic history of this dark sector, where coupling of the dark mediator to the SM was sufficient to keep the two sectors in thermal equilibrium at early times. In the well-motivated case where the dark mediators couple to the Standard Model (SM) via renormalizable interactions, the requirement of thermal equilibrium provides a minimal, UV-insensitive, and predictive cosmology for hidden sector dark matter. We call DM that freezes out of a dark radiation bath in thermal equilibrium with the SM a WIMP next door, and demonstrate that the parameter space for such WIMPs next door is sharply defined, bounded, and in large part potentially accessible. This parameter space, and the corresponding signals, depend on the leading interaction between the SM and the dark mediator; we establish it for both Higgs and vector portal interactions. In particular, there is a cosmological lower bound on the portal coupling strength necessary to thermalize the two sectors in the early universe. We determine this thermalization floor as a function of equilibration temperature for the first time. We demonstrate that direct detection experiments are currently probing this cosmological lower bound in some regions of parameter space, while indirect detection signals and terrestrial searches for the mediator cut further into the viable parameter space. We present regions of interest for both direct detection and dark mediator searches, including motivated parameter space for the direct detection of sub-GeV DM.

Access to Experimental Cancer Drugs

Cancer.gov

An experimental drug has been tested in the lab and with animals and approved for testing in people by the FDA, but can’t yet be advertised, sold, or prescribed. Experimental drugs may be available through clinical trials or expanded access programs - learn more about these programs and how to talk to your doctor.

Invited Review Article: Pump-probe microscopy.

PubMed

Fischer, Martin C; Wilson, Jesse W; Robles, Francisco E; Warren, Warren S

2016-03-01

Multiphoton microscopy has rapidly gained popularity in biomedical imaging and materials science because of its ability to provide three-dimensional images at high spatial and temporal resolution even in optically scattering environments. Currently the majority of commercial and home-built devices are based on two-photon fluorescence and harmonic generation contrast. These two contrast mechanisms are relatively easy to measure but can access only a limited range of endogenous targets. Recent developments in fast laser pulse generation, pulse shaping, and detection technology have made accessible a wide range of optical contrasts that utilize multiple pulses of different colors. Molecular excitation with multiple pulses offers a large number of adjustable parameters. For example, in two-pulse pump-probe microscopy, one can vary the wavelength of each excitation pulse, the detection wavelength, the timing between the excitation pulses, and the detection gating window after excitation. Such a large parameter space can provide much greater molecular specificity than existing single-color techniques and allow for structural and functional imaging without the need for exogenous dyes and labels, which might interfere with the system under study. In this review, we provide a tutorial overview, covering principles of pump-probe microscopy and experimental setup, challenges associated with signal detection and data processing, and an overview of applications.

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

Fischer, Martin C., E-mail: Martin.Fischer@duke.edu; Wilson, Jesse W.; Robles, Francisco E.

Multiphoton microscopy has rapidly gained popularity in biomedical imaging and materials science because of its ability to provide three-dimensional images at high spatial and temporal resolution even in optically scattering environments. Currently the majority of commercial and home-built devices are based on two-photon fluorescence and harmonic generation contrast. These two contrast mechanisms are relatively easy to measure but can access only a limited range of endogenous targets. Recent developments in fast laser pulse generation, pulse shaping, and detection technology have made accessible a wide range of optical contrasts that utilize multiple pulses of different colors. Molecular excitation with multiple pulsesmore » offers a large number of adjustable parameters. For example, in two-pulse pump-probe microscopy, one can vary the wavelength of each excitation pulse, the detection wavelength, the timing between the excitation pulses, and the detection gating window after excitation. Such a large parameter space can provide much greater molecular specificity than existing single-color techniques and allow for structural and functional imaging without the need for exogenous dyes and labels, which might interfere with the system under study. In this review, we provide a tutorial overview, covering principles of pump-probe microscopy and experimental setup, challenges associated with signal detection and data processing, and an overview of applications.« less

Invited Review Article: Pump-probe microscopy

PubMed Central

Wilson, Jesse W.; Robles, Francisco E.; Warren, Warren S.

2016-01-01

Multiphoton microscopy has rapidly gained popularity in biomedical imaging and materials science because of its ability to provide three-dimensional images at high spatial and temporal resolution even in optically scattering environments. Currently the majority of commercial and home-built devices are based on two-photon fluorescence and harmonic generation contrast. These two contrast mechanisms are relatively easy to measure but can access only a limited range of endogenous targets. Recent developments in fast laser pulse generation, pulse shaping, and detection technology have made accessible a wide range of optical contrasts that utilize multiple pulses of different colors. Molecular excitation with multiple pulses offers a large number of adjustable parameters. For example, in two-pulse pump-probe microscopy, one can vary the wavelength of each excitation pulse, the detection wavelength, the timing between the excitation pulses, and the detection gating window after excitation. Such a large parameter space can provide much greater molecular specificity than existing single-color techniques and allow for structural and functional imaging without the need for exogenous dyes and labels, which might interfere with the system under study. In this review, we provide a tutorial overview, covering principles of pump-probe microscopy and experimental setup, challenges associated with signal detection and data processing, and an overview of applications. PMID:27036751

The Role of Genome Accessibility in Transcription Factor Binding in Bacteria.

PubMed

Gomes, Antonio L C; Wang, Harris H

2016-04-01

ChIP-seq enables genome-scale identification of regulatory regions that govern gene expression. However, the biological insights generated from ChIP-seq analysis have been limited to predictions of binding sites and cooperative interactions. Furthermore, ChIP-seq data often poorly correlate with in vitro measurements or predicted motifs, highlighting that binding affinity alone is insufficient to explain transcription factor (TF)-binding in vivo. One possibility is that binding sites are not equally accessible across the genome. A more comprehensive biophysical representation of TF-binding is required to improve our ability to understand, predict, and alter gene expression. Here, we show that genome accessibility is a key parameter that impacts TF-binding in bacteria. We developed a thermodynamic model that parameterizes ChIP-seq coverage in terms of genome accessibility and binding affinity. The role of genome accessibility is validated using a large-scale ChIP-seq dataset of the M. tuberculosis regulatory network. We find that accounting for genome accessibility led to a model that explains 63% of the ChIP-seq profile variance, while a model based in motif score alone explains only 35% of the variance. Moreover, our framework enables de novo ChIP-seq peak prediction and is useful for inferring TF-binding peaks in new experimental conditions by reducing the need for additional experiments. We observe that the genome is more accessible in intergenic regions, and that increased accessibility is positively correlated with gene expression and anti-correlated with distance to the origin of replication. Our biophysically motivated model provides a more comprehensive description of TF-binding in vivo from first principles towards a better representation of gene regulation in silico, with promising applications in systems biology.

Effects of Filtering on Experimental Blast Overpressure Measurements.

PubMed

Alphonse, Vanessa D; Kemper, Andrew R; Duma, Stefan M

2015-01-01

When access to live-fire test facilities is limited, experimental studies of blast-related injuries necessitate the use of a shock tube or Advanced Blast Simulator (ABS) to mimic free-field blast overpressure. However, modeling blast overpressure in a laboratory setting potentially introduces experimental artifacts in measured responses. Due to the high sampling rates required to capture a blast overpressure event, proximity to alternating current (AC-powered electronics) and poorly strain-relieved or unshielded wires can result in artifacts in the recorded overpressure trace. Data in this study were collected for tests conducted on an empty ABS (“Empty Tube”) using high frequency pressure sensors specifically designed for blast loading rates (n=5). Additionally, intraocular overpressure data (“IOP”) were collected for porcine eyes potted inside synthetic orbits located inside the ABS using an unshielded miniature pressure sensor (n=3). All tests were conducted at a 30 psi static overpressure level. A 4th order phaseless low pass Butterworth software filter was applied to the data. Various cutoff frequencies were examined to determine if the raw shock wave parameters values could be preserved while eliminating noise and artifacts. A Fast Fourier Transform (FFT) was applied to each test to examine the frequency spectra of the raw and filtered signals. Shock wave parameters (time of arrival, peak overpressure, positive duration, and positive impulse) were quantified using a custom MATLAB® script. Lower cutoff frequencies attenuated the raw signal, effectively decreasing the peak overpressure and increasing the positive duration. Rise time was not preserved the filtered data. A CFC 6000 filter preserved the remaining shock wave parameters within ±2.5% of the average raw values for the Empty Tube test data. A CFC 7000 filter removed experimental high-frequency artifacts and preserved the remaining shock wave parameters within ±2.5% of the average raw values for test IOP test data. Though the region of interest of the signals examined in the current study did not contain extremely high frequency content, it is possible that live-fire testing may produce shock waves with higher frequency content. While post-processing filtering can remove experimental artifacts, special care should be taken to minimize or eliminate the possibility of recording these artifacts in the first place.

A Microfluidics and Agent-Based Modeling Framework for Investigating Spatial Organization in Bacterial Colonies: The Case of Pseudomonas Aeruginosa and H1-Type VI Secretion Interactions

DOE PAGES

Wilmoth, Jared L.; Doak, Peter W.; Timm, Andrea; ...

2018-02-06

The factors leading to changes in the organization of microbial assemblages at fine spatial scales are not well characterized or understood. However, they are expected to guide the succession of community development and function toward specific outcomes that could impact human health and the environment. In this study, we put forward a combined experimental and agent-based modeling framework and use it to interpret unique spatial organization patterns of H1-Type VI secretion system (T6SS) mutants of P. aeruginosa under spatial confinement. We find that key parameters, such as T6SS-mediated cell contact and lysis, spatial localization, relative species abundance, cell density andmore » local concentrations of growth substrates and metabolites are influenced by spatial confinement. The model, written in the accessible programming language NetLogo, can be adapted to a variety of biological systems of interest and used to simulate experiments across a broad parameter space. It was implemented and run in a high-throughput mode by deploying it across multiple CPUs, with each simulation representing an individual well within a high-throughput microwell array experimental platform. The microfluidics and agent-based modeling framework we present in this paper provides an effective means by which to connect experimental studies in microbiology to model development. The work demonstrates progress in coupling experimental results to simulation while also highlighting potential sources of discrepancies between real-world experiments and idealized models.« less

A Microfluidics and Agent-Based Modeling Framework for Investigating Spatial Organization in Bacterial Colonies: The Case of Pseudomonas Aeruginosa and H1-Type VI Secretion Interactions

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

Wilmoth, Jared L.; Doak, Peter W.; Timm, Andrea

The factors leading to changes in the organization of microbial assemblages at fine spatial scales are not well characterized or understood. However, they are expected to guide the succession of community development and function toward specific outcomes that could impact human health and the environment. In this study, we put forward a combined experimental and agent-based modeling framework and use it to interpret unique spatial organization patterns of H1-Type VI secretion system (T6SS) mutants of P. aeruginosa under spatial confinement. We find that key parameters, such as T6SS-mediated cell contact and lysis, spatial localization, relative species abundance, cell density andmore » local concentrations of growth substrates and metabolites are influenced by spatial confinement. The model, written in the accessible programming language NetLogo, can be adapted to a variety of biological systems of interest and used to simulate experiments across a broad parameter space. It was implemented and run in a high-throughput mode by deploying it across multiple CPUs, with each simulation representing an individual well within a high-throughput microwell array experimental platform. The microfluidics and agent-based modeling framework we present in this paper provides an effective means by which to connect experimental studies in microbiology to model development. The work demonstrates progress in coupling experimental results to simulation while also highlighting potential sources of discrepancies between real-world experiments and idealized models.« less

Microscopic insights into the NMR relaxation based protein conformational entropy meter

PubMed Central

Kasinath, Vignesh; Sharp, Kim A.; Wand, A. Joshua

2013-01-01

Conformational entropy is a potentially important thermodynamic parameter contributing to protein function. Quantitative measures of conformational entropy are necessary for an understanding of its role but have been difficult to obtain. An empirical method that utilizes changes in conformational dynamics as a proxy for changes in conformational entropy has recently been introduced. Here we probe the microscopic origins of the link between conformational dynamics and conformational entropy using molecular dynamics simulations. Simulation of seven pro! teins gave an excellent correlation with measures of side-chain motion derived from NMR relaxation. The simulations show that the motion of methyl-bearing side-chains are sufficiently coupled to that of other side chains to serve as excellent reporters of the overall side-chain conformational entropy. These results tend to validate the use of experimentally accessible measures of methyl motion - the NMR-derived generalized order parameters - as a proxy from which to derive changes in protein conformational entropy. PMID:24007504

Particle Image Velocimetry During Injection Molding

NASA Astrophysics Data System (ADS)

Bress, Thomas; Dowling, David

2012-11-01

Injection molding involves the unsteady non-isothermal flow of a non-Newtonian polymer melt. An optical-access mold has been used to perform particle image velocimetry (PIV) on molten polystyrene during injection molding. Velocimetry data of the mold-filling flow will be presented. Statistical assessments of the velocimetry data and scaled residuals of the continuity equation suggest that PIV can be conducted in molten plastics with an uncertainty of +/-2 percent. Simulations are often used to model polymer flow during injection molding to design molds and select processing parameters but it is difficult to determine the accuracy of these simulations due to a lack of in-mold velocimetry and melt-front progression data. Moldflow was used to simulate the filling of the optical-access mold, and these simulated results are compared to the appropriately-averaged time-varying velocity field measurements. Simulated results for melt-front progression are also compared with the experimentally observed flow fronts. The ratio of the experimentally measured average velocity magnitudes to the simulation magnitudes was found on average to be 0.99 with a standard deviation of 0.25, and the difference in velocity orientations was found to be 0.9 degree with a standard deviation of 3.2 degrees. formerly at the University of Michigan.

Noncritical generation of nonclassical frequency combs via spontaneous rotational symmetry breaking

NASA Astrophysics Data System (ADS)

Navarrete-Benlloch, Carlos; Patera, Giuseppe; de Valcárcel, Germán J.

2017-10-01

Synchronously pumped optical parametric oscillators (SPOPOs) are optical cavities driven by mode-locked lasers, and containing a nonlinear crystal capable of down-converting a frequency comb to lower frequencies. SPOPOs have received a lot of attention lately because their intrinsic multimode nature makes them compact sources of quantum correlated light with promising applications in modern quantum information technologies. In this work we show that SPOPOs are also capable of accessing the challenging and interesting regime where spontaneous symmetry breaking confers strong nonclassical properties to the emitted light, which has eluded experimental observation so far. Apart from opening the possibility of studying experimentally this elusive regime of dissipative phase transitions, our predictions will have a practical impact, since we show that spontaneous symmetry breaking provides a specific spatiotemporal mode with large quadrature squeezing for any value of the system parameters, turning SPOPOs into robust sources of highly nonclassical light above threshold.

Enhanced nonlinear interactions in quantum optomechanics via mechanical amplification

PubMed Central

Lemonde, Marc-Antoine; Didier, Nicolas; Clerk, Aashish A.

2016-01-01

The quantum nonlinear regime of optomechanics is reached when nonlinear effects of the radiation pressure interaction are observed at the single-photon level. This requires couplings larger than the mechanical frequency and cavity-damping rate, and is difficult to achieve experimentally. Here we show how to exponentially enhance the single-photon optomechanical coupling strength using only additional linear resources. Our method is based on using a large-amplitude, strongly detuned mechanical parametric drive to amplify mechanical zero-point fluctuations and hence enhance the radiation pressure interaction. It has the further benefit of allowing time-dependent control, enabling pulsed schemes. For a two-cavity optomechanical set-up, we show that our scheme generates photon blockade for experimentally accessible parameters, and even makes the production of photonic states with negative Wigner functions possible. We discuss how our method is an example of a more general strategy for enhancing boson-mediated two-particle interactions and nonlinearities. PMID:27108814

Overview and recent progress of the Magnetized Shock Experiment (MSX)

NASA Astrophysics Data System (ADS)

Weber, T. E.; Intrator, T. P.; Smith, R. J.; Hutchinson, T. M.; Boguski, J. C.; Sears, J. A.; Swan, H. O.; Gao, K. W.; Chapdelaine, L. J.; Winske, D.; Dunn, J. P.

2013-10-01

The Magnetized Shock Experiment (MSX) has been constructed to study the physics of super-Alfvènic, supercritical, magnetized shocks. Exhibiting transitional length and time scales much smaller than can be produced through collisional processes, these shocks are observed to create non-thermal distributions, amplify magnetic fields, and accelerate particles to relativistic velocities. Shocks are produced through the acceleration and subsequent stagnation of Field Reversed Configuration (FRC) plasmoids against a high-flux magnetic mirror with a conducting boundary or a plasma target with embedded field. Adjustable shock velocity, density, and magnetic geometry (B parallel, perpendicular, or oblique to k) provide unique access to a wide range of dimensionless parameters relevant to astrophysical shocks. Information regarding the experimental configuration, diagnostics suite, recent simulations, experimental results, and physics goals will be presented. This work is supported by DOE OFES and NNSA under LANS contract DE-AC52-06NA25369 Approved for Public Release: LA-UR-13-24859.

Experimental determination of spin-dependent electron density by joint refinement of X-ray and polarized neutron diffraction data.

PubMed

Deutsch, Maxime; Claiser, Nicolas; Pillet, Sébastien; Chumakov, Yurii; Becker, Pierre; Gillet, Jean Michel; Gillon, Béatrice; Lecomte, Claude; Souhassou, Mohamed

2012-11-01

New crystallographic tools were developed to access a more precise description of the spin-dependent electron density of magnetic crystals. The method combines experimental information coming from high-resolution X-ray diffraction (XRD) and polarized neutron diffraction (PND) in a unified model. A new algorithm that allows for a simultaneous refinement of the charge- and spin-density parameters against XRD and PND data is described. The resulting software MOLLYNX is based on the well known Hansen-Coppens multipolar model, and makes it possible to differentiate the electron spins. This algorithm is validated and demonstrated with a molecular crystal formed by a bimetallic chain, MnCu(pba)(H(2)O)(3)·2H(2)O, for which XRD and PND data are available. The joint refinement provides a more detailed description of the spin density than the refinement from PND data alone.

Generalized polarizabilities of the nucleon in baryon chiral perturbation theory

NASA Astrophysics Data System (ADS)

Lensky, Vadim; Pascalutsa, Vladimir; Vanderhaeghen, Marc

2017-02-01

The nucleon generalized polarizabilities (GPs), probed in virtual Compton scattering (VCS), describe the spatial distribution of the polarization density in a nucleon. They are accessed experimentally via the process of electron-proton bremsstrahlung (ep→ epγ ) at electron-beam facilities, such as MIT-Bates, CEBAF (Jefferson Lab), and MAMI (Mainz). We present the calculation of the nucleon GPs and VCS observables at next-to-leading order in baryon chiral perturbation theory (Bχ PT), and confront the results with the empirical information. At this order our results are predictions, in the sense that all the parameters are well known from elsewhere. Within the relatively large uncertainties of our calculation we find good agreement with the experimental observations of VCS and the empirical extractions of the GPs. We find large discrepancies with previous chiral calculations - all done in heavy-baryon χ PT (HBχ PT) - and discuss the differences between Bχ PT and HBχ PT responsible for these discrepancies.

On the Measurement of Power Law Creep Parameters from Instrumented Indentation

NASA Astrophysics Data System (ADS)

Sudharshan Phani, P.; Oliver, W. C.; Pharr, G. M.

2017-11-01

Recently the measurement of the creep response of materials at small scales has received renewed interest largely because the equipment required to perform high-temperature nanomechanical testing has become available to an increasing number of researchers. Despite that increased access, there remain several significant experimental and modeling challenges in small-scale mechanical testing at elevated temperatures that are as yet unresolved. In this regard, relating the creep response observed with high-temperature instrumented indentation experiments to macroscopic uniaxial creep response is of great practical value. In this review, we present an overview of various methods currently being used to measure creep with instrumented indentation, with a focus on geometrically self-similar indenters, and their relative merits and demerits from an experimental perspective. A comparison of the various methods to use those instrumented indentation results to predict the uniaxial power law creep response of a wide range of materials will be presented to assess their validity.

Relative Fluid Novelty Differentially Alters the Time Course of Limited-Access Ethanol and Water Intake in Selectively Bred High Alcohol Preferring Mice

PubMed Central

Linsenbardt, David N.; Boehm, Stephen L.

2015-01-01

Background The influence of previous alcohol (ethanol) drinking experience on increasing the rate and amount of future ethanol consumption might be a genetically-regulated phenomenon critical to the development and maintenance of repeated excessive ethanol abuse. We have recently found evidence supporting this view, wherein inbred C57BL/6J (B6) mice develop progressive increases in the rate of binge-ethanol consumption over repeated Drinking-in-the-Dark (DID) ethanol access sessions (i.e. ‘front-loading’). The primary goal of the present study was to evaluate identical parameters in High Alcohol Preferring (HAP) mice to determine if similar temporal alterations in limited-access ethanol drinking develop in a population selected for high ethanol preference/intake under continuous (24hr) access conditions. Methods Using specialized volumetric drinking devices, HAP mice received 14 daily 2 hour DID ethanol or water access sessions. A subset of these mice was then given one day access to the opposite assigned fluid on day 15. Home cage locomotor activity was recorded concomitantly on each day of these studies. The possibility of behavioral/metabolic tolerance was evaluated on day 16 using experimenter administered ethanol. Results The amount of ethanol consumed within the first 15 minutes of access increased markedly over days. However, in contrast to previous observations in B6 mice, ethanol front-loading was also observed on day 15 in mice that only had previous DID experience with water. Furthermore, a decrease in the amount of water consumed within the first 15 minutes of access compared to animals given repeated water access was observed on day 15 in mice with 14 previous days of ethanol access. Conclusions These data further illustrate the complexity and importance of the temporal aspects of limited-access ethanol consumption, and suggest that previous procedural/fluid experience in HAP mice selectively alters the time course of ethanol and water consumption. PMID:25833024

Purification and switching protocols for dissipatively stabilized entangled qubit states

NASA Astrophysics Data System (ADS)

Hein, Sven M.; Aron, Camille; Türeci, Hakan E.

2016-06-01

Pure dephasing processes limit the fidelities achievable in driven-dissipative schemes for stabilization of entangled states of qubits. We propose a scheme which, combined with already existing entangling methods, purifies the desired entangled state by driving out of equilibrium auxiliary dissipative cavity modes coupled to the qubits. We lay out the specifics of our scheme and compute its efficiency in the particular context of two superconducting qubits in a cavity-QED architecture, where the strongly coupled auxiliary modes provided by collective cavity excitations can drive and sustain the qubits in maximally entangled Bell states with fidelities reaching 90% for experimentally accessible parameters.

Development of test specimens to obtain the transmission factors to attenuate photons of 0.511 MeV

NASA Astrophysics Data System (ADS)

Costa, J. J. S.; Cardoso, D. D.; Gavazza, S.; Oliveira, C. L.; Morales, R. K.; Amorim, A. S.; Balthar, M. C. V.; Oliveira, L. S. R.

2018-03-01

For designing a shielding, it is necessary, mainly, to determine or have access to the following parameters: transmission factors of the material used and type of radiation to be shielded. Cylindrical test specimens with different thicknesses were developed for experimentally obtaining the material transmission factor for shielding calculation. The cylindrical test specimens were made considering the geometric characteristics of the detector, the ease of production and the energy of 0.511 MeV from the 18F-FDG decay. A type of concrete widely used in Brazil was used in the preparation of the cylindrical test specimens.

Molecular surface area based predictive models for the adsorption and diffusion of disperse dyes in polylactic acid matrix.

PubMed

Xu, Suxin; Chen, Jiangang; Wang, Bijia; Yang, Yiqi

2015-11-15

Two predictive models were presented for the adsorption affinities and diffusion coefficients of disperse dyes in polylactic acid matrix. Quantitative structure-sorption behavior relationship would not only provide insights into sorption process, but also enable rational engineering for desired properties. The thermodynamic and kinetic parameters for three disperse dyes were measured. The predictive model for adsorption affinity was based on two linear relationships derived by interpreting the experimental measurements with molecular structural parameters and compensation effect: ΔH° vs. dye size and ΔS° vs. ΔH°. Similarly, the predictive model for diffusion coefficient was based on two derived linear relationships: activation energy of diffusion vs. dye size and logarithm of pre-exponential factor vs. activation energy of diffusion. The only required parameters for both models are temperature and solvent accessible surface area of the dye molecule. These two predictive models were validated by testing the adsorption and diffusion properties of new disperse dyes. The models offer fairly good predictive ability. The linkage between structural parameter of disperse dyes and sorption behaviors might be generalized and extended to other similar polymer-penetrant systems. Copyright © 2015 Elsevier Inc. All rights reserved.

Probing protein surface with a solvent mimetic carbene coupled to detection by mass spectrometry.

PubMed

Gómez, Gabriela E; Mundo, Mariana R; Craig, Patricio O; Delfino, José M

2012-01-01

Much knowledge into protein folding, ligand binding, and complex formation can be derived from the examination of the nature and size of the accessible surface area (SASA) of the polypeptide chain, a key parameter in protein science not directly measurable in an experimental fashion. To this end, an ideal chemical approach should aim at exerting solvent mimicry and achieving minimal selectivity to probe the protein surface regardless of its chemical nature. The choice of the photoreagent diazirine to fulfill these goals arises from its size comparable to water and from being a convenient source of the extremely reactive methylene carbene (:CH(2)). The ensuing methylation depends primarily on the solvent accessibility of the polypeptide chain, turning it into a valuable signal to address experimentally the measurement of SASA in proteins. The superb sensitivity and high resolution of modern mass spectrometry techniques allows us to derive a quantitative signal proportional to the extent of modification (EM) of the sample. Thus, diazirine labeling coupled to electrospray mass spectrometry (ESI-MS) detection can shed light on conformational features of the native as well as non-native states, not easily addressable by other methods. Enzymatic fragmentation of the polypeptide chain at the level of small peptides allows us to locate the covalent tag along the amino acid sequence, therefore enabling the construction of a map of solvent accessibility. Moreover, by subsequent MS/MS analysis of peptides, we demonstrate here the feasibility of attaining amino acid resolution in defining the target sites. © American Society for Mass Spectrometry, 2011

VMS-ROT: A New Module of the Virtual Multifrequency Spectrometer for Simulation, Interpretation, and Fitting of Rotational Spectra

PubMed Central

2017-01-01

The Virtual Multifrequency Spectrometer (VMS) is a tool that aims at integrating a wide range of computational and experimental spectroscopic techniques with the final goal of disclosing the static and dynamic physical–chemical properties “hidden” in molecular spectra. VMS is composed of two parts, namely, VMS-Comp, which provides access to the latest developments in the field of computational spectroscopy, and VMS-Draw, which provides a powerful graphical user interface (GUI) for an intuitive interpretation of theoretical outcomes and a direct comparison to experiment. In the present work, we introduce VMS-ROT, a new module of VMS that has been specifically designed to deal with rotational spectroscopy. This module offers an integrated environment for the analysis of rotational spectra: from the assignment of spectral transitions to the refinement of spectroscopic parameters and the simulation of the spectrum. While bridging theoretical and experimental rotational spectroscopy, VMS-ROT is strongly integrated with quantum-chemical calculations, and it is composed of four independent, yet interacting units: (1) the computational engine for the calculation of the spectroscopic parameters that are employed as a starting point for guiding experiments and for the spectral interpretation, (2) the fitting-prediction engine for the refinement of the molecular parameters on the basis of the assigned transitions and the prediction of the rotational spectrum of the target molecule, (3) the GUI module that offers a powerful set of tools for a vis-à-vis comparison between experimental and simulated spectra, and (4) the new assignment tool for the assignment of experimental transitions in terms of quantum numbers upon comparison with the simulated ones. The implementation and the main features of VMS-ROT are presented, and the software is validated by means of selected test cases ranging from isolated molecules of different sizes to molecular complexes. VMS-ROT therefore offers an integrated environment for the analysis of the rotational spectra, with the innovative perspective of an intimate connection to quantum-chemical calculations that can be exploited at different levels of refinement, as an invaluable support and complement for experimental studies. PMID:28742339

Systematic parameter inference in stochastic mesoscopic modeling

NASA Astrophysics Data System (ADS)

Lei, Huan; Yang, Xiu; Li, Zhen; Karniadakis, George Em

2017-02-01

We propose a method to efficiently determine the optimal coarse-grained force field in mesoscopic stochastic simulations of Newtonian fluid and polymer melt systems modeled by dissipative particle dynamics (DPD) and energy conserving dissipative particle dynamics (eDPD). The response surfaces of various target properties (viscosity, diffusivity, pressure, etc.) with respect to model parameters are constructed based on the generalized polynomial chaos (gPC) expansion using simulation results on sampling points (e.g., individual parameter sets). To alleviate the computational cost to evaluate the target properties, we employ the compressive sensing method to compute the coefficients of the dominant gPC terms given the prior knowledge that the coefficients are "sparse". The proposed method shows comparable accuracy with the standard probabilistic collocation method (PCM) while it imposes a much weaker restriction on the number of the simulation samples especially for systems with high dimensional parametric space. Fully access to the response surfaces within the confidence range enables us to infer the optimal force parameters given the desirable values of target properties at the macroscopic scale. Moreover, it enables us to investigate the intrinsic relationship between the model parameters, identify possible degeneracies in the parameter space, and optimize the model by eliminating model redundancies. The proposed method provides an efficient alternative approach for constructing mesoscopic models by inferring model parameters to recover target properties of the physics systems (e.g., from experimental measurements), where those force field parameters and formulation cannot be derived from the microscopic level in a straight forward way.

Can high quality overcome consumer resistance to restricted provider access? Evidence from a health plan choice experiment.

PubMed

Harris, Katherine M

2002-06-01

To investigate the impact of quality information on the willingness of consumers to enroll in health plans that restrict provider access. A survey administered to respondents between the ages of 25 and 64 in the West Los Angeles area with private health insurance. An experimental approach is used to measure the effect of variation in provider network features and information about the quality of network physicians on hypothetical plan choices. Conditional logit models are used to analyze the experimental choice data. Next, choice model parameter estimates are used to simulate the impact of changes in plan features on the market shares of competing health plans and to calculate the quality level required to make consumers indifferent to changes in provider access. The presence of quality information reduced the importance of provider network features in plan choices as hypothesized. However, there were not statistically meaningful differences by type of quality measure (i.e., consumer assessed versus expert assessed). The results imply that large quality differences are required to make consumers indifferent to changes in provider access. The impact of quality on plan choices depended more on the particular measure and less on the type of measure. Quality ratings based on the proportion of survey respondents "extremely satisfied with results of care" had the greatest impact on plan choice while the proportion of network doctors "affiliated with university medical centers" had the least. Other consumer and expert assessed measures had more comparable effects. Overall the results provide empirical evidence that consumers are willing to trade high quality for restrictions on provider access. This willingness to trade implies that relatively small plans that place restrictions on provider access can successfully compete against less restrictive plans when they can demonstrate high quality. However, the results of this study suggest that in many cases, the level of quality required for consumers to accept access restrictions may be so high as to be unattainable. The results provide empirical support for the current focus of decision support efforts on consumer assessed quality measures. At the same time, however, the results suggest that consumers would also value quality measures based on expert assessments. This finding is relevant given the lack of comparative quality information based on expert judgment and research suggesting that consumers have apprehensions about their ability to meaningfully interpret performance-based quality measures.

S&MPO - An information system for ozone spectroscopy on the WEB

NASA Astrophysics Data System (ADS)

Babikov, Yurii L.; Mikhailenko, Semen N.; Barbe, Alain; Tyuterev, Vladimir G.

2014-09-01

Spectroscopy and Molecular Properties of Ozone ("S&MPO") is an Internet accessible information system devoted to high resolution spectroscopy of the ozone molecule, related properties and data sources. S&MPO contains information on original spectroscopic data (line positions, line intensities, energies, transition moments, spectroscopic parameters) recovered from comprehensive analyses and modeling of experimental spectra as well as associated software for data representation written in PHP Java Script, C++ and FORTRAN. The line-by-line list of vibration-rotation transitions and other information is organized as a relational database under control of MySQL database tools. The main S&MPO goal is to provide access to all available information on vibration-rotation molecular states and transitions under extended conditions based on extrapolations of laboratory measurements using validated theoretical models. Applications for the S&MPO may include: education/training in molecular physics, radiative processes, laser physics; spectroscopic applications (analysis, Fourier transform spectroscopy, atmospheric optics, optical standards, spectroscopic atlases); applications to environment studies and atmospheric physics (remote sensing); data supply for specific databases; and to photochemistry (laser excitation, multiphoton processes). The system is accessible via Internet on two sites: http://smpo.iao.ru and http://smpo.univ-reims.fr.

Fiber Bragg grating based arterial localization device

NASA Astrophysics Data System (ADS)

Ho, Siu Chun Michael; Li, Weijie; Razavi, Mehdi; Song, Gangbing

2017-06-01

A critical first step to many surgical procedures is locating and gaining access to a patients vascular system. Vascular access allows the deployment of other surgical instruments and also the monitoring of many physiological parameters. Current methods to locate blood vessels are predominantly based on the landmark technique coupled with ultrasound, fluoroscopy, or Doppler. However, even with experience and technological assistance, locating the required blood vessel is not always an easy task, especially with patients that present atypical anatomy or suffer from conditions such as weak pulsation or obesity that make vascular localization difficult. With recent advances in fiber optic sensors, there is an opportunity to develop a new tool that can make vascular localization safer and easier. In this work, the authors present a new fiber Bragg grating (FBG) based vascular access device that specializes in arterial localization. The device estimates the location towards a local artery based on the bending of a needle inserted near the tissue surrounding the artery. Experimental results obtained from an artificial circulatory loop and a mock artery show the device works best for lower angles of needle insertion and can provide an approximately 40° range of estimation towards the location of a pulsating source (e.g. an artery).

Development and Use of a Virtual NMR Facility

NASA Astrophysics Data System (ADS)

Keating, Kelly A.; Myers, James D.; Pelton, Jeffrey G.; Bair, Raymond A.; Wemmer, David E.; Ellis, Paul D.

2000-03-01

We have developed a "virtual NMR facility" (VNMRF) to enhance access to the NMR spectrometers in Pacific Northwest National Laboratory's Environmental Molecular Sciences Laboratory (EMSL). We use the term virtual facility to describe a real NMR facility made accessible via the Internet. The VNMRF combines secure remote operation of the EMSL's NMR spectrometers over the Internet with real-time videoconferencing, remotely controlled laboratory cameras, real-time computer display sharing, a Web-based electronic laboratory notebook, and other capabilities. Remote VNMRF users can see and converse with EMSL researchers, directly and securely control the EMSL spectrometers, and collaboratively analyze results. A customized Electronic Laboratory Notebook allows interactive Web-based access to group notes, experimental parameters, proposed molecular structures, and other aspects of a research project. This paper describes our experience developing a VNMRF and details the specific capabilities available through the EMSL VNMRF. We show how the VNMRF has evolved during a test project and present an evaluation of its impact in the EMSL and its potential as a model for other scientific facilities. All Collaboratory software used in the VNMRF is freely available from http://www.emsl.pnl.gov:2080/docs/collab.

Pertinent parameters in photo-generation of electrons: Comparative study of anatase-based nano-TiO2 suspensions.

PubMed

Martel, D; Guerra, A; Turek, P; Weiss, J; Vileno, B

2016-04-01

In the field of solar fuel cells, the development of efficient photo-converting semiconductors remains a major challenge. A rational analysis of experimental photocatalytic results obtained with material in colloïdal suspensions is needed to access fundamental knowledge required to improve the design and properties of new materials. In this study, a simple system electron donor/nano-TiO2 is considered and examined via spin scavenging electron paramagnetic resonance as well as a panel of analytical techniques (composition, optical spectroscopy and dynamic light scattering) for selected type of nano-TiO2. Independent variables (pH, electron donor concentration and TiO2 amount) have been varied and interdependent variables (aggregate size, aggregate surface vs. volume and acid/base groups distribution) are discussed. This work shows that reliable understanding involves thoughtful combination of interdependent parameters, whereas the specific surface area seems not a pertinent parameter. The conclusion emphasizes the difficulty to identify the key features of the mechanisms governing photocatalytic properties in nano-TiO2. Copyright © 2016 Elsevier Inc. All rights reserved.

Large amplitude Fourier transformed ac voltammetry at a rotating disc electrode: a versatile technique for covering Levich and flow rate insensitive regimes in a single experiment.

PubMed

Bano, Kiran; Kennedy, Gareth F; Zhang, Jie; Bond, Alan M

2012-04-14

The theory for large amplitude Fourier transformed ac voltammetry at a rotating disc electrode is described. Resolution of time domain data into dc and ac harmonic components reveals that the mass transport for the dc component is controlled by convective-diffusion, while the background free higher order harmonic components are flow rate insensitive and mainly governed by linear diffusion. Thus, remarkable versatility is available; Levich behaviour of the dc component limiting current provides diffusion coefficient values and access to higher harmonics allows fast electrode kinetics to be probed. Two series of experiments (dc and ac voltammetry) have been required to extract these parameters; here large amplitude ac voltammetry with RDE methodology is used to demonstrate that kinetics and diffusion coefficient information can be extracted from a single experiment. To demonstrate the power of this approach, theoretical and experimental comparisons of data obtained for the reversible [Ru(NH(3))(6)](3+/2+) and quasi-reversible [Fe(CN)(6)](3-/4-) electron transfer processes are presented over a wide range of electrode rotation rates and with different concentrations and electrode materials. Excellent agreement of experimental and simulated data is achieved, which allows parameters such as electron transfer rate, diffusion coefficient, uncompensated resistance and others to be determined using a strategically applied approach that takes into account the different levels of sensitivity of each parameter to the dc or the ac harmonic.

Optimizing Muscle Parameters in Musculoskeletal Modeling Using Monte Carlo Simulations

NASA Technical Reports Server (NTRS)

Hanson, Andrea; Reed, Erik; Cavanagh, Peter

2011-01-01

Astronauts assigned to long-duration missions experience bone and muscle atrophy in the lower limbs. The use of musculoskeletal simulation software has become a useful tool for modeling joint and muscle forces during human activity in reduced gravity as access to direct experimentation is limited. Knowledge of muscle and joint loads can better inform the design of exercise protocols and exercise countermeasure equipment. In this study, the LifeModeler(TM) (San Clemente, CA) biomechanics simulation software was used to model a squat exercise. The initial model using default parameters yielded physiologically reasonable hip-joint forces. However, no activation was predicted in some large muscles such as rectus femoris, which have been shown to be active in 1-g performance of the activity. Parametric testing was conducted using Monte Carlo methods and combinatorial reduction to find a muscle parameter set that more closely matched physiologically observed activation patterns during the squat exercise. Peak hip joint force using the default parameters was 2.96 times body weight (BW) and increased to 3.21 BW in an optimized, feature-selected test case. The rectus femoris was predicted to peak at 60.1% activation following muscle recruitment optimization, compared to 19.2% activation with default parameters. These results indicate the critical role that muscle parameters play in joint force estimation and the need for exploration of the solution space to achieve physiologically realistic muscle activation.

High accuracy experimental determination of copper and zinc mass attenuation coefficients in the 100 eV to 30 keV photon energy range

NASA Astrophysics Data System (ADS)

Ménesguen, Y.; Gerlach, M.; Pollakowski, B.; Unterumsberger, R.; Haschke, M.; Beckhoff, B.; Lépy, M.-C.

2016-02-01

The knowledge of atomic fundamental parameters such as mass attenuation coefficients with low uncertainties, is of decisive importance in elemental quantification using x-ray fluorescence analysis techniques. Several databases are accessible and frequently used within a large community of users. These compilations are most often in good agreement for photon energies in the hard x-ray ranges. However, they significantly differ for low photon energies and around the absorption edges of any element. In a joint cooperation of the metrology institutes of France and Germany, mass attenuation coefficients of copper and zinc were determined experimentally in the photon energy range from 100 eV to 30 keV by independent approaches using monochromatized synchrotron radiation at SOLEIL (France) and BESSY II (Germany), respectively. The application of high-accuracy experimental techniques resulted in mass attenuation coefficient datasets determined with low uncertainties that are directly compared to existing databases. The novel datasets are expected to enhance the reliability of mass attenuation coefficients.

The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data

PubMed Central

Koscielny, Gautier; Yaikhom, Gagarine; Iyer, Vivek; Meehan, Terrence F.; Morgan, Hugh; Atienza-Herrero, Julian; Blake, Andrew; Chen, Chao-Kung; Easty, Richard; Di Fenza, Armida; Fiegel, Tanja; Grifiths, Mark; Horne, Alan; Karp, Natasha A.; Kurbatova, Natalja; Mason, Jeremy C.; Matthews, Peter; Oakley, Darren J.; Qazi, Asfand; Regnart, Jack; Retha, Ahmad; Santos, Luis A.; Sneddon, Duncan J.; Warren, Jonathan; Westerberg, Henrik; Wilson, Robert J.; Melvin, David G.; Smedley, Damian; Brown, Steve D. M.; Flicek, Paul; Skarnes, William C.; Mallon, Ann-Marie; Parkinson, Helen

2014-01-01

The International Mouse Phenotyping Consortium (IMPC) web portal (http://www.mousephenotype.org) provides the biomedical community with a unified point of access to mutant mice and rich collection of related emerging and existing mouse phenotype data. IMPC mouse clinics worldwide follow rigorous highly structured and standardized protocols for the experimentation, collection and dissemination of data. Dedicated ‘data wranglers’ work with each phenotyping center to collate data and perform quality control of data. An automated statistical analysis pipeline has been developed to identify knockout strains with a significant change in the phenotype parameters. Annotation with biomedical ontologies allows biologists and clinicians to easily find mouse strains with phenotypic traits relevant to their research. Data integration with other resources will provide insights into mammalian gene function and human disease. As phenotype data become available for every gene in the mouse, the IMPC web portal will become an invaluable tool for researchers studying the genetic contributions of genes to human diseases. PMID:24194600

Adsorption site analysis of impurity embedded single-walled carbon nanotube bundles

USGS Publications Warehouse

Agnihotri, S.; Mota, J.P.B.; Rostam-Abadi, M.; Rood, M.J.

2006-01-01

Bundle morphology and adsorptive contributions from nanotubes and impurities are studied both experimentally and by simulation using a computer-aided methodology, which employs a small physisorbed probe molecule to explore the porosity of nanotube samples. Grand canonical Monte Carlo simulation of nitrogen adsorption on localized sites of a bundle is carried out to predict adsorption in its accessible internal pore volume and on its external surface as a function of tube diameter. External adsorption is split into the contributions from the clean surface of the outermost nanotubes of the bundle and from the surface of the impurities. The site-specific isotherms are then combined into a global isotherm for a given sample using knowledge of its tube-diameter distribution obtained by Raman spectroscopy. The structural parameters of the sample, such as the fraction of open-ended nanotubes and the contributions from impurities and nanotube bundles to total external surface area, are determined by fitting the experimental nitrogen adsorption data to the simulated isotherm. The degree of closure between experimental and calculated adsorption isotherms for samples manufactured by two different methods, to provide different nanotube morphology and contamination level, further strengthens the validity and resulting interpretations based on the proposed approach. The average number of nanotubes per bundle and average bundle size, within a sample, are also quantified. The proposed method allows for extrapolation of adsorption properties to conditions where the purification process is 100% effective at removing all impurities and opening access to all intrabundle adsorption sites. ?? 2006 Elsevier Ltd. All rights reserved.

Data services providing by the Ukrainian NODC (MHI NASU)

NASA Astrophysics Data System (ADS)

Eremeev, V.; Godin, E.; Khaliulin, A.; Ingerov, A.; Zhuk, E.

2009-04-01

At modern stage of the World Ocean study information support of investigation based on ad-vanced computer technologies becomes of particular importance. These abstracts are devoted to presentation of several data services developed in the Ukrainian NODC on the base of the Ma-rine Environmental and Information Technologies Department of MHI NASU. The Data Quality Control Service Using experience of international collaboration in the field of data collection and quality check we have developed the quality control (QC) software providing both preliminary(automatic) and expert(manual) data quality check procedures. The current version of the QC software works for the Mediterranean and Black seas and includes the climatic arrays for hydrological and few hydrochemical parameters based on such products as MEDAR/MEDATLAS II, Physical Oceanography of the Black Sea and Climatic Atlas of Oxygen and Hydrogen Sulfide in the Black sea. The data quality check procedure includes metadata control and hydrological and hydrochemical data control. Metadata control provides checking of duplicate cruises and pro-files, date and chronology, ship velocity, station location, sea depth and observation depth. Data QC procedure includes climatic (or range for parameters with small number of observations) data QC, density inversion check for hydrological data and searching for spikes. Using of cli-matic fields and profiles prepared by regional oceanography experts leads to more reliable results of data quality check procedure. The Data Access Services The Ukrainian NODC provides two products for data access - on-line software and data access module for the MHI NASU local net. This software allows select-ing data on rectangle area, on date, on months, on cruises. The result of query is metadata which are presented in the table and the visual presentation of stations on the map. It is possible to see both metadata and data. For this purpose it is necessary to select station in the table of metadata or on the map. There is also an opportunity to export data in ODV format. The product is avail-able on http://www.ocean.nodc.org.ua/DataAccess.php The local net version provides access to the oceanological database of the MHI NASU. The cur-rent version allows selecting data by spatial and temporal limits, depth, values of parameters, quality flags and works for the Mediterranean and Black seas. It provides visualization of meta-data and data, statistics of data selection, data export into several data formats. The Operational Data Management Services The collaborators of the MHI Experimental Branch developed a system of obtaining information on water pressure and temperature, as well as on atmospheric pressure. Sea level observations are also conducted. The obtained data are transferred online. The interface for operation data access was developed. It allows to select parameters (sea level, water temperature, atmospheric pressure, wind and wa-ter pressure) and time interval to see parameter graphics. The product is available on http://www.ocean.nodc.org.ua/Katsively.php . The Climatic products The current version of the Climatic Atlas includes maps on such pa-rameters as temperature, salinity, density, heat storage, dynamic heights, upper boundary of hy-drogen sulfide and lower boundary of oxygen for the Black sea basin. Maps for temperature, sa-linity, density were calculated on 19 standard depths and averaged monthly for depths 0 - 300 m and annually for lower depth values. The climatic maps of upper boundary of hydrogen sulfide and lower boundary of oxygen were averaged by decades from 20 till 90 of the XX century and by seasons. Two versions of climatic atlas viewer - on-line and desktop for presentation of the climatic maps were developed. They provide similar functions of selection and viewing maps by parameter, month and depth and saving maps in various formats. On-line version of atlas is available on http://www.ocean.nodc.org.ua/Main_Atlas.php .

A Quantitative Theoretical Framework For Protein-Induced Fluorescence Enhancement-Förster-Type Resonance Energy Transfer (PIFE-FRET).

PubMed

Lerner, Eitan; Ploetz, Evelyn; Hohlbein, Johannes; Cordes, Thorben; Weiss, Shimon

2016-07-07

Single-molecule, protein-induced fluorescence enhancement (PIFE) serves as a molecular ruler at molecular distances inaccessible to other spectroscopic rulers such as Förster-type resonance energy transfer (FRET) or photoinduced electron transfer. In order to provide two simultaneous measurements of two distances on different molecular length scales for the analysis of macromolecular complexes, we and others recently combined measurements of PIFE and FRET (PIFE-FRET) on the single molecule level. PIFE relies on steric hindrance of the fluorophore Cy3, which is covalently attached to a biomolecule of interest, to rotate out of an excited-state trans isomer to the cis isomer through a 90° intermediate. In this work, we provide a theoretical framework that accounts for relevant photophysical and kinetic parameters of PIFE-FRET, show how this framework allows the extraction of the fold-decrease in isomerization mobility from experimental data, and show how these results provide information on changes in the accessible volume of Cy3. The utility of this model is then demonstrated for experimental results on PIFE-FRET measurement of different protein-DNA interactions. The proposed model and extracted parameters could serve as a benchmark to allow quantitative comparison of PIFE effects in different biological systems.

Effects of larval growth condition and water availability on desiccation resistance and its physiological basis in adult Anopheles gambiae sensu stricto

PubMed Central

2010-01-01

Background Natural populations of the malaria mosquito Anopheles gambiae s.s. are exposed to large seasonal and daily fluctuations in relative humidity and temperature, which makes coping with drought a crucial aspect of their ecology. Methods To better understand natural variation in desiccation resistance in this species, the effects of variation in larval food availability and access to water as an adult on subsequent phenotypic quality and desiccation resistance of adult females of the Mopti chromosomal form were tested experimentally. Results It was found that, under normal conditions, larval food availability and adult access to water had only small direct effects on female wet mass, dry mass, and water, glycogen and body lipid contents corrected for body size. In contrast, when females subsequently faced a strong desiccation challenge, larval food availability and adult access to water had strong carry-over effects on most measured physiological and metabolic parameters, and affected female survival. Glycogen and water content were the most used physiological reserves in relative terms, but their usage significantly depended on female phenotypic quality. Adult access to water significantly influenced the use of water and body lipid reserves, which subsequently affected desiccation resistance. Conclusions These results demonstrate the importance of growth conditions and water availability on adult physiological status and subsequent resistance to desiccation. PMID:20691104

34 CFR 98.3 - Access to instructional material used in a research or experimentation program.

Code of Federal Regulations, 2012 CFR

2012-07-01

... RIGHTS IN RESEARCH, EXPERIMENTAL PROGRAMS, AND TESTING § 98.3 Access to instructional material used in a... designed to explore or develop new or unproven teaching methods or techniques. (c) For the purpose of the...

34 CFR 98.3 - Access to instructional material used in a research or experimentation program.

Code of Federal Regulations, 2013 CFR

2013-07-01

... RIGHTS IN RESEARCH, EXPERIMENTAL PROGRAMS, AND TESTING § 98.3 Access to instructional material used in a... designed to explore or develop new or unproven teaching methods or techniques. (c) For the purpose of the...

34 CFR 98.3 - Access to instructional material used in a research or experimentation program.

Code of Federal Regulations, 2010 CFR

2010-07-01

... RIGHTS IN RESEARCH, EXPERIMENTAL PROGRAMS, AND TESTING § 98.3 Access to instructional material used in a... designed to explore or develop new or unproven teaching methods or techniques. (c) For the purpose of the...

34 CFR 98.3 - Access to instructional material used in a research or experimentation program.

Code of Federal Regulations, 2014 CFR

2014-07-01

... RIGHTS IN RESEARCH, EXPERIMENTAL PROGRAMS, AND TESTING § 98.3 Access to instructional material used in a... designed to explore or develop new or unproven teaching methods or techniques. (c) For the purpose of the...

34 CFR 98.3 - Access to instructional material used in a research or experimentation program.

Code of Federal Regulations, 2011 CFR

2011-07-01

... RIGHTS IN RESEARCH, EXPERIMENTAL PROGRAMS, AND TESTING § 98.3 Access to instructional material used in a... designed to explore or develop new or unproven teaching methods or techniques. (c) For the purpose of the...

Effect of membranes on oxygen transfer rate and consumption within a newly developed three-compartment bioartificial liver device: Advanced experimental and theoretical studies.

PubMed

Hilal-Alnaqbi, Ali; Mourad, Abdel-Hamid I; Yousef, Basem F

2014-01-01

A mathematical model is developed to predict oxygen transfer in the fiber-in-fiber (FIF) bioartificial liver device. The model parameters are taken from the constructed and tested FIF modules. We extended the Krogh cylinder model by including one more zone for oxygen transfer. Cellular oxygen uptake was based on Michaelis-Menten kinetics. The effect of varying a number of important model parameters is investigated, including (1) oxygen partial pressure at the inlet, (2) the hydraulic permeability of compartment B (cell region), (3) the hydraulic permeability of the inner membrane, and (4) the oxygen diffusivity of the outer membrane. The mathematical model is validated by comparing its output against the experimentally acquired values of an oxygen transfer rate and the hydrostatic pressure drop. Three governing simultaneous linear differential equations are derived to predict and validate the experimental measurements, e.g., the flow rate and the hydrostatic pressure drop. The model output simulated the experimental measurements to a high degree of accuracy. The model predictions show that the cells in the annulus can be oxygenated well even at high cell density or at a low level of gas phase PG if the value of the oxygen diffusion coefficient Dm is 16 × 10(-5) . The mathematical model also shows that the performance of the FIF improves by increasing the permeability of polypropylene membrane (inner fiber). Moreover, the model predicted that 60% of plasma has access to the cells in the annulus within the first 10% of the FIF bioreactor axial length for a specific polypropylene membrane permeability and can reach 95% within the first 30% of its axial length. © 2013 International Union of Biochemistry and Molecular Biology, Inc.

Evaluation of accessible mineral surface areas for improved prediction of mineral reaction rates in porous media

NASA Astrophysics Data System (ADS)

Beckingham, Lauren E.; Steefel, Carl I.; Swift, Alexander M.; Voltolini, Marco; Yang, Li; Anovitz, Lawrence M.; Sheets, Julia M.; Cole, David R.; Kneafsey, Timothy J.; Mitnick, Elizabeth H.; Zhang, Shuo; Landrot, Gautier; Ajo-Franklin, Jonathan B.; DePaolo, Donald J.; Mito, Saeko; Xue, Ziqiu

2017-05-01

The rates of mineral dissolution reactions in porous media are difficult to predict, in part because of a lack of understanding of mineral reactive surface area in natural porous media. Common estimates of mineral reactive surface area used in reactive transport models for porous media are typically ad hoc and often based on average grain size, increased to account for surface roughness or decreased by several orders of magnitude to account for reduced surface reactivity of field as opposed to laboratory samples. In this study, accessible mineral surface areas are determined for a sample from the reservoir formation at the Nagaoka pilot CO2 injection site (Japan) using a multi-scale image analysis based on synchrotron X-ray microCT, SEM QEMSCAN, XRD, SANS, and FIB-SEM. This analysis not only accounts for accessibility of mineral surfaces to macro-pores, but also accessibility through connected micro-pores in smectite, the most abundant clay mineral in this sample. While the imaging analysis reveals that most of the micro- and macro-pores are well connected, some pore regions are unconnected and thus inaccessible to fluid flow and diffusion. To evaluate whether mineral accessible surface area accurately reflects reactive surface area a flow-through core experiment is performed and modeled at the continuum scale. The core experiment is performed under conditions replicating the pilot site and the evolution of effluent solutes in the aqueous phase is tracked. Various reactive surface area models are evaluated for their ability to capture the observed effluent chemistry, beginning with parameter values determined as a best fit to a disaggregated sediment experiment (Beckingham et al., 2016) described previously. Simulations that assume that all mineral surfaces are accessible (as in the disaggregated sediment experiment) over-predict the observed mineral reaction rates, suggesting that a reduction of RSA by a factor of 10-20 is required to match the core flood experimental data. While the fit of the effluent chemistry (and inferred mineral dissolution rates) greatly improve when the pore-accessible mineral surface areas are used, it was also necessary to include highly reactive glass phases to match the experimental observations, in agreement with conclusions from the disaggregated sediment experiment. It is hypothesized here that the 10-20 reduction in reactive surface areas based on the limited pore accessibility of reactive phases in core flood experiment may be reasonable for poorly sorted and cemented sediments like those at the Nagaoka site, although this reflects pore rather than larger scale heterogeneity.

Transcription factor target site search and gene regulation in a background of unspecific binding sites.

PubMed

Hettich, J; Gebhardt, J C M

2018-06-02

Response time and transcription level are vital parameters of gene regulation. They depend on how fast transcription factors (TFs) find and how efficient they occupy their specific target sites. It is well known that target site search is accelerated by TF binding to and sliding along unspecific DNA and that unspecific associations alter the occupation frequency of a gene. However, whether target site search time and occupation frequency can be optimized simultaneously is mostly unclear. We developed a transparent and intuitively accessible state-based formalism to calculate search times to target sites on and occupation frequencies of promoters of arbitrary state structure. Our formalism is based on dissociation rate constants experimentally accessible in live cell experiments. To demonstrate our approach, we consider promoters activated by a single TF, by two coactivators or in the presence of a competitive inhibitor. We find that target site search time and promoter occupancy differentially vary with the unspecific dissociation rate constant. Both parameters can be harmonized by adjusting the specific dissociation rate constant of the TF. However, while measured DNA residence times of various eukaryotic TFs correspond to a fast search time, the occupation frequencies of target sites are generally low. Cells might tolerate low target site occupancies as they enable timely gene regulation in response to a changing environment. Copyright © 2018 The Author(s). Published by Elsevier Ltd.. All rights reserved.

A Measurement Plane for Optical Networks to Manage Emergency Events

NASA Astrophysics Data System (ADS)

Tego, E.; Carciofi, C.; Grazioso, P.; Petrini, V.; Pompei, S.; Matera, F.; Attanasio, V.; Nastri, E.; Restuccia, E.

2017-11-01

In this work, we show a wide geographical area optical network test bed, adopting the mPlane measurement plane for monitoring its performance and to manage software defined network approaches, with some specific tests and procedures dedicated to respond to disaster events and to support emergency networks. Such a test bed includes FTTX accesses, and it is currently implemented to support future 5G wireless services with slicing procedures based on Carrier Ethernet. The characteristics of this platform have been experimentally tested in the case of a damage-causing link failure and traffic congestion, showing a fast reactions to these disastrous events, allowing the user to recharge the initial QoS parameters.

Database of Novel and Emerging Adsorbent Materials

National Institute of Standards and Technology Data Gateway

SRD 205 NIST/ARPA-E Database of Novel and Emerging Adsorbent Materials (Web, free access)   The NIST/ARPA-E Database of Novel and Emerging Adsorbent Materials is a free, web-based catalog of adsorbent materials and measured adsorption properties of numerous materials obtained from article entries from the scientific literature. Search fields for the database include adsorbent material, adsorbate gas, experimental conditions (pressure, temperature), and bibliographic information (author, title, journal), and results from queries are provided as a list of articles matching the search parameters. The database also contains adsorption isotherms digitized from the cataloged articles, which can be compared visually online in the web application or exported for offline analysis.

NASA participation in the 1980 PEPE/NEROS project: Data archive

NASA Technical Reports Server (NTRS)

Brewer, D. A.; Remsberg, E. E.; Loar, G. R.; Bendura, R. J.

1982-01-01

Eight experimental air quality measurement systems were investigated during July and August 1980 as part of the EPA PEPE/NEROS fiel measurement program. Data from those efforts have been entered into an archive that may be accessed by other researchers. The data sets consists of airborne measurements of regional mixed layer heights and aerosol and ozone distributions as well as point measurements of meteorological parameters and ozone obtained during diurnal transitions in the planetary boundary layer. This report gives a discussion of each measurement system, a preliminary assessment of data quality, a description of the archive format for each data set, and a summary of several proposed scientific studies which will utilize these data.

Systematic parameter inference in stochastic mesoscopic modeling

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

Lei, Huan; Yang, Xiu; Li, Zhen

2017-02-01

We propose a method to efficiently determine the optimal coarse-grained force field in mesoscopic stochastic simulations of Newtonian fluid and polymer melt systems modeled by dissipative particle dynamics (DPD) and energy conserving dissipative particle dynamics (eDPD). The response surfaces of various target properties (viscosity, diffusivity, pressure, etc.) with respect to model parameters are constructed based on the generalized polynomial chaos (gPC) expansion using simulation results on sampling points (e.g., individual parameter sets). To alleviate the computational cost to evaluate the target properties, we employ the compressive sensing method to compute the coefficients of the dominant gPC terms given the priormore » knowledge that the coefficients are “sparse”. The proposed method shows comparable accuracy with the standard probabilistic collocation method (PCM) while it imposes a much weaker restriction on the number of the simulation samples especially for systems with high dimensional parametric space. Fully access to the response surfaces within the confidence range enables us to infer the optimal force parameters given the desirable values of target properties at the macroscopic scale. Moreover, it enables us to investigate the intrinsic relationship between the model parameters, identify possible degeneracies in the parameter space, and optimize the model by eliminating model redundancies. The proposed method provides an efficient alternative approach for constructing mesoscopic models by inferring model parameters to recover target properties of the physics systems (e.g., from experimental measurements), where those force field parameters and formulation cannot be derived from the microscopic level in a straight forward way.« less

A case study of tuning MapReduce for efficient Bioinformatics in the cloud

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

Shi, Lizhen; Wang, Zhong; Yu, Weikuan

The combination of the Hadoop MapReduce programming model and cloud computing allows biological scientists to analyze next-generation sequencing (NGS) data in a timely and cost-effective manner. Cloud computing platforms remove the burden of IT facility procurement and management from end users and provide ease of access to Hadoop clusters. However, biological scientists are still expected to choose appropriate Hadoop parameters for running their jobs. More importantly, the available Hadoop tuning guidelines are either obsolete or too general to capture the particular characteristics of bioinformatics applications. In this paper, we aim to minimize the cloud computing cost spent on bioinformatics datamore » analysis by optimizing the extracted significant Hadoop parameters. When using MapReduce-based bioinformatics tools in the cloud, the default settings often lead to resource underutilization and wasteful expenses. We choose k-mer counting, a representative application used in a large number of NGS data analysis tools, as our study case. Experimental results show that, with the fine-tuned parameters, we achieve a total of 4× speedup compared with the original performance (using the default settings). Finally, this paper presents an exemplary case for tuning MapReduce-based bioinformatics applications in the cloud, and documents the key parameters that could lead to significant performance benefits.« less

Derivation of site-specific relationships between hydraulic parameters and p-wave velocities based on hydraulic and seismic tomography

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

Brauchler, R.; Doetsch, J.; Dietrich, P.

2012-01-10

In this study, hydraulic and seismic tomographic measurements were used to derive a site-specific relationship between the geophysical parameter p-wave velocity and the hydraulic parameters, diffusivity and specific storage. Our field study includes diffusivity tomograms derived from hydraulic travel time tomography, specific storage tomograms, derived from hydraulic attenuation tomography, and p-wave velocity tomograms, derived from seismic tomography. The tomographic inversion was performed in all three cases with the SIRT (Simultaneous Iterative Reconstruction Technique) algorithm, using a ray tracing technique with curved trajectories. The experimental set-up was designed such that the p-wave velocity tomogram overlaps the hydraulic tomograms by half. Themore » experiments were performed at a wellcharacterized sand and gravel aquifer, located in the Leine River valley near Göttingen, Germany. Access to the shallow subsurface was provided by direct-push technology. The high spatial resolution of hydraulic and seismic tomography was exploited to derive representative site-specific relationships between the hydraulic and geophysical parameters, based on the area where geophysical and hydraulic tests were performed. The transformation of the p-wave velocities into hydraulic properties was undertaken using a k-means cluster analysis. Results demonstrate that the combination of hydraulic and geophysical tomographic data is a promising approach to improve hydrogeophysical site characterization.« less

Suppression of anomalous synchronization and nonstationary behavior of neural network under small-world topology

NASA Astrophysics Data System (ADS)

Boaretto, B. R. R.; Budzinski, R. C.; Prado, T. L.; Kurths, J.; Lopes, S. R.

2018-05-01

It is known that neural networks under small-world topology can present anomalous synchronization and nonstationary behavior for weak coupling regimes. Here, we propose methods to suppress the anomalous synchronization and also to diminish the nonstationary behavior occurring in weakly coupled neural network under small-world topology. We consider a network of 2000 thermally sensitive identical neurons, based on the model of Hodgkin-Huxley in a small-world topology, with the probability of adding non local connection equal to p = 0 . 001. Based on experimental protocols to suppress anomalous synchronization, as well as nonstationary behavior of the neural network dynamics, we make use of (i) external stimulus (pulsed current); (ii) biologic parameters changing (neuron membrane conductance changes); and (iii) body temperature changes. Quantification analysis to evaluate phase synchronization makes use of the Kuramoto's order parameter, while recurrence quantification analysis, particularly the determinism, computed over the easily accessible mean field of network, the local field potential (LFP), is used to evaluate nonstationary states. We show that the methods proposed can control the anomalous synchronization and nonstationarity occurring for weak coupling parameter without any effect on the individual neuron dynamics, neither in the expected asymptotic synchronized states occurring for large values of the coupling parameter.

Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects.

PubMed

Lomize, Andrei L; Pogozheva, Irina D; Mosberg, Henry I

2011-04-25

A new implicit solvation model was developed for calculating free energies of transfer of molecules from water to any solvent with defined bulk properties. The transfer energy was calculated as a sum of the first solvation shell energy and the long-range electrostatic contribution. The first term was proportional to solvent accessible surface area and solvation parameters (σ(i)) for different atom types. The electrostatic term was computed as a product of group dipole moments and dipolar solvation parameter (η) for neutral molecules or using a modified Born equation for ions. The regression coefficients in linear dependencies of solvation parameters σ(i) and η on dielectric constant, solvatochromic polarizability parameter π*, and hydrogen-bonding donor and acceptor capacities of solvents were optimized using 1269 experimental transfer energies from 19 organic solvents to water. The root-mean-square errors for neutral compounds and ions were 0.82 and 1.61 kcal/mol, respectively. Quantification of energy components demonstrates the dominant roles of hydrophobic effect for nonpolar atoms and of hydrogen-bonding for polar atoms. The estimated first solvation shell energy outweighs the long-range electrostatics for most compounds including ions. The simplicity and computational efficiency of the model allows its application for modeling of macromolecules in anisotropic environments, such as biological membranes.

Rapid and precise determination of zero-field splittings by terahertz time-domain electron paramagnetic resonance spectroscopy.

PubMed

Lu, Jian; Ozel, I Ozge; Belvin, Carina A; Li, Xian; Skorupskii, Grigorii; Sun, Lei; Ofori-Okai, Benjamin K; Dincă, Mircea; Gedik, Nuh; Nelson, Keith A

2017-11-01

Zero-field splitting (ZFS) parameters are fundamentally tied to the geometries of metal ion complexes. Despite their critical importance for understanding the magnetism and spectroscopy of metal complexes, they are not routinely available through general laboratory-based techniques, and are often inferred from magnetism data. Here we demonstrate a simple tabletop experimental approach that enables direct and reliable determination of ZFS parameters in the terahertz (THz) regime. We report time-domain measurements of electron paramagnetic resonance (EPR) signals associated with THz-frequency ZFSs in molecular complexes containing high-spin transition-metal ions. We measure the temporal profiles of the free-induction decays of spin resonances in the complexes at zero and nonzero external magnetic fields, and we derive the EPR spectra via numerical Fourier transformation of the time-domain signals. In most cases, absolute values of the ZFS parameters are extracted from the measured zero-field EPR frequencies, and the signs can be determined by zero-field measurements at two different temperatures. Field-dependent EPR measurements further allow refined determination of the ZFS parameters and access to the g -factor. The results show good agreement with those obtained by other methods. The simplicity of the method portends wide applicability in chemistry, biology and material science.

Dynamical vanishing of the order parameter in a confined Bardeen-Cooper-Schrieffer Fermi gas after an interaction quench

NASA Astrophysics Data System (ADS)

Hannibal, S.; Kettmann, P.; Croitoru, M. D.; Axt, V. M.; Kuhn, T.

2018-01-01

We present a numerical study of the Higgs mode in an ultracold confined Fermi gas after an interaction quench and find a dynamical vanishing of the superfluid order parameter. Our calculations are done within a microscopic density-matrix approach in the Bogoliubov-de Gennes framework which takes the three-dimensional cigar-shaped confinement explicitly into account. In this framework, we study the amplitude mode of the order parameter after interaction quenches starting on the BCS side of the BEC-BCS crossover close to the transition and ending in the BCS regime. We demonstrate the emergence of a dynamically vanishing superfluid order parameter in the spatiotemporal dynamics in a three-dimensional trap. Further, we show that the signal averaged over the whole trap mirrors the spatiotemporal behavior and allows us to systematically study the effects of the system size and aspect ratio on the observed dynamics. Our analysis enables us to connect the confinement-induced modifications of the dynamics to the pairing properties of the system. Finally, we demonstrate that the signature of the Higgs mode is contained in the dynamical signal of the condensate fraction, which, therefore, might provide a new experimental access to the nonadiabatic regime of the Higgs mode.

SCOPE: a web server for practical de novo motif discovery.

PubMed

Carlson, Jonathan M; Chakravarty, Arijit; DeZiel, Charles E; Gross, Robert H

2007-07-01

SCOPE is a novel parameter-free method for the de novo identification of potential regulatory motifs in sets of coordinately regulated genes. The SCOPE algorithm combines the output of three component algorithms, each designed to identify a particular class of motifs. Using an ensemble learning approach, SCOPE identifies the best candidate motifs from its component algorithms. In tests on experimentally determined datasets, SCOPE identified motifs with a significantly higher level of accuracy than a number of other web-based motif finders run with their default parameters. Because SCOPE has no adjustable parameters, the web server has an intuitive interface, requiring only a set of gene names or FASTA sequences and a choice of species. The most significant motifs found by SCOPE are displayed graphically on the main results page with a table containing summary statistics for each motif. Detailed motif information, including the sequence logo, PWM, consensus sequence and specific matching sites can be viewed through a single click on a motif. SCOPE's efficient, parameter-free search strategy has enabled the development of a web server that is readily accessible to the practising biologist while providing results that compare favorably with those of other motif finders. The SCOPE web server is at .

Experimental/Analytical Characterization of the RBCC Rocket-Ejector Mode

NASA Technical Reports Server (NTRS)

Ruf, J. H.; Lehman, M.; Pal, S.; Santoro, R. J.

2000-01-01

The experimental/analytical research work described here addresses the rocket-ejector mode (Mach 0-2 operational range) of the RBCC engine. The experimental phase of the program includes studying the mixing and combustion characteristics of the rocket-ejector system utilizing state-of-the-art diagnostic techniques. A two-dimensional variable geometry rocket-ejector system with enhanced optical access was utilized as the experimental platform. The goals of the experimental phase of the research being conducted at Penn State are to: (a) systematically increase the range of rocket-ejector understanding over a wide range of flow/geometry parameters and (b) provide a comprehensive data base for evaluating and anchoring CFD codes. Concurrent with the experimental activities, a CFD code benchmarking effort at Marshall Space Flight Center is also being used to further investigate the RBCC rocket-ejector mode. Experiments involving the single rocket based optically-accessible rocket-ejector system have been conducted for Diffusion and Afterburning (DAB) as well as Simultaneous Mixing and Combustion configurations. For the DAB configuration, air is introduced (direct-connect) or ejected (sea-level static) into a constant area mixer section with a centrally located gaseous oxygen (GO2)/gaseous hydrogen (GH2) rocket combustor. The downstream flowpath for this configuration includes a diffuser, an afterburner and a final converging nozzle. For the SMC configuration, the rocket is centrally located in a slightly divergent duct. For all tested configurations, global measurements of the axial pressure and heat transfer profiles as well as the overall engine thrust were made. Detailed measurements include major species concentration (H2 O2 N2 and H2O) profiles at various mixer locations made using Raman spectroscopy. Complementary CFD calculations of the flowfield at the experimental conditions also provide additional information on the physics of the problem. These calculations are being conducted at Marshall Space Flight Center to benchmark the FDNS code for RBCC engine operations for such configurations. The primary fluid physics of interests are the mixing and interaction of the rocket plume and secondary flow, subsequent combustion of the fuel rich rocket exhaust with the secondary flow and combustion of the injected afterburner flow. The CFD results are compared to static pressure along the RBCC duct walls, Raman Spectroscopy specie distribution data at several axial locations, net engine thrust and entrained air for the SLS cases. The CFD results compare reasonably well with the experimental results.

Relative fluid novelty differentially alters the time course of limited-access ethanol and water intake in selectively bred high-alcohol-preferring mice.

PubMed

Linsenbardt, David N; Boehm, Stephen L

2015-04-01

The influence of previous alcohol (ethanol [EtOH])-drinking experience on increasing the rate and amount of future EtOH consumption might be a genetically regulated phenomenon critical to the development and maintenance of repeated excessive EtOH abuse. We have recently found evidence supporting this view, wherein inbred C57BL/6J (B6) mice develop progressive increases in the rate of binge EtOH consumption over repeated drinking-in-the-dark (DID) EtOH access sessions (i.e., "front loading"). The primary goal of this study was to evaluate identical parameters in high-alcohol-preferring (HAP) mice to determine whether similar temporal alterations in limited-access EtOH drinking develop in a population selected for high EtOH preference/intake under continuous (24-hour) access conditions. Using specialized volumetric drinking devices, HAP mice received 14 daily 2-hour DID EtOH or water access sessions. A subset of these mice was then given 1 day access to the opposite assigned fluid on day 15. Home cage locomotor activity was recorded concomitantly on each day of these studies. The possibility of behavioral/metabolic tolerance was evaluated on day 16 using experimenter-administered EtOH. The amount of EtOH consumed within the first 15 minutes of access increased markedly over days. However, in contrast to previous observations in B6 mice, EtOH front loading was also observed on day 15 in mice that only had previous DID experience with water. Furthermore, a decrease in the amount of water consumed within the first 15 minutes of access compared to animals given repeated water access was observed on day 15 in mice with 14 previous days of EtOH access. These data further illustrate the complexity and importance of the temporal aspects of limited-access EtOH consumption and suggest that previous procedural/fluid experience in HAP mice selectively alters the time course of EtOH and water consumption. Copyright © 2015 by the Research Society on Alcoholism.

Interfacial tensiometry and dilational surface visco-elasticity of biological liquids in medicine.

PubMed

Fainerman, V B; Trukhin, D V; Zinkovych, Igor I; Miller, R

2018-05-01

Dynamic surface tensions and dilational visco-elasticity are easy accessible parameters of liquids. For human body liquids, such as urine, blood serum, amniotic fluid, gastric juice, saliva and others, these parameters are very characteristic for the health status of people. In case of a disease the composition of certain liquids specifically changes and the measured characteristics of dynamic surface tension of the dilational surface elasticity and viscosity reflect these changes in a clear way. Thus, this kind of physico-chemical measurements represent sensitive tools for evaluating the severity of a disease and can serve as control tool for the efficiency of applied therapies. The overview summarises the results of a successful work over about 25years on this subject and gives specific insight into a number of diseases for which the diagnostics as well as the therapy control have been significantly improved by the application of physico-chemical experimental techniques. Copyright © 2017 Elsevier B.V. All rights reserved.

Origin of Disagreements in Tandem Mass Spectra Interpretation by Search Engines.

PubMed

Tessier, Dominique; Lollier, Virginie; Larré, Colette; Rogniaux, Hélène

2016-10-07

Several proteomic database search engines that interpret LC-MS/MS data do not identify the same set of peptides. These disagreements occur even when the scores of the peptide-to-spectrum matches suggest good confidence in the interpretation. Our study shows that these disagreements observed for the interpretations of a given spectrum are almost exclusively due to the variation of what we call the "peptide space", i.e., the set of peptides that are actually compared to the experimental spectra. We discuss the potential difficulties of precisely defining the "peptide space." Indeed, although several parameters that are generally reported in publications can easily be set to the same values, many additional parameters-with much less straightforward user access-might impact the "peptide space" used by each program. Moreover, in a configuration where each search engine identifies the same candidates for each spectrum, the inference of the proteins may remain quite different depending on the false discovery rate selected.

Hydrodynamics of isotropic and liquid crystalline active polymer solutions.

PubMed

Ahmadi, Aphrodite; Marchetti, M C; Liverpool, T B

2006-12-01

We describe the large-scale collective behavior of solutions of polar biofilaments and stationary and mobile crosslinkers. Both mobile and stationary crosslinkers induce filament alignment promoting either polar or nematic order. In addition, mobile crosslinkers, such as clusters of motor proteins, exchange forces and torques among the filaments and render the homogeneous states unstable via filament bundling. We start from a Smoluchowski equation for rigid filaments in solutions, where pairwise crosslink-mediated interactions among the filaments yield translational and rotational currents. The large-scale properties of the system are described in terms of continuum equations for filament and motor densities, polarization, and alignment tensor obtained by coarse-graining the Smoluchovski equation. The possible homogeneous and inhomogeneous states of the systems are obtained as stable solutions of the dynamical equations and are characterized in terms of experimentally accessible parameters. We make contact with work by other authors and show that our model allows for an estimate of the various parameters in the hydrodynamic equations in terms of physical properties of the crosslinkers.

Simulation of the ozone pretreatment of wheat straw.

PubMed

Bhattarai, Sujala; Bottenus, Danny; Ivory, Cornelius F; Gao, Allan Haiming; Bule, Mahesh; Garcia-Perez, Manuel; Chen, Shulin

2015-11-01

Wheat straw is a potential feedstock in biorefinery for sugar production. However, the cellulose, which is the major source of sugar, is protected by lignin. Ozonolysis deconstructs the lignin and makes cellulose accessible to enzymatic digestion. In this study, the change in lignin concentration with different ozonolysis times (0, 1, 2, 3, 5, 7, 10, 15, 20, 30, 60min) was fit to two different kinetic models: one using the model developed by Garcia-Cubero et al. (2012) and another including an outer mass transfer barrier or "cuticle" region where ozone mass transport is reduced in proportion to the mass of unreacted insoluble lignin in the cuticle. The kinetic parameters of two mathematical models for predicting the soluble and insoluble lignin at different pretreatment time were determined. The results showed that parameters derived from the cuticle-based model provided a better fit to experimental results compared to a model without a cuticle layer. Copyright © 2015 Elsevier Ltd. All rights reserved.

Numerical-experimental observation of shape bistability of red blood cells flowing in a microchannel

NASA Astrophysics Data System (ADS)

Guckenberger, Achim; Kihm, Alexander; John, Thomas; Wagner, Christian; Gekle, Stephan

Red blood cells flowing through capillaries assume a wide variety of different shapes owing to their high deformability. Predicting the realized shapes is a complex field as they are determined by the intricate interplay between the flow conditions and the membrane mechanics. In this work we construct the shape phase diagram of a single red blood cell with a physiological viscosity ratio flowing in a microchannel. We use both experimental in-vitro measurements as well as 3D numerical simulations to complement the respective other one. Numerically, we have easy control over the initial starting configuration and natural access to the full 3D shape. With this information we obtain the phase diagram as a function of initial position, starting shape and cell velocity. Experimentally, we measure the occurrence frequency of the different shapes as a function of the cell velocity to construct the experimental diagram which is in good agreement with the numerical observations. Two different major shapes are found, namely croissants and slippers. Notably, both shapes show coexistence at low (<1 mm/s) and high velocities (>3 mm/s) while in-between only croissants are stable. This pronounced bistability indicates that RBC shapes are not only determined by system parameters such as flow velocity or channel size, but also strongly depend on the initial conditions.

Theoretical Investigation of Kinetic Processes in Small Radicals of Importance in Combustion

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

Alexander, Millard; Dagdigian, Paul J.

Our group studies inelastic and reactive collisions of small molecules, focusing on radicals important in combustion environments. The goal is the better understanding of kinetic processes that may be difficult to access experimentally. An essential component is the accurate determination and fitting of potential energy surfaces (PESs). After fitting the ab initio points to obtain global PESs, we treat the dynamics using time-independent (close-coupling) methods. Cross sections and rate constants for collisions of are determined with our Hibridon program suite . We have studied energy transfer (rotationally, vibrationally, and/or electronically inelastic) in small hydrocarbon radicals (CH 2 and CH 3)more » and the CN radical. We have made a comparison with experimental measurements of relevant rate constants for collisions of these radicals. Also, we have calculated accurate transport properties using state-of-the-art PESs and to investigate the sensitivity to these parameters in 1-dimensional flame simulations. Of particular interest are collision pairs involving the light H atom.« less

Cyber-physical experiments on the efficiency of swimming protocols

NASA Astrophysics Data System (ADS)

Wei, Nathaniel; Floryan, Daniel; van Buren, Tyler; Smits, Alexander

2016-11-01

We present results from experiments on a biologically inspired cyber-physical system, composed of a two-dimensional heaving and pitching rigid airfoil attached to a six component load cell, mounted to a traverse that can move along a water channel. A feedback controller, influenced by the apparatus of Mackowski and Williamson, introduces the effects of a fictional drag force specified by a virtual body profile and drives the traverse accordingly. Free-swimming protocols using the force-feedback system are compared with similar motions on a motionless traverse. The propulsive efficiency of burst-and-coast kinematics is also considered. Of particular interest are (1) the implementation of the cyber-physical control system with respect to the accessible experimental parameter space, (2) the impact of force-based streamwise actuation on experimental data, and (3) the effects of burst-and-coast motions on propulsive efficiency. The work was supported by the Office of Naval Research (ONR) under MURI Grant N00014-14-1-0533.

Experimental results of superimposing 9.9 GHz extraordinary mode microwaves on 2.45 GHz ECRIS plasma

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

Nishiokada, Takuya, E-mail: nishiokada@nf.eie.eng.osaka-u.ac.jp; Nagaya, Tomoki; Hagino, Shogo

2016-02-15

Efficient production of multicharged ions has been investigated on the tandem-type ECRIS in Osaka University. According to the consideration of the accessibility conditions of microwaves to resonance and cutoff regions, it was suggested that the upper hybrid resonance (UHR) heating contributed to enhancement of ion beam intensity. In order to enhance multicharged ion beams efficiently, injecting higher frequency microwave with extraordinary (X-mode) toward UHR region has been tried. In this study, 2.45 GHz frequency microwaves are used for conventional ECR discharge, and 9.9 GHz frequency microwaves with X-mode are superimposed for UHR heating. The effects of additive microwave injection aremore » investigated experimentally in terms of plasma parameters and electron energy distribution function (EEDF) measured by Langmuir probe and ion beam current. As the results show, it is confirmed that the electrons in the high energy region are affected by 9.9 GHz X-mode microwave injection from the detailed analysis of EEDF.« less

Theory for controlling individual self-propelled micro-swimmers by photon nudging I: directed transport.

PubMed

Selmke, Markus; Khadka, Utsab; Bregulla, Andreas P; Cichos, Frank; Yang, Haw

2018-04-18

Photon nudging is a new experimental method which enables the force-free manipulation and localization of individual self-propelled artificial micro-swimmers in fluidic environments. It uses a weak laser to stochastically and adaptively turn on and off the swimmer's propulsion when the swimmer, through rotational diffusion, points towards or away from its target, respectively. This contribution presents a theoretical framework for the statistics of both 2D and 3D controls. The main results are: the on- and off-time distributions for the controlling laser, the arrival time statistics for the swimmer to reach a remote target, and how the experimentally accessible control parameters influence the control, e.g., the optimal acceptance angle for directed transport. The results are general in that they are independent of the propulsion or the actuation mechanisms. They provide a concrete physical picture for how a single artificial micro-swimmer could be navigated under thermal fluctuations-insights that could also be useful for understanding biological micro-swimmers.

In silico screening of drug-membrane thermodynamics reveals linear relations between bulk partitioning and the potential of mean force

NASA Astrophysics Data System (ADS)

Menichetti, Roberto; Kanekal, Kiran H.; Kremer, Kurt; Bereau, Tristan

2017-09-01

The partitioning of small molecules in cell membranes—a key parameter for pharmaceutical applications—typically relies on experimentally available bulk partitioning coefficients. Computer simulations provide a structural resolution of the insertion thermodynamics via the potential of mean force but require significant sampling at the atomistic level. Here, we introduce high-throughput coarse-grained molecular dynamics simulations to screen thermodynamic properties. This application of physics-based models in a large-scale study of small molecules establishes linear relationships between partitioning coefficients and key features of the potential of mean force. This allows us to predict the structure of the insertion from bulk experimental measurements for more than 400 000 compounds. The potential of mean force hereby becomes an easily accessible quantity—already recognized for its high predictability of certain properties, e.g., passive permeation. Further, we demonstrate how coarse graining helps reduce the size of chemical space, enabling a hierarchical approach to screening small molecules.

Glass transition of charged particles in two-dimensional confinement.

PubMed

Yazdi, Anoosheh; Heinen, Marco; Ivlev, Alexei; Löwen, Hartmut; Sperl, Matthias

2015-05-01

The glass transition of mesoscopic charged particles in two-dimensional confinement is studied by mode-coupling theory. We consider two types of effective interactions between the particles, corresponding to two different models for the distribution of surrounding ions that are integrated out in coarse-grained descriptions. In the first model, a planar monolayer of charged particles is immersed in an unbounded isotropic bath of ions, giving rise to an isotropically screened Debye-Hückel (Yukawa)-type effective interaction. The second, experimentally more relevant system is a monolayer of negatively charged particles that levitate atop a flat horizontal electrode, as frequently encountered in laboratory experiments with complex (dusty) plasmas. A steady plasma current toward the electrode gives rise to an anisotropic effective interaction potential between the particles, with an algebraically long-ranged in-plane decay. In a comprehensive parameter scan that covers the typical range of experimentally accessible plasma conditions, we calculate and compare the mode-coupling predictions for the glass transition in both kinds of systems.

Experimental results of superimposing 9.9 GHz extraordinary mode microwaves on 2.45 GHz ECRIS plasma.

PubMed

Nishiokada, Takuya; Nagaya, Tomoki; Hagino, Shogo; Otsuka, Takuro; Muramatsu, Masayuki; Sato, Fuminobu; Kitagawa, Atsushi; Kato, Yushi

2016-02-01

Efficient production of multicharged ions has been investigated on the tandem-type ECRIS in Osaka University. According to the consideration of the accessibility conditions of microwaves to resonance and cutoff regions, it was suggested that the upper hybrid resonance (UHR) heating contributed to enhancement of ion beam intensity. In order to enhance multicharged ion beams efficiently, injecting higher frequency microwave with extraordinary (X-mode) toward UHR region has been tried. In this study, 2.45 GHz frequency microwaves are used for conventional ECR discharge, and 9.9 GHz frequency microwaves with X-mode are superimposed for UHR heating. The effects of additive microwave injection are investigated experimentally in terms of plasma parameters and electron energy distribution function (EEDF) measured by Langmuir probe and ion beam current. As the results show, it is confirmed that the electrons in the high energy region are affected by 9.9 GHz X-mode microwave injection from the detailed analysis of EEDF.

Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions

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

Changlani, Hitesh J.; Zheng, Huihuo; Wagner, Lucas K.

2015-09-14

We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U{sup ∗}/t tomore » be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.« less

A suite of diagnostics to validate and optimize the prototype ITER neutral beam injector

NASA Astrophysics Data System (ADS)

Pasqualotto, R.; Agostini, M.; Barbisan, M.; Brombin, M.; Cavazzana, R.; Croci, G.; Dalla Palma, M.; Delogu, R. S.; De Muri, M.; Muraro, A.; Peruzzo, S.; Pimazzoni, A.; Pomaro, N.; Rebai, M.; Rizzolo, A.; Sartori, E.; Serianni, G.; Spagnolo, S.; Spolaore, M.; Tardocchi, M.; Zaniol, B.; Zaupa, M.

2017-10-01

The ITER project requires additional heating provided by two neutral beam injectors using 40 A negative deuterium ions accelerated at 1 MV. As the beam requirements have never been experimentally met, a test facility is under construction at Consorzio RFX, which hosts two experiments: SPIDER, full-size 100 kV ion source prototype, and MITICA, 1 MeV full-size ITER injector prototype. Since diagnostics in ITER injectors will be mainly limited to thermocouples, due to neutron and gamma radiation and to limited access, it is crucial to thoroughly investigate and characterize in more accessible experiments the key parameters of source plasma and beam, using several complementary diagnostics assisted by modelling. In SPIDER and MITICA the ion source parameters will be measured by optical emission spectroscopy, electrostatic probes, cavity ring down spectroscopy for H^- density and laser absorption spectroscopy for cesium density. Measurements over multiple lines-of-sight will provide the spatial distribution of the parameters over the source extension. The beam profile uniformity and its divergence are studied with beam emission spectroscopy, complemented by visible tomography and neutron imaging, which are novel techniques, while an instrumented calorimeter based on custom unidirectional carbon fiber composite tiles observed by infrared cameras will measure the beam footprint on short pulses with the highest spatial resolution. All heated components will be monitored with thermocouples: as these will likely be the only measurements available in ITER injectors, their capabilities will be investigated by comparison with other techniques. SPIDER and MITICA diagnostics are described in the present paper with a focus on their rationale, key solutions and most original and effective implementations.

Experimental design to understand the interaction of stellar radiation with molecular clouds

NASA Astrophysics Data System (ADS)

Vandervort, Robert; Davis, Josh; Trantham, Matt; Klein, Sallee; Frank, Yechiel; Raicher, Erez; Fraenkel, Moshe; Shvarts, Dov; Keiter, Paul; Drake, R. Paul

2016-10-01

Enhanced star formation triggered by local O and B type stars is an astrophysical problem of interest. O and B type stars are massive, hot stars that emit an enormous amount of radiation. This radiation acts to either compress or blow apart clumps of gas in the interstellar media. For example, in the optically thick limit, when the x-ray radiation in the gas clump has a short mean free path length the x-ray radiation is absorbed near the clump edge and compresses the clump. In the optically thin limit, when the mean free path is long, the radiation is absorbed throughout acting to heat the clump. This heating explodes the gas clump. Careful selection of parameters, such as foam density or source temperature, allow the experimental platform to access different hydrodynamic regimes. The stellar radiation source is mimicked by a laser irradiated thin gold foil. This will provide a source of thermal x-rays (around 100 eV). The gas clump is mimicked by a low-density foam around 0.12 g/cc. Simulations were done using radiation hydrodynamics codes to tune the experimental parameters. The experiment will be carried out at the Omega laser facility on OMEGA 60. Funding acknowledgements: This work is funded by the U.S. DOE, through the NNSA-DS and SC-OFES Joint Program in HEDPLP, Grant No. DE-NA0001840, and the NLUF Program, Grant No. DE-NA0000850, and through LLE, University of Rochester by the NNSA/OICF under Agreement No. DE-FC52-08NA28302.

On Increasing Network Lifetime in Body Area Networks Using Global Routing with Energy Consumption Balancing

PubMed Central

Tsouri, Gill R.; Prieto, Alvaro; Argade, Nikhil

2012-01-01

Global routing protocols in wireless body area networks are considered. Global routing is augmented with a novel link cost function designed to balance energy consumption across the network. The result is a substantial increase in network lifetime at the expense of a marginal increase in energy per bit. Network maintenance requirements are reduced as well, since balancing energy consumption means all batteries need to be serviced at the same time and less frequently. The proposed routing protocol is evaluated using a hardware experimental setup comprising multiple nodes and an access point. The setup is used to assess network architectures, including an on-body access point and an off-body access point with varying number of antennas. Real-time experiments are conducted in indoor environments to assess performance gains. In addition, the setup is used to record channel attenuation data which are then processed in extensive computer simulations providing insight on the effect of protocol parameters on performance. Results demonstrate efficient balancing of energy consumption across all nodes, an average increase of up to 40% in network lifetime corresponding to a modest average increase of 0.4 dB in energy per bit, and a cutoff effect on required transmission power to achieve reliable connectivity. PMID:23201987

On increasing network lifetime in body area networks using global routing with energy consumption balancing.

PubMed

Tsouri, Gill R; Prieto, Alvaro; Argade, Nikhil

2012-09-26

Global routing protocols in wireless body area networks are considered. Global routing is augmented with a novel link cost function designed to balance energy consumption across the network. The result is a substantial increase in network lifetime at the expense of a marginal increase in energy per bit. Network maintenance requirements are reduced as well, since balancing energy consumption means all batteries need to be serviced at the same time and less frequently. The proposed routing protocol is evaluated using a hardware experimental setup comprising multiple nodes and an access point. The setup is used to assess network architectures, including an on-body access point and an off-body access point with varying number of antennas. Real-time experiments are conducted in indoor environments to assess performance gains. In addition, the setup is used to record channel attenuation data which are then processed in extensive computer simulations providing insight on the effect of protocol parameters on performance. Results demonstrate efficient balancing of energy consumption across all nodes, an average increase of up to 40% in network lifetime corresponding to a modest average increase of 0.4 dB in energy per bit, and a cutoff effect on required transmission power to achieve reliable connectivity.

Experimental realization of an entanglement access network and secure multi-party computation

NASA Astrophysics Data System (ADS)

Chang, X.-Y.; Deng, D.-L.; Yuan, X.-X.; Hou, P.-Y.; Huang, Y.-Y.; Duan, L.-M.

2016-07-01

To construct a quantum network with many end users, it is critical to have a cost-efficient way to distribute entanglement over different network ends. We demonstrate an entanglement access network, where the expensive resource, the entangled photon source at the telecom wavelength and the core communication channel, is shared by many end users. Using this cost-efficient entanglement access network, we report experimental demonstration of a secure multiparty computation protocol, the privacy-preserving secure sum problem, based on the network quantum cryptography.

Experimental realization of an entanglement access network and secure multi-party computation

NASA Astrophysics Data System (ADS)

Chang, Xiuying; Deng, Donglin; Yuan, Xinxing; Hou, Panyu; Huang, Yuanyuan; Duan, Luming; Department of Physics, University of Michigan Collaboration; CenterQuantum Information in Tsinghua University Team

2017-04-01

To construct a quantum network with many end users, it is critical to have a cost-efficient way to distribute entanglement over different network ends. We demonstrate an entanglement access network, where the expensive resource, the entangled photon source at the telecom wavelength and the core communication channel, is shared by many end users. Using this cost-efficient entanglement access network, we report experimental demonstration of a secure multiparty computation protocol, the privacy-preserving secure sum problem, based on the network quantum cryptography.

In silico characterization of cell-cell interactions using a cellular automata model of cell culture.

PubMed

Kihara, Takanori; Kashitani, Kosuke; Miyake, Jun

2017-07-14

Cell proliferation is a key characteristic of eukaryotic cells. During cell proliferation, cells interact with each other. In this study, we developed a cellular automata model to estimate cell-cell interactions using experimentally obtained images of cultured cells. We used four types of cells; HeLa cells, human osteosarcoma (HOS) cells, rat mesenchymal stem cells (MSCs), and rat smooth muscle A7r5 cells. These cells were cultured and stained daily. The obtained cell images were binarized and clipped into squares containing about 10 4 cells. These cells showed characteristic cell proliferation patterns. The growth curves of these cells were generated from the cell proliferation images and we determined the doubling time of these cells from the growth curves. We developed a simple cellular automata system with an easily accessible graphical user interface. This system has five variable parameters, namely, initial cell number, doubling time, motility, cell-cell adhesion, and cell-cell contact inhibition (of proliferation). Within these parameters, we obtained initial cell numbers and doubling times experimentally. We set the motility at a constant value because the effect of the parameter for our simulation was restricted. Therefore, we simulated cell proliferation behavior with cell-cell adhesion and cell-cell contact inhibition as variables. By comparing growth curves and proliferation cell images, we succeeded in determining the cell-cell interaction properties of each cell. Simulated HeLa and HOS cells exhibited low cell-cell adhesion and weak cell-cell contact inhibition. Simulated MSCs exhibited high cell-cell adhesion and positive cell-cell contact inhibition. Simulated A7r5 cells exhibited low cell-cell adhesion and strong cell-cell contact inhibition. These simulated results correlated with the experimental growth curves and proliferation images. Our simulation approach is an easy method for evaluating the cell-cell interaction properties of cells.

Recent advances in continuum plasticity: phenomenological modeling and experimentation using X-ray diffraction

NASA Astrophysics Data System (ADS)

Edmiston, John Kearney

This work explores the field of continuum plasticity from two fronts. On the theory side, we establish a complete specification of a phenomenological theory of plasticity for single crystals. The model serves as an alternative to the popular crystal plasticity formulation. Such a model has been previously proposed in the literature; the new contribution made here is the constitutive framework and resulting simulations. We calibrate the model to available data and use a simple numerical method to explore resulting predictions in plane strain boundary value problems. Results show promise for further investigation of the plasticity model. Conveniently, this theory comes with a corresponding experimental tool in X-ray diffraction. Recent advances in hardware technology at synchrotron sources have led to an increased use of the technique for studies of plasticity in the bulk of materials. The method has been successful in qualitative observations of material behavior, but its use in quantitative studies seeking to extract material properties is open for investigation. Therefore in the second component of the thesis several contributions are made to synchrotron X-ray diffraction experiments, in terms of method development as well as the quantitative reporting of constitutive parameters. In the area of method development, analytical tools are developed to determine the available precision of this type of experiment—a crucial aspect to determine if the method is to be used for quantitative studies. We also extract kinematic information relating to intragranular inhomogeneity which is not accessible with traditional methods of data analysis. In the area of constitutive parameter identification, we use the method to extract parameters corresponding to the proposed formulation of plasticity for a titanium alloy (HCP) which is continuously sampled by X-ray diffraction during uniaxial extension. These results and the lessons learned from the efforts constitute early reporting of the quantitative profitability of undertaking such a line of experimentation for the study of plastic deformation processes.

Response of broilers to feeding low-calcium and phosphorus diets plus phytase under different environmental conditions: body weight and tibiotarsus mineralization.

PubMed

Catalá-Gregori, P; García, V; Hernández, F; Madrid, J; Cerón, J J

2006-11-01

Three experiments on Ross broiler chickens were conducted in 3 locations: cages (Experiment 1), floor pens (Experiment 2), and commercial farms (Experiment 3). The effect of low-total P (TP) wheat-soybean based diets plus microbial phytase (Natuphos) was evaluated. Four experimental starter and finisher diets were used in a 2-phase feeding program, as follows: control diet (SC until 21 d, FC from 22 to 42 d); 2 diets (SL400 and SL600 until 21 d, FL400 and FL600 from 22 to 42 d) with low TP (0.61% for starter and 0.54% for finisher), including 400 and 600 U/kg of phytase, respectively; and a very low-TP (0.52% for starter and 0.44% for finisher) diet (SVL600 until 21 d, FVL600 from 22 to 42 d) with 600 U/kg of phytase. In Experiment 1 (broilers in cages had movement limitation and no access to litter), no differences in BW, tibiotarsus mineralization, or mineral metabolism were observed among diets. In Experiment 2 (broilers in floor pens had movement limitation and access to litter), at 21 d of age, the lowest tibiotarsus ash percentage and BW were shown by birds fed the SVL600 diet. At 42 d of age, broilers fed the FC diet were the lightest. For the rest of the parameters of tibiotarsus mineralization and mineral metabolism measured in Experiment 2, no differences were shown. In Experiment 3 (broilers in commercial farms had access to litter without movement limitation), the BW of broilers fed the SC diet was the highest at 21 d of age. At 42 d of age, the broilers fed FL400 and FL600 diets were the heaviest. At the end of Experiment 3, broilers fed the FC diet had the highest dry litter Ca and P, whereas broilers fed the FVL600 diet had the lowest values. In conclusion, the very low-TP wheat-soybean based diet supplemented with 600 U/kg of phytase was sufficient to optimize all the parameters measured in Experiment 1 but not in Experiments 2 and 3. Therefore, when evaluating Ca and P in phytase-supplemented diets for broilers, it is necessary to bear in mind the environmental conditions of experimentation.

Ten new predicted covalent organic frameworks with strong optical response in the visible and near infrared

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

Yang, Li-Ming, E-mail: lmyang.uio@gmail.com, E-mail: ganzx001@umn.edu; Frauenheim, Thomas; Dornfeld, Matthew

2015-06-28

We use density functional theory to predict and evaluate 10 novel covalent organic frameworks (COFs), labeled (X{sub 4}Y)(BDC){sub 3}, (X = C/Si; Y = C, Si, Ge, Sn, and Pb), with topology based on metal organic framework isoreticular metal-organic framework (IRMOF-1), but with new elements substituted for the corner atoms. We show that these new materials are stable structures using frequency calculations. For two structures, (C{sub 4}C and Si{sub 4}C) molecular dynamics simulations were performed to demonstrate stability of the systems up to 600 K for 10 ps. This demonstrates the remarkable stability of these systems, some of which maymore » be experimentally accessible. For the C{sub 4}C material, we also explored the stability of isolated corners and linkers and vacuum and started to build the structure from these pieces. We discuss the equilibrium lattice parameters, formation enthalpies, electronic structures, chemical bonding, and mechanical and optical properties. The predicted bulk moduli of these COFs range from 18.9 to 23.9 GPa, larger than that of IRMOF-1 (ca. 15.4 GPa), and larger than many existing 3D COF materials. The band gaps range from 1.5 to 2.1 eV, corresponding to 600–830 nm wavelength (orange through near infrared). The negative values of the formation enthalpy suggest that they are stable and should be experimentally accessible under suitable conditions. Seven materials distort the crystal structure to a lower space group symmetry Fm-3, while three materials maintain the original Fm-3m space group symmetry. All of the new materials are highly luminescent. We hope that this work will inspire efforts for experimental synthesis of these new materials.« less

Can High Quality Overcome Consumer Resistance to Restricted Provider Access? Evidence from a Health Plan Choice Experiment

PubMed Central

Harris, Katherine M

2002-01-01

Objective To investigate the impact of quality information on the willingness of consumers to enroll in health plans that restrict provider access. Data Sources and Setting A survey administered to respondents between the ages of 25 and 64 in the West Los Angeles area with private health insurance. Study Design An experimental approach is used to measure the effect of variation in provider network features and information about the quality of network physicians on hypothetical plan choices. Conditional logit models are used to analyze the experimental choice data. Next, choice model parameter estimates are used to simulate the impact of changes in plan features on the market shares of competing health plans and to calculate the quality level required to make consumers indifferent to changes in provider access. Principal Findings The presence of quality information reduced the importance of provider network features in plan choices as hypothesized. However, there were not statistically meaningful differences by type of quality measure (i.e., consumer assessed versus expert assessed). The results imply that large quality differences are required to make consumers indifferent to changes in provider access. The impact of quality on plan choices depended more on the particular measure and less on the type of measure. Quality ratings based on the proportion of survey respondents “extremely satisfied with results of care” had the greatest impact on plan choice while the proportion of network doctors “affiliated with university medical centers” had the least. Other consumer and expert assessed measures had more comparable effects. Conclusions Overall the results provide empirical evidence that consumers are willing to trade high quality for restrictions on provider access. This willingness to trade implies that relatively small plans that place restrictions on provider access can successfully compete against less restrictive plans when they can demonstrate high quality. However, the results of this study suggest that in many cases, the level of quality required for consumers to accept access restrictions may be so high as to be unattainable. The results provide empirical support for the current focus of decision support efforts on consumer assessed quality measures. At the same time, however, the results suggest that consumers would also value quality measures based on expert assessments. This finding is relevant given the lack of comparative quality information based on expert judgment and research suggesting that consumers have apprehensions about their ability to meaningfully interpret performance-based quality measures. PMID:12132595

Optimal experimental design for improving the estimation of growth parameters of Lactobacillus viridescens from data under non-isothermal conditions.

PubMed

Longhi, Daniel Angelo; Martins, Wiaslan Figueiredo; da Silva, Nathália Buss; Carciofi, Bruno Augusto Mattar; de Aragão, Gláucia Maria Falcão; Laurindo, João Borges

2017-01-02

In predictive microbiology, the model parameters have been estimated using the sequential two-step modeling (TSM) approach, in which primary models are fitted to the microbial growth data, and then secondary models are fitted to the primary model parameters to represent their dependence with the environmental variables (e.g., temperature). The Optimal Experimental Design (OED) approach allows reducing the experimental workload and costs, and the improvement of model identifiability because primary and secondary models are fitted simultaneously from non-isothermal data. Lactobacillus viridescens was selected to this study because it is a lactic acid bacterium of great interest to meat products preservation. The objectives of this study were to estimate the growth parameters of L. viridescens in culture medium from TSM and OED approaches and to evaluate both the number of experimental data and the time needed in each approach and the confidence intervals of the model parameters. Experimental data for estimating the model parameters with TSM approach were obtained at six temperatures (total experimental time of 3540h and 196 experimental data of microbial growth). Data for OED approach were obtained from four optimal non-isothermal profiles (total experimental time of 588h and 60 experimental data of microbial growth), two profiles with increasing temperatures (IT) and two with decreasing temperatures (DT). The Baranyi and Roberts primary model and the square root secondary model were used to describe the microbial growth, in which the parameters b and T min (±95% confidence interval) were estimated from the experimental data. The parameters obtained from TSM approach were b=0.0290 (±0.0020) [1/(h 0.5 °C)] and T min =-1.33 (±1.26) [°C], with R 2 =0.986 and RMSE=0.581, and the parameters obtained with the OED approach were b=0.0316 (±0.0013) [1/(h 0.5 °C)] and T min =-0.24 (±0.55) [°C], with R 2 =0.990 and RMSE=0.436. The parameters obtained from OED approach presented smaller confidence intervals and best statistical indexes than those from TSM approach. Besides, less experimental data and time were needed to estimate the model parameters with OED than TSM. Furthermore, the OED model parameters were validated with non-isothermal experimental data with great accuracy. In this way, OED approach is feasible and is a very useful tool to improve the prediction of microbial growth under non-isothermal condition. Copyright © 2016 Elsevier B.V. All rights reserved.

Observation of Prethermalization in Long-Range Interacting Spin Chains (Open Access, Author’s Manuscript)

DTIC Science & Technology

2016-08-03

instance, quantum systems that are near-integrable usually fail to thermalize in an experimentally realistic time scale and, instead, relax to quasi ...However, it is possible to observe quasi -stationary states, often called prethermal, that emerge within an experimentally accessible time scale. Previous...generalized Gibbs ensemble (GGE) [10–13]. Here we experimentally study the relaxation dynamics of a chain of up to 22 spins evolving under a long-range

Comparison between different thickness umbrella-shaped expandable radiofrequency electrodes (SuperSlim and CoAccess): Experimental and clinical study

PubMed Central

KODA, MASAHIKO; TOKUNAGA, SHIHO; MATONO, TOMOMITSU; SUGIHARA, TAKAAKI; NAGAHARA, TAKAKAZU; MURAWAKI, YOSHIKAZU

2011-01-01

The purpose of the present study was to compare the size and configuration of the ablation zones created by SuperSlim and CoAccess electrodes, using various ablation algorithms in ex vivo bovine liver and in clinical cases. In the experimental study, we ablated explanted bovine liver using 2 types of electrodes and 4 ablation algorithms (combinations of incremental power supply, stepwise expansion and additional low-power ablation) and evaluated the ablation area and time. In the clinical study, we compared the ablation volume and the shape of the ablation zone between both electrodes in 23 hepatocellular carcinoma (HCC) cases with the best algorithm (incremental power supply, stepwise expansion and additional low-power ablation) as derived from the experimental study. In the experimental study, the ablation area and time by the CoAccess electrode were significantly greater compared to those by the SuperSlim electrode for the single-step (algorithm 1, p=0.0209 and 0.0325, respectively) and stepwise expansion algorithms (algorithm 2, p=0.0002 and <0.0001, respectively; algorithm 3, p= 0.006 and 0.0407, respectively). However, differences were not significant for the additional low-power ablation algorithm. In the clinical study, the ablation volume and time in the CoAccess group were significantly larger and longer, respectively, compared to those in the SuperSlim group (p=0.0242 and 0.009, respectively). Round ablation zones were acquired in 91.7% of the CoAccess group, while irregular ablation zones were obtained in 45.5% of the SuperSlim group (p=0.0428). In conclusion, the CoAccess electrode achieves larger and more uniform ablation zones compared with the SuperSlim electrode, though it requires longer ablation times in experimental and clinical studies. PMID:22977647

Potential description of charmonium and charmed-strange mesons from lattice QCD

NASA Astrophysics Data System (ADS)

Kawanai, Taichi; Sasaki, Shoichi

2015-11-01

We present spin-independent and spin-spin interquark potentials for the charmonium and charmed-strange mesons, which are calculated in 2 +1 flavor lattice QCD simulations using the PACS-CS gauge configurations generated at the lightest pion mass (Mπ≈156 (7 ) MeV ) with a lattice cutoff of a-1≈2.2 GeV and a spatial volume of (3 fm )3 . For the charm quark, we use a relativistic heavy quark (RHQ) action with fine tuned RHQ parameters, which closely reproduce both the experimental spin-averaged mass and hyperfine splitting of the 1 S charmonium. The interquark potential and the quark kinetic mass, both of which are key ingredients within the potential description of heavy-heavy and heavy-light mesons, are determined from the equal-time Bethe-Salpeter (BS) amplitude. The charmonium potentials are obtained from the BS wave function of 1 S charmonia (ηc and J /ψ mesons), while the charmed-strange potential are calculated from the Ds and Ds* heavy-light mesons. We then use resulting potentials and quark masses as purely theoretical inputs so as to solve the nonrelativistic Schrödinger equation for calculating accessible energy levels of charmonium and charmed-strange mesons without unknown parameters. The resultant spectra below the D D ¯ and D K thresholds excellently agree with well-established experimental data.

Field-Theoretic Simulations

NASA Astrophysics Data System (ADS)

Ganesan, Venkat; Fredrickson, Glenn H.

The science and engineering of materials is entering a new era of so-called "designer materials", wherein, based upon the properties required for a particular application, a material is designed by exploiting the self-assembly of appropriately chosen molecular constituents [1]. The desirable and marketable properties of such materials, which include plastic alloys, block and graft copolymers, and polyelectrolyte solutions, complexes, and gels, depend critically on the ability to control and manipulate morphology by adjusting a combination of molecular and macroscopic variables. For example, styrenebutadiene block copolymers can be devised that serve either as rigid, tough, transparent thermoplastics or as soft, flexible, thermoplastic elastomers, by appropriate control of copolymer architecture and styrene/butadiene ratio. In this case, the property profiles are intimately connected to the extent and type of nanoscale self-assembly that is established within the material. One of the main challenges confronting the successful design of nano-structured polymers is the development of a basic understanding of the relationship between the molecular details of the polymer formulation and the morphology that is achieved. Unfortunately, such relationships are still mainly determined by trial and error experimentation. A purely experimental-based program in pursuit of this objective proves cumbersome — primarily, due to the broad parameter space accessible at the time of synthesis and formulation. Consequently, there is a significant motivation for the development of computational tools that can enable a rational exploration of the parameter space.

Noisy Oscillations in the Actin Cytoskeleton of Chemotactic Amoeba.

PubMed

Negrete, Jose; Pumir, Alain; Hsu, Hsin-Fang; Westendorf, Christian; Tarantola, Marco; Beta, Carsten; Bodenschatz, Eberhard

2016-09-30

Biological systems with their complex biochemical networks are known to be intrinsically noisy. Here we investigate the dynamics of actin polymerization of amoeboid cells, which are close to the onset of oscillations. We show that the large phenotypic variability in the polymerization dynamics can be accurately captured by a generic nonlinear oscillator model in the presence of noise. We determine the relative role of the noise with a single dimensionless, experimentally accessible parameter, thus providing a quantitative description of the variability in a population of cells. Our approach, which rests on a generic description of a system close to a Hopf bifurcation and includes the effect of noise, can characterize the dynamics of a large class of noisy systems close to an oscillatory instability.

Towards a data-driven analysis of hadronic light-by-light scattering

NASA Astrophysics Data System (ADS)

Colangelo, Gilberto; Hoferichter, Martin; Kubis, Bastian; Procura, Massimiliano; Stoffer, Peter

2014-11-01

The hadronic light-by-light contribution to the anomalous magnetic moment of the muon was recently analyzed in the framework of dispersion theory, providing a systematic formalism where all input quantities are expressed in terms of on-shell form factors and scattering amplitudes that are in principle accessible in experiment. We briefly review the main ideas behind this framework and discuss the various experimental ingredients needed for the evaluation of one- and two-pion intermediate states. In particular, we identify processes that in the absence of data for doubly-virtual pion-photon interactions can help constrain parameters in the dispersive reconstruction of the relevant input quantities, the pion transition form factor and the helicity partial waves for γ*γ* → ππ.

THE Role OF Anisotropy AND Intermittency IN Solar Wind/Magnetosphere Coupling

NASA Astrophysics Data System (ADS)

Jankovicova, D.; Voros, Z.

2006-12-01

Turbulent fluctuations are common in the solar wind as well as in the Earth's magnetosphere. The fluctuations of both magnetic field and plasma parameters exhibit non-Gaussian statistics. Neither the amplitude of these fluctuations nor their spectral characteristics can provide a full statistical description of multi-scale features in turbulence. It substantiates a statistical approach including the estimation of experimentally accessible statistical moments. In this contribution, we will directly estimate the third (skewness) and the fourth (kurtosis) statistical moments from the available time series of magnetic measurements in the solar wind (ACE and WIND spacecraft) and in the Earth's magnetosphere (SYM-H index). Then we evaluate how the statistical moments change during strong and weak solar wind/magnetosphere coupling intervals.

Acoustic environmental accuracy requirements for response determination

NASA Technical Reports Server (NTRS)

Pettitt, M. R.

1983-01-01

A general purpose computer program was developed for the prediction of vehicle interior noise. This program, named VIN, has both modal and statistical energy analysis capabilities for structural/acoustic interaction analysis. The analytic models and their computer implementation were verified through simple test cases with well-defined experimental results. The model was also applied in a space shuttle payload bay launch acoustics prediction study. The computer program processes large and small problems with equal efficiency because all arrays are dynamically sized by program input variables at run time. A data base is built and easily accessed for design studies. The data base significantly reduces the computational costs of such studies by allowing the reuse of the still-valid calculated parameters of previous iterations.

Noisy Oscillations in the Actin Cytoskeleton of Chemotactic Amoeba

NASA Astrophysics Data System (ADS)

Negrete, Jose; Pumir, Alain; Hsu, Hsin-Fang; Westendorf, Christian; Tarantola, Marco; Beta, Carsten; Bodenschatz, Eberhard

2016-09-01

Biological systems with their complex biochemical networks are known to be intrinsically noisy. Here we investigate the dynamics of actin polymerization of amoeboid cells, which are close to the onset of oscillations. We show that the large phenotypic variability in the polymerization dynamics can be accurately captured by a generic nonlinear oscillator model in the presence of noise. We determine the relative role of the noise with a single dimensionless, experimentally accessible parameter, thus providing a quantitative description of the variability in a population of cells. Our approach, which rests on a generic description of a system close to a Hopf bifurcation and includes the effect of noise, can characterize the dynamics of a large class of noisy systems close to an oscillatory instability.

Metamaterial-inspired silicon nanophotonics

NASA Astrophysics Data System (ADS)

Staude, Isabelle; Schilling, Jörg

2017-04-01

The prospect of creating metamaterials with optical properties greatly exceeding the parameter space accessible with natural materials has been inspiring intense research efforts in nanophotonics for more than a decade. Following an era of plasmonic metamaterials, low-loss dielectric nanostructures have recently moved into the focus of metamaterial-related research. This development was mainly triggered by the experimental observation of electric and magnetic multipolar Mie-type resonances in high-refractive-index dielectric nanoparticles. Silicon in particular has emerged as a popular material choice, due to not only its high refractive index and very low absorption losses in the telecom spectral range, but also its paramount technological relevance. This Review overviews recent progress on metamaterial-inspired silicon nanostructures, including Mie-resonant and off-resonant regimes.

Space Station tethered elevator system

NASA Technical Reports Server (NTRS)

Haddock, Michael H.; Anderson, Loren A.; Hosterman, K.; Decresie, E.; Miranda, P.; Hamilton, R.

1989-01-01

The optimized conceptual engineering design of a space station tethered elevator is presented. The tethered elevator is an unmanned, mobile structure which operates on a ten-kilometer tether spanning the distance between Space Station Freedom and a platform. Its capabilities include providing access to residual gravity levels, remote servicing, and transportation to any point along a tether. The report discusses the potential uses, parameters, and evolution of the spacecraft design. Emphasis is placed on the elevator's structural configuration and three major subsystem designs. First, the design of elevator robotics used to aid in elevator operations and tethered experimentation is presented. Second, the design of drive mechanisms used to propel the vehicle is discussed. Third, the design of an onboard self-sufficient power generation and transmission system is addressed.

High Density Memory Based on Quantum Device Technology

NASA Technical Reports Server (NTRS)

vanderWagt, Paul; Frazier, Gary; Tang, Hao

1995-01-01

We explore the feasibility of ultra-high density memory based on quantum devices. Starting from overall constraints on chip area, power consumption, access speed, and noise margin, we deduce boundaries on single cell parameters such as required operating voltage and standby current. Next, the possible role of quantum devices is examined. Since the most mature quantum device, the resonant tunneling diode (RTD) can easily be integrated vertically, it naturally leads to the issue of 3D integrated memory. We propose a novel method of addressing vertically integrated bistable two-terminal devices, such as resonant tunneling diodes (RTD) and Esaki diodes, that avoids individual physical contacts. The new concept has been demonstrated experimentally in memory cells of field effect transistors (FET's) and stacked RTD's.

Research related to roads in USDA experimental forests [Chapter 16

Treesearch

W. J. Elliot; P. J. Edwards; R. B. Foltz

2014-01-01

Forest roads are essential in experimental forests and rangelands (EFRs) to allow researchers and the public access to research sites and for fire suppression, timber extraction, and fuel management. Sediment from roads can adversely impact watershed health. Since the 1930s, the design and management of forest roads has addressed both access issues and watershed health...

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

A novel and lightweight system to secure wireless medical sensor networks.

PubMed

He, Daojing; Chan, Sammy; Tang, Shaohua

2014-01-01

Wireless medical sensor networks (MSNs) are a key enabling technology in e-healthcare that allows the data of a patient's vital body parameters to be collected by the wearable or implantable biosensors. However, the security and privacy protection of the collected data is a major unsolved issue, with challenges coming from the stringent resource constraints of MSN devices, and the high demand for both security/privacy and practicality. In this paper, we propose a lightweight and secure system for MSNs. The system employs hash-chain based key updating mechanism and proxy-protected signature technique to achieve efficient secure transmission and fine-grained data access control. Furthermore, we extend the system to provide backward secrecy and privacy preservation. Our system only requires symmetric-key encryption/decryption and hash operations and is thus suitable for the low-power sensor nodes. This paper also reports the experimental results of the proposed system in a network of resource-limited motes and laptop PCs, which show its efficiency in practice. To the best of our knowledge, this is the first secure data transmission and access control system for MSNs until now.

Experimental realization of an entanglement access network and secure multi-party computation

PubMed Central

Chang, X.-Y.; Deng, D.-L.; Yuan, X.-X.; Hou, P.-Y.; Huang, Y.-Y.; Duan, L.-M.

2016-01-01

To construct a quantum network with many end users, it is critical to have a cost-efficient way to distribute entanglement over different network ends. We demonstrate an entanglement access network, where the expensive resource, the entangled photon source at the telecom wavelength and the core communication channel, is shared by many end users. Using this cost-efficient entanglement access network, we report experimental demonstration of a secure multiparty computation protocol, the privacy-preserving secure sum problem, based on the network quantum cryptography. PMID:27404561

Right-to-try laws and individual patient "compassionate use" of experimental oncology medications: A call for improved provider-patient communication.

PubMed

Hoerger, Michael

2016-01-01

The U.S. Food and Drug Administration's Expanded Access program allows patients with life-threatening diagnoses, such as advanced cancer, to use experimental medications without participating in clinical research (colloquially, "Compassionate Use"). Sixteen U.S. states recently passed "right-to-try" legislation aimed at promoting Expanded Access. Acknowledging popular support, Expanded Access could undermine clinical trials that benefit public health. Moreover, existing norms in oncologic care, for example, often lead patients to pursue intense treatments near the end of life, at the expense of palliation, and improved communication about the risks and benefits of Expanded Access would more often discourage its use.

A miniaturized, optically accessible bioreactor for systematic 3D tissue engineering research.

PubMed

Laganà, Matteo; Raimondi, Manuela T

2012-02-01

Perfusion bioreactors are widely used in tissue engineering and pharmaceutical research to provide reliable models of tissue growth under controlled conditions. Destructive assays are not able to follow the evolution of the growing tissue on the same construct, so it is necessary to adopt non-destructive analysis. We have developed a miniaturized, optically accessible bioreactor for interstitial perfusion of 3D cell-seeded scaffolds. The scaffold adopted was optically transparent, with highly defined architecture. Computational fluid dynamics (CFD) analysis was useful to predict the flow behavior in the bioreactor scaffold chamber (that was laminar flow, Re = 0.179, with mean velocity equal to 100 microns/s). Moreover, experimental characterization of the bioreactor performance gave that the maximum allowable pressure was 0.06 MPa and allowable flow rate up to 25 ml/min. A method, to estimate quantitatively and non destructively the cell proliferation (from 15 to 43 thousand cells) and tissue growth (from 2% to 43%) during culture time, was introduced and validated. An end point viability test was performed to check the experimental set-up overall suitability for cell culture with successful results. Morphological analysis was performed at the end time point to show the complex tridimensional pattern of the biological tissue growth. Our system, characterized by controlled conditions in a wide range of allowable flow rate and pressure, permits to systematically study the influence of several parameters on engineered tissue growth, using viable staining and a standard fluorescence microscope.

Wireless Technology Recognition Based on RSSI Distribution at Sub-Nyquist Sampling Rate for Constrained Devices.

PubMed

Liu, Wei; Kulin, Merima; Kazaz, Tarik; Shahid, Adnan; Moerman, Ingrid; De Poorter, Eli

2017-09-12

Driven by the fast growth of wireless communication, the trend of sharing spectrum among heterogeneous technologies becomes increasingly dominant. Identifying concurrent technologies is an important step towards efficient spectrum sharing. However, due to the complexity of recognition algorithms and the strict condition of sampling speed, communication systems capable of recognizing signals other than their own type are extremely rare. This work proves that multi-model distribution of the received signal strength indicator (RSSI) is related to the signals' modulation schemes and medium access mechanisms, and RSSI from different technologies may exhibit highly distinctive features. A distinction is made between technologies with a streaming or a non-streaming property, and appropriate feature spaces can be established either by deriving parameters such as packet duration from RSSI or directly using RSSI's probability distribution. An experimental study shows that even RSSI acquired at a sub-Nyquist sampling rate is able to provide sufficient features to differentiate technologies such as Wi-Fi, Long Term Evolution (LTE), Digital Video Broadcasting-Terrestrial (DVB-T) and Bluetooth. The usage of the RSSI distribution-based feature space is illustrated via a sample algorithm. Experimental evaluation indicates that more than 92% accuracy is achieved with the appropriate configuration. As the analysis of RSSI distribution is straightforward and less demanding in terms of system requirements, we believe it is highly valuable for recognition of wideband technologies on constrained devices in the context of dynamic spectrum access.

Mesoscopic fluctuations in biharmonically driven flux qubits

NASA Astrophysics Data System (ADS)

Ferrón, Alejandro; Domínguez, Daniel; Sánchez, María José

2017-01-01

We investigate flux qubits driven by a biharmonic magnetic signal, with a phase lag that acts as an effective time reversal broken parameter. The driving induced transition rate between the ground and the excited state of the flux qubit can be thought of as an effective transmittance, profiting from a direct analogy between interference effects at avoided level crossings and scattering events in disordered electronic systems. For time scales prior to full relaxation, but large compared to the decoherence time, this characteristic rate has been accessed experimentally by Gustavsson et al. [Phys. Rev. Lett. 110, 016603 (2013)], 10.1103/PhysRevLett.110.016603 and its sensitivity with both the phase lag and the dc flux detuning explored. In this way, signatures of universal conductance fluctuationslike effects have been analyzed and compared with predictions from a phenomenological model that only accounts for decoherence, as a classical noise. Here we go beyond the classical noise model and solve the full dynamics of the driven flux qubit in contact with a quantum bath employing the Floquet-Born-Markov master equation. Within this formalism, the computed relaxation and decoherence rates turn out to be strongly dependent on both the phase lag and the dc flux detuning. Consequently, the associated pattern of fluctuations in the characteristic rates display important differences with those obtained within the mentioned phenomenological model. In particular, we demonstrate the weak localizationlike effect in the average values of the relaxation rate. Our predictions can be tested for accessible but longer time scales than the current experimental times.

Wireless Technology Recognition Based on RSSI Distribution at Sub-Nyquist Sampling Rate for Constrained Devices

PubMed Central

Liu, Wei; Kulin, Merima; Kazaz, Tarik; De Poorter, Eli

2017-01-01

Driven by the fast growth of wireless communication, the trend of sharing spectrum among heterogeneous technologies becomes increasingly dominant. Identifying concurrent technologies is an important step towards efficient spectrum sharing. However, due to the complexity of recognition algorithms and the strict condition of sampling speed, communication systems capable of recognizing signals other than their own type are extremely rare. This work proves that multi-model distribution of the received signal strength indicator (RSSI) is related to the signals’ modulation schemes and medium access mechanisms, and RSSI from different technologies may exhibit highly distinctive features. A distinction is made between technologies with a streaming or a non-streaming property, and appropriate feature spaces can be established either by deriving parameters such as packet duration from RSSI or directly using RSSI’s probability distribution. An experimental study shows that even RSSI acquired at a sub-Nyquist sampling rate is able to provide sufficient features to differentiate technologies such as Wi-Fi, Long Term Evolution (LTE), Digital Video Broadcasting-Terrestrial (DVB-T) and Bluetooth. The usage of the RSSI distribution-based feature space is illustrated via a sample algorithm. Experimental evaluation indicates that more than 92% accuracy is achieved with the appropriate configuration. As the analysis of RSSI distribution is straightforward and less demanding in terms of system requirements, we believe it is highly valuable for recognition of wideband technologies on constrained devices in the context of dynamic spectrum access. PMID:28895879

Formation and field-driven dynamics of nematic spheroids.

PubMed

Fu, Fred; Abukhdeir, Nasser Mohieddin

2017-07-19

Unlike the canonical application of liquid crystals (LCs), LC displays, emerging technologies based on LC materials are increasingly leveraging the presence of nanoscale defects. The inherent nanoscale characteristics of LC defects present both significant opportunities as well as barriers for the application of this fascinating class of materials. Simulation-based approaches to the study of the effects of confinement and interface anchoring conditions on LC domains has resulted in significant progress over the past decade, where simulations are now able to access experimentally-relevant length scales while simultaneously capturing nanoscale defect structures. In this work, continuum simulations were performed in order to study the dynamics of micron-scale nematic LC spheroids of varying shape. Nematic spheroids are one of the simplest inherently defect-containing LC structures and are relevant to polymer-dispersed LC-based "smart" window technology. Simulation results include nematic phase formation and external field-switching dynamics of nematic spheroids ranging in shape from oblate to prolate. Results include both qualitative and quantitative insight into the complex coupling of nanoscale defect dynamics and structure transitions to micron-scale reorientation. Dynamic mechanisms are presented and related to structural transitions in LC defects present in the nematic domain. Domain-averaged metrics including order parameters and response times are determined for a range of experimentally-accessible electric field strengths. These results have both fundamental and technological relevance, in that increased understanding of LC dynamics in the presence of defects is a key barrier to continued advancement in the field.

PyCoTools: A Python Toolbox for COPASI.

PubMed

Welsh, Ciaran M; Fullard, Nicola; Proctor, Carole J; Martinez-Guimera, Alvaro; Isfort, Robert J; Bascom, Charles C; Tasseff, Ryan; Przyborski, Stefan A; Shanley, Daryl P

2018-05-22

COPASI is an open source software package for constructing, simulating and analysing dynamic models of biochemical networks. COPASI is primarily intended to be used with a graphical user interface but often it is desirable to be able to access COPASI features programmatically, with a high level interface. PyCoTools is a Python package aimed at providing a high level interface to COPASI tasks with an emphasis on model calibration. PyCoTools enables the construction of COPASI models and the execution of a subset of COPASI tasks including time courses, parameter scans and parameter estimations. Additional 'composite' tasks which use COPASI tasks as building blocks are available for increasing parameter estimation throughput, performing identifiability analysis and performing model selection. PyCoTools supports exploratory data analysis on parameter estimation data to assist with troubleshooting model calibrations. We demonstrate PyCoTools by posing a model selection problem designed to show case PyCoTools within a realistic scenario. The aim of the model selection problem is to test the feasibility of three alternative hypotheses in explaining experimental data derived from neonatal dermal fibroblasts in response to TGF-β over time. PyCoTools is used to critically analyse the parameter estimations and propose strategies for model improvement. PyCoTools can be downloaded from the Python Package Index (PyPI) using the command 'pip install pycotools' or directly from GitHub (https://github.com/CiaranWelsh/pycotools). Documentation at http://pycotools.readthedocs.io. Supplementary data are available at Bioinformatics.

A Quasi-Experimental Evaluation of Parents as Sexual Health Educators Resulting in Delayed Sexual Initiation and Increased Access to Condoms

ERIC Educational Resources Information Center

Campero, Lourdes; Walker, Dilys; Atienzo, Erika E.; Gutierrez, Juan Pablo

2011-01-01

Objective: To evaluate the effectiveness of an educational intervention for parents of first year high school students in the State of Morelos, Mexico, whose aim was to impact adolescents' sexual behavior, knowledge and access to contraception. Material and methods: Quasi-experimental prospective study with eleven control and eleven intervention…

Effect of processing parameters on FDM process

NASA Astrophysics Data System (ADS)

Chari, V. Srinivasa; Venkatesh, P. R.; Krupashankar, Dinesh, Veena

2018-04-01

This paper focused on the process parameters on fused deposition modeling (FDM). Infill, resolution, temperature are the process variables considered for experimental studies. Compression strength, Hardness test microstructure are the outcome parameters, this experimental study done based on the taguchi's L9 orthogonal array is used. Taguchi array used to build the 9 different models and also to get the effective output results on the under taken parameters. The material used for this experimental study is Polylactic Acid (PLA).

Rapid and precise determination of zero-field splittings by terahertz time-domain electron paramagnetic resonance spectroscopy† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc00830a Click here for additional data file.

PubMed Central

Lu, Jian; Ozel, I. Ozge; Belvin, Carina A.; Li, Xian; Skorupskii, Grigorii; Sun, Lei; Ofori-Okai, Benjamin K.; Dincă, Mircea; Gedik, Nuh

2017-01-01

Zero-field splitting (ZFS) parameters are fundamentally tied to the geometries of metal ion complexes. Despite their critical importance for understanding the magnetism and spectroscopy of metal complexes, they are not routinely available through general laboratory-based techniques, and are often inferred from magnetism data. Here we demonstrate a simple tabletop experimental approach that enables direct and reliable determination of ZFS parameters in the terahertz (THz) regime. We report time-domain measurements of electron paramagnetic resonance (EPR) signals associated with THz-frequency ZFSs in molecular complexes containing high-spin transition-metal ions. We measure the temporal profiles of the free-induction decays of spin resonances in the complexes at zero and nonzero external magnetic fields, and we derive the EPR spectra via numerical Fourier transformation of the time-domain signals. In most cases, absolute values of the ZFS parameters are extracted from the measured zero-field EPR frequencies, and the signs can be determined by zero-field measurements at two different temperatures. Field-dependent EPR measurements further allow refined determination of the ZFS parameters and access to the g-factor. The results show good agreement with those obtained by other methods. The simplicity of the method portends wide applicability in chemistry, biology and material science. PMID:29163882

Topological superconductivity in an ultrathin, magnetically-doped topological insulator proximity coupled to a conventional superconductor

NASA Astrophysics Data System (ADS)

Kim, Youngseok; Philip, Timothy M.; Park, Moon Jip; Gilbert, Matthew J.

2016-12-01

As a promising candidate system to realize topological superconductivity, the system of a 3D topological insulator (TI) grown on top of the s -wave superconductor has been extensively studied. To access the topological superconductivity experimentally, the 3D TI sample must be thin enough to allow for Cooper pair tunneling to the exposed surface of TI. The use of magnetically ordered dopants to break time-reversal symmetry may allow the surface of a TI to host Majorana fermion, which are believed to be a signature of topological superconductivity. In this work, we study a magnetically-doped thin film TI-superconductor hybrid system. Considering the proximity induced order parameter in thin film of TI, we analyze the gap closing points of the Hamiltonian and draw the phase diagram as a function of relevant parameters: the hybridization gap, Zeeman energy, and chemical potential of the TI system. Our findings provide a useful guide in choosing relevant parameters to facilitate the observation of topological superconductivity in thin film TI-superconductor hybrid systems. In addition, we further perform numerical analysis on a TI proximity coupled to an s -wave superconductor and find that, due to the spin-momentum locked nature of the surface states in TI, the induced s -wave order parameter of the surface states persists even at large magnitude of the Zeeman energy.

Data publication with the structural biology data grid supports live analysis

DOE PAGES

Meyer, Peter A.; Socias, Stephanie; Key, Jason; ...

2016-03-07

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of themore » original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. In conclusion, it is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.« less

Data publication with the structural biology data grid supports live analysis

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

Meyer, Peter A.; Socias, Stephanie; Key, Jason

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of themore » original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. In conclusion, it is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.« less

Data publication with the structural biology data grid supports live analysis.

PubMed

Meyer, Peter A; Socias, Stephanie; Key, Jason; Ransey, Elizabeth; Tjon, Emily C; Buschiazzo, Alejandro; Lei, Ming; Botka, Chris; Withrow, James; Neau, David; Rajashankar, Kanagalaghatta; Anderson, Karen S; Baxter, Richard H; Blacklow, Stephen C; Boggon, Titus J; Bonvin, Alexandre M J J; Borek, Dominika; Brett, Tom J; Caflisch, Amedeo; Chang, Chung-I; Chazin, Walter J; Corbett, Kevin D; Cosgrove, Michael S; Crosson, Sean; Dhe-Paganon, Sirano; Di Cera, Enrico; Drennan, Catherine L; Eck, Michael J; Eichman, Brandt F; Fan, Qing R; Ferré-D'Amaré, Adrian R; Fromme, J Christopher; Garcia, K Christopher; Gaudet, Rachelle; Gong, Peng; Harrison, Stephen C; Heldwein, Ekaterina E; Jia, Zongchao; Keenan, Robert J; Kruse, Andrew C; Kvansakul, Marc; McLellan, Jason S; Modis, Yorgo; Nam, Yunsun; Otwinowski, Zbyszek; Pai, Emil F; Pereira, Pedro José Barbosa; Petosa, Carlo; Raman, C S; Rapoport, Tom A; Roll-Mecak, Antonina; Rosen, Michael K; Rudenko, Gabby; Schlessinger, Joseph; Schwartz, Thomas U; Shamoo, Yousif; Sondermann, Holger; Tao, Yizhi J; Tolia, Niraj H; Tsodikov, Oleg V; Westover, Kenneth D; Wu, Hao; Foster, Ian; Fraser, James S; Maia, Filipe R N C; Gonen, Tamir; Kirchhausen, Tom; Diederichs, Kay; Crosas, Mercè; Sliz, Piotr

2016-03-07

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.

Data publication with the structural biology data grid supports live analysis

PubMed Central

Meyer, Peter A.; Socias, Stephanie; Key, Jason; Ransey, Elizabeth; Tjon, Emily C.; Buschiazzo, Alejandro; Lei, Ming; Botka, Chris; Withrow, James; Neau, David; Rajashankar, Kanagalaghatta; Anderson, Karen S.; Baxter, Richard H.; Blacklow, Stephen C.; Boggon, Titus J.; Bonvin, Alexandre M. J. J.; Borek, Dominika; Brett, Tom J.; Caflisch, Amedeo; Chang, Chung-I; Chazin, Walter J.; Corbett, Kevin D.; Cosgrove, Michael S.; Crosson, Sean; Dhe-Paganon, Sirano; Di Cera, Enrico; Drennan, Catherine L.; Eck, Michael J.; Eichman, Brandt F.; Fan, Qing R.; Ferré-D'Amaré, Adrian R.; Christopher Fromme, J.; Garcia, K. Christopher; Gaudet, Rachelle; Gong, Peng; Harrison, Stephen C.; Heldwein, Ekaterina E.; Jia, Zongchao; Keenan, Robert J.; Kruse, Andrew C.; Kvansakul, Marc; McLellan, Jason S.; Modis, Yorgo; Nam, Yunsun; Otwinowski, Zbyszek; Pai, Emil F.; Pereira, Pedro José Barbosa; Petosa, Carlo; Raman, C. S.; Rapoport, Tom A.; Roll-Mecak, Antonina; Rosen, Michael K.; Rudenko, Gabby; Schlessinger, Joseph; Schwartz, Thomas U.; Shamoo, Yousif; Sondermann, Holger; Tao, Yizhi J.; Tolia, Niraj H.; Tsodikov, Oleg V.; Westover, Kenneth D.; Wu, Hao; Foster, Ian; Fraser, James S.; Maia, Filipe R. N C.; Gonen, Tamir; Kirchhausen, Tom; Diederichs, Kay; Crosas, Mercè; Sliz, Piotr

2016-01-01

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis. PMID:26947396

A flexible, interactive software tool for fitting the parameters of neuronal models.

PubMed

Friedrich, Péter; Vella, Michael; Gulyás, Attila I; Freund, Tamás F; Káli, Szabolcs

2014-01-01

The construction of biologically relevant neuronal models as well as model-based analysis of experimental data often requires the simultaneous fitting of multiple model parameters, so that the behavior of the model in a certain paradigm matches (as closely as possible) the corresponding output of a real neuron according to some predefined criterion. Although the task of model optimization is often computationally hard, and the quality of the results depends heavily on technical issues such as the appropriate choice (and implementation) of cost functions and optimization algorithms, no existing program provides access to the best available methods while also guiding the user through the process effectively. Our software, called Optimizer, implements a modular and extensible framework for the optimization of neuronal models, and also features a graphical interface which makes it easy for even non-expert users to handle many commonly occurring scenarios. Meanwhile, educated users can extend the capabilities of the program and customize it according to their needs with relatively little effort. Optimizer has been developed in Python, takes advantage of open-source Python modules for nonlinear optimization, and interfaces directly with the NEURON simulator to run the models. Other simulators are supported through an external interface. We have tested the program on several different types of problems of varying complexity, using different model classes. As targets, we used simulated traces from the same or a more complex model class, as well as experimental data. We successfully used Optimizer to determine passive parameters and conductance densities in compartmental models, and to fit simple (adaptive exponential integrate-and-fire) neuronal models to complex biological data. Our detailed comparisons show that Optimizer can handle a wider range of problems, and delivers equally good or better performance than any other existing neuronal model fitting tool.

A flexible, interactive software tool for fitting the parameters of neuronal models

PubMed Central

Friedrich, Péter; Vella, Michael; Gulyás, Attila I.; Freund, Tamás F.; Káli, Szabolcs

2014-01-01

The construction of biologically relevant neuronal models as well as model-based analysis of experimental data often requires the simultaneous fitting of multiple model parameters, so that the behavior of the model in a certain paradigm matches (as closely as possible) the corresponding output of a real neuron according to some predefined criterion. Although the task of model optimization is often computationally hard, and the quality of the results depends heavily on technical issues such as the appropriate choice (and implementation) of cost functions and optimization algorithms, no existing program provides access to the best available methods while also guiding the user through the process effectively. Our software, called Optimizer, implements a modular and extensible framework for the optimization of neuronal models, and also features a graphical interface which makes it easy for even non-expert users to handle many commonly occurring scenarios. Meanwhile, educated users can extend the capabilities of the program and customize it according to their needs with relatively little effort. Optimizer has been developed in Python, takes advantage of open-source Python modules for nonlinear optimization, and interfaces directly with the NEURON simulator to run the models. Other simulators are supported through an external interface. We have tested the program on several different types of problems of varying complexity, using different model classes. As targets, we used simulated traces from the same or a more complex model class, as well as experimental data. We successfully used Optimizer to determine passive parameters and conductance densities in compartmental models, and to fit simple (adaptive exponential integrate-and-fire) neuronal models to complex biological data. Our detailed comparisons show that Optimizer can handle a wider range of problems, and delivers equally good or better performance than any other existing neuronal model fitting tool. PMID:25071540

Dissolution study of active pharmaceutical ingredients using molecular dynamics simulations with classical force fields

NASA Astrophysics Data System (ADS)

Greiner, Maximilian; Elts, Ekaterina; Schneider, Julian; Reuter, Karsten; Briesen, Heiko

2014-11-01

The CHARMM, general Amber and OPLS force fields are evaluated for their suitability in simulating the molecular dynamics of the dissolution of the hydrophobic, small-molecule active pharmaceutical ingredients aspirin, ibuprofen, and paracetamol in aqueous media. The force fields are evaluated by comparison with quantum chemical simulations or experimental references on the basis of the following capabilities: accurately representing intra- and intermolecular interactions, appropriately reproducing crystal lattice parameters, adequately describing thermodynamic properties, and the qualitative description of the dissolution behavior. To make this approach easily accessible for evaluating the dissolution properties of novel drug candidates in the early stage of drug development, the force field parameter files are generated using online resources such as the SWISS PARAM servers, and the software packages ACPYPE and Maestro. All force fields are found to reproduce the intermolecular interactions with a reasonable degree of accuracy, with the general Amber and CHARMM force fields showing the best agreement with quantum mechanical calculations. A stable crystal bulk structure is obtained for all model substances, except for ibuprofen, where the reproductions of the lattice parameters and observed crystal stability are considerably poor for all force fields. The heat of solution used to evaluate the solid-to-solution phase transitions is found to be in qualitative agreement with the experimental data for all combinations tested, with the results being quantitatively optimum for the general Amber and CHARMM force fields. For aspirin and paracetamol, stable crystal-water interfaces were obtained. The (100), (110), (011) and (001) interfaces of aspirin or paracetamol and water were simulated for each force field for 30 ns. Although generally expected as a rare event, in some of the simulations, dissolution is observed at 310 K and ambient pressure conditions.

An NMR database for simulations of membrane dynamics.

PubMed

Leftin, Avigdor; Brown, Michael F

2011-03-01

Computational methods are powerful in capturing the results of experimental studies in terms of force fields that both explain and predict biological structures. Validation of molecular simulations requires comparison with experimental data to test and confirm computational predictions. Here we report a comprehensive database of NMR results for membrane phospholipids with interpretations intended to be accessible by non-NMR specialists. Experimental ¹³C-¹H and ²H NMR segmental order parameters (S(CH) or S(CD)) and spin-lattice (Zeeman) relaxation times (T(1Z)) are summarized in convenient tabular form for various saturated, unsaturated, and biological membrane phospholipids. Segmental order parameters give direct information about bilayer structural properties, including the area per lipid and volumetric hydrocarbon thickness. In addition, relaxation rates provide complementary information about molecular dynamics. Particular attention is paid to the magnetic field dependence (frequency dispersion) of the NMR relaxation rates in terms of various simplified power laws. Model-free reduction of the T(1Z) studies in terms of a power-law formalism shows that the relaxation rates for saturated phosphatidylcholines follow a single frequency-dispersive trend within the MHz regime. We show how analytical models can guide the continued development of atomistic and coarse-grained force fields. Our interpretation suggests that lipid diffusion and collective order fluctuations are implicitly governed by the viscoelastic nature of the liquid-crystalline ensemble. Collective bilayer excitations are emergent over mesoscopic length scales that fall between the molecular and bilayer dimensions, and are important for lipid organization and lipid-protein interactions. Future conceptual advances and theoretical reductions will foster understanding of biomembrane structural dynamics through a synergy of NMR measurements and molecular simulations. Copyright © 2010 Elsevier B.V. All rights reserved.

Investigating the Energetic Ordering of Stable and Metastable TiO 2 Polymorphs Using DFT+ U and Hybrid Functionals

DOE PAGES

Curnan, Matthew T.; Kitchin, John R.

2015-08-12

Prediction of transition metal oxide BO 2 (B = Ti, V, etc.) polymorph energetic properties is critical to tunable material design and identifying thermodynamically accessible structures. Determining procedures capable of synthesizing particular polymorphs minimally requires prior knowledge of their relative energetic favorability. Information concerning TiO 2 polymorph relative energetic favorability has been ascertained from experimental research. In this study, the consistency of first-principles predictions and experimental results involving the relative energetic ordering of stable (rutile), metastable (anatase and brookite), and unstable (columbite) TiO 2 polymorphs is assessed via density functional theory (DFT). Considering the issues involving electron–electron interaction and chargemore » delocalization in TiO 2 calculations, relative energetic ordering predictions are evaluated over trends varying Ti Hubbard U 3d or exact exchange fraction parameter values. Energetic trends formed from varying U 3d predict experimentally consistent energetic ordering over U 3d intervals when using GGA-based functionals, regardless of pseudopotential selection. Given pertinent linear response calculated Hubbard U values, these results enable TiO 2 polymorph energetic ordering prediction. Here, the hybrid functional calculations involving rutile–anatase relative energetics, though demonstrating experimentally consistent energetic ordering over exact exchange fraction ranges, are not accompanied by predicted fractions, for a first-principles methodology capable of calculating exact exchange fractions precisely predicting TiO 2 polymorph energetic ordering is not available.« less

Ab initio thermodynamic model for magnesium carbonates and hydrates.

PubMed

Chaka, Anne M; Felmy, Andrew R

2014-09-04

An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first-principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogues of Ca-based hydrated carbonates monohydrocalcite and ikaite, which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.

Thermodynamically consistent model calibration in chemical kinetics

PubMed Central

2011-01-01

Background The dynamics of biochemical reaction systems are constrained by the fundamental laws of thermodynamics, which impose well-defined relationships among the reaction rate constants characterizing these systems. Constructing biochemical reaction systems from experimental observations often leads to parameter values that do not satisfy the necessary thermodynamic constraints. This can result in models that are not physically realizable and may lead to inaccurate, or even erroneous, descriptions of cellular function. Results We introduce a thermodynamically consistent model calibration (TCMC) method that can be effectively used to provide thermodynamically feasible values for the parameters of an open biochemical reaction system. The proposed method formulates the model calibration problem as a constrained optimization problem that takes thermodynamic constraints (and, if desired, additional non-thermodynamic constraints) into account. By calculating thermodynamically feasible values for the kinetic parameters of a well-known model of the EGF/ERK signaling cascade, we demonstrate the qualitative and quantitative significance of imposing thermodynamic constraints on these parameters and the effectiveness of our method for accomplishing this important task. MATLAB software, using the Systems Biology Toolbox 2.1, can be accessed from http://www.cis.jhu.edu/~goutsias/CSS lab/software.html. An SBML file containing the thermodynamically feasible EGF/ERK signaling cascade model can be found in the BioModels database. Conclusions TCMC is a simple and flexible method for obtaining physically plausible values for the kinetic parameters of open biochemical reaction systems. It can be effectively used to recalculate a thermodynamically consistent set of parameter values for existing thermodynamically infeasible biochemical reaction models of cellular function as well as to estimate thermodynamically feasible values for the parameters of new models. Furthermore, TCMC can provide dimensionality reduction, better estimation performance, and lower computational complexity, and can help to alleviate the problem of data overfitting. PMID:21548948

Experimental realization of a multiplexed quantum memory with 225 individually accessible memory cells.

PubMed

Pu, Y-F; Jiang, N; Chang, W; Yang, H-X; Li, C; Duan, L-M

2017-05-08

To realize long-distance quantum communication and quantum network, it is required to have multiplexed quantum memory with many memory cells. Each memory cell needs to be individually addressable and independently accessible. Here we report an experiment that realizes a multiplexed DLCZ-type quantum memory with 225 individually accessible memory cells in a macroscopic atomic ensemble. As a key element for quantum repeaters, we demonstrate that entanglement with flying optical qubits can be stored into any neighboring memory cells and read out after a programmable time with high fidelity. Experimental realization of a multiplexed quantum memory with many individually accessible memory cells and programmable control of its addressing and readout makes an important step for its application in quantum information technology.

Right-to-Try Laws and Individual Patient “Compassionate Use” of Experimental Oncology Medications: A Call for Improved Provider-Patient Communication

PubMed Central

Hoerger, Michael

2016-01-01

The U.S. Food and Drug Administration’s Expanded Access program allows patients with life-threatening diagnoses, such as advanced cancer, to use experimental medications without participating in clinical research (colloquially, “Compassionate Use”). Sixteen U.S. states recently passed “right-to-try” legislation aimed at promoting Expanded Access. Acknowledging popular support, Expanded Access could undermine clinical trials that benefit public health. Moreover, existing norms in oncologic care, for example, often lead patients to pursue intense treatments near the end of life, at the expense of palliation, and improved communication about the risks and benefits of Expanded Access would more often discourage its use. PMID:26313583

A Lab Assembled Microcontroller-Based Sensor Module for Continuous Oxygen Measurement in Portable Hypoxia Chambers

PubMed Central

Mathupala, Saroj P.; Kiousis, Sam; Szerlip, Nicholas J.

2016-01-01

Background Hypoxia-based cell culture experiments are routine and essential components of in vitro cancer research. Most laboratories use low-cost portable modular chambers to achieve hypoxic conditions for cell cultures, where the sealed chambers are purged with a gas mixture of preset O2 concentration. Studies are conducted under the assumption that hypoxia remains unaltered throughout the 48 to 72 hour duration of such experiments. Since these chambers lack any sensor or detection system to monitor gas-phase O2, the cell-based data tend to be non-uniform due to the ad hoc nature of the experimental setup. Methodology With the availability of low-cost open-source microcontroller-based electronic project kits, it is now possible for researchers to program these with easy-to-use software, link them to sensors, and place them in basic scientific apparatus to monitor and record experimental parameters. We report here the design and construction of a small-footprint kit for continuous measurement and recording of O2 concentration in modular hypoxia chambers. The low-cost assembly (US$135) consists of an Arduino-based microcontroller, data-logging freeware, and a factory pre-calibrated miniature O2 sensor. A small, intuitive software program was written by the authors to control the data input and output. The basic nature of the kit will enable any student in biology with minimal experience in hobby-electronics to assemble the system and edit the program parameters to suit individual experimental conditions. Results/Conclusions We show the kit’s utility and stability of data output via a series of hypoxia experiments. The studies also demonstrated the critical need to monitor and adjust gas-phase O2 concentration during hypoxia-based experiments to prevent experimental errors or failure due to partial loss of hypoxia. Thus, incorporating the sensor-microcontroller module to a portable hypoxia chamber provides a researcher a capability that was previously available only to labs with access to sophisticated (and expensive) cell culture incubators. PMID:26862760

A Lab Assembled Microcontroller-Based Sensor Module for Continuous Oxygen Measurement in Portable Hypoxia Chambers.

PubMed

Mathupala, Saroj P; Kiousis, Sam; Szerlip, Nicholas J

2016-01-01

Hypoxia-based cell culture experiments are routine and essential components of in vitro cancer research. Most laboratories use low-cost portable modular chambers to achieve hypoxic conditions for cell cultures, where the sealed chambers are purged with a gas mixture of preset O2 concentration. Studies are conducted under the assumption that hypoxia remains unaltered throughout the 48 to 72 hour duration of such experiments. Since these chambers lack any sensor or detection system to monitor gas-phase O2, the cell-based data tend to be non-uniform due to the ad hoc nature of the experimental setup. With the availability of low-cost open-source microcontroller-based electronic project kits, it is now possible for researchers to program these with easy-to-use software, link them to sensors, and place them in basic scientific apparatus to monitor and record experimental parameters. We report here the design and construction of a small-footprint kit for continuous measurement and recording of O2 concentration in modular hypoxia chambers. The low-cost assembly (US$135) consists of an Arduino-based microcontroller, data-logging freeware, and a factory pre-calibrated miniature O2 sensor. A small, intuitive software program was written by the authors to control the data input and output. The basic nature of the kit will enable any student in biology with minimal experience in hobby-electronics to assemble the system and edit the program parameters to suit individual experimental conditions. We show the kit's utility and stability of data output via a series of hypoxia experiments. The studies also demonstrated the critical need to monitor and adjust gas-phase O2 concentration during hypoxia-based experiments to prevent experimental errors or failure due to partial loss of hypoxia. Thus, incorporating the sensor-microcontroller module to a portable hypoxia chamber provides a researcher a capability that was previously available only to labs with access to sophisticated (and expensive) cell culture incubators.

Elasticity of short DNA molecules: theory and experiment for contour lengths of 0.6-7 microm.

PubMed

Seol, Yeonee; Li, Jinyu; Nelson, Philip C; Perkins, Thomas T; Betterton, M D

2007-12-15

The wormlike chain (WLC) model currently provides the best description of double-stranded DNA elasticity for micron-sized molecules. This theory requires two intrinsic material parameters-the contour length L and the persistence length p. We measured and then analyzed the elasticity of double-stranded DNA as a function of L (632 nm-7.03 microm) using the classic solution to the WLC model. When the elasticity data were analyzed using this solution, the resulting fitted value for the persistence length p(wlc) depended on L; even for moderately long DNA molecules (L = 1300 nm), this apparent persistence length was 10% smaller than its limiting value for long DNA. Because p is a material parameter, and cannot depend on length, we sought a new solution to the WLC model, which we call the "finite wormlike chain (FWLC)," to account for effects not considered in the classic solution. Specifically we accounted for the finite chain length, the chain-end boundary conditions, and the bead rotational fluctuations inherent in optical trapping assays where beads are used to apply the force. After incorporating these corrections, we used our FWLC solution to generate force-extension curves, and then fit those curves with the classic WLC solution, as done in the standard experimental analysis. These results qualitatively reproduced the apparent dependence of p(wlc) on L seen in experimental data when analyzed with the classic WLC solution. Directly fitting experimental data to the FWLC solution reduces the apparent dependence of p(fwlc) on L by a factor of 3. Thus, the FWLC solution provides a significantly improved theoretical framework in which to analyze single-molecule experiments over a broad range of experimentally accessible DNA lengths, including both short (a few hundred nanometers in contour length) and very long (microns in contour length) molecules.

Convergence in parameters and predictions using computational experimental design.

PubMed

Hagen, David R; White, Jacob K; Tidor, Bruce

2013-08-06

Typically, biological models fitted to experimental data suffer from significant parameter uncertainty, which can lead to inaccurate or uncertain predictions. One school of thought holds that accurate estimation of the true parameters of a biological system is inherently problematic. Recent work, however, suggests that optimal experimental design techniques can select sets of experiments whose members probe complementary aspects of a biochemical network that together can account for its full behaviour. Here, we implemented an experimental design approach for selecting sets of experiments that constrain parameter uncertainty. We demonstrated with a model of the epidermal growth factor-nerve growth factor pathway that, after synthetically performing a handful of optimal experiments, the uncertainty in all 48 parameters converged below 10 per cent. Furthermore, the fitted parameters converged to their true values with a small error consistent with the residual uncertainty. When untested experimental conditions were simulated with the fitted models, the predicted species concentrations converged to their true values with errors that were consistent with the residual uncertainty. This paper suggests that accurate parameter estimation is achievable with complementary experiments specifically designed for the task, and that the resulting parametrized models are capable of accurate predictions.

Nucleosome stability and accessibility of its DNA to proteins.

PubMed

Prinsen, Peter; Schiessel, Helmut

2010-12-01

In this paper we present a theoretical description of the accessibility of nucleosomal DNA to proteins. We reassess the classical analysis of Polach and Widom (1995) who demonstrated that proteins (in their case restriction enzymes) gain access to buried binding sites inside a nucleosome through spontaneous unwrapping of DNA from the protein spool. We introduce a straightforward nucleosome model the predictions of which show good agreement with experimental data. By fitting the model to the data we obtain the values of two quantities: the adsorption energy to the histone octamer per length of DNA and the extra length that the DNA needs to unwrap beyond the binding site of an enzyme before the enzyme can act as effectively as on bare DNA. Our results indicate that the effective binding energy is surprisingly low which suggests that the nucleosomal parameters are tuned such that two large energies, the DNA bending energy and the pure adsorption energy, nearly cancel. This paper is based on a lecture presented at the summer school "DNA and Chromosomes 2009: Physical and Biological Applications". We follow the lecture as closely as possible which is why we spend more time than usual on issues that are already well-known in the field, and why we discuss some well-known results from a different perspective. Copyright © 2010 Elsevier Masson SAS. All rights reserved.

Evidence that attitude accessibility augments the relationship between speeding attitudes and speeding behavior: a test of the MODE model in the context of driving.

PubMed

Elliott, Mark A; Lee, Emme; Robertson, Jamie S; Innes, Rhona

2015-01-01

According to the MODE model of attitude-to-behavior processes, attitude accessibility augments attitude-behavior correspondence, reflecting an automatic influence of attitudes on behavior. We therefore tested whether attitude accessibility moderates the attitude-behavior relationship in a context that is governed by characteristically automatic behavior, namely driving. In study 1 (correlational design), participants (N=130) completed online questionnaire measures of the valences and accessibilities of their attitudes towards speeding. Two weeks later, online questionnaire measures of subsequent speeding behavior were obtained. Attitude valence was a significantly better predictor of behavior at high (mean+1SD) versus low (mean-1SD) levels of attitude accessibility. In study 2 (experimental design), attitude accessibility was manipulated with a repeated attitude expression task. Immediately after the manipulation, participants (N=122) completed online questionnaire measures of attitude valence and accessibility, and two weeks later, subsequent speeding behavior. Increased attitude accessibility in the experimental (versus control) condition generated an increase in attitude-behavior correspondence. The findings are consistent with the MODE model's proposition that attitudes can exert an automatic influence on behavior. Interventions to reduce speeding could usefully increase the accessibility of anti-speeding attitudes and reduce the accessibility of pro-speeding attitudes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Right-to-Try Investigational Therapies for Incurable Disorders.

PubMed

Simmons, Zachary

2017-10-01

Patients with life-threatening disorders such as amyotrophic lateral sclerosis, for which only minimally effective medical therapies currently exist, often seek treatments not proven to be effective and not approved by regulatory agencies for use outside of experimental treatment trials. The expanded access (compassionate use) provisions of the US Food and Drug Administration (FDA) for access to such therapies are often perceived as being inadequate. In response, states have passed right-to-try laws designed to improve access to experimental therapies for patients willing to assume the risks associated with such treatments. This situation has resulted in conflicts between those who perceive access to such treatments as their right as autonomous individuals and those who believe that the principles of beneficence and nonmaleficence justify actions of physicians and regulators in controlling access to such treatments. A variety of factors also contribute to the inequitable distribution of such treatments. Better systems are needed to improve access to promising new treatments while protecting these vulnerable patients from the abuses associated with human research in the preregulatory era.

On the generalization of attitude accessibility after repeated attitude expression

PubMed Central

Spruyt, Adriaan; Fazio, Russell H.; Hermans, Dirk

2016-01-01

Abstract The more accessible an attitude is, the stronger is its influence on information processing and behavior. Accessibility can be increased through attitude rehearsal, but it remains unknown whether attitude rehearsal also affects the accessibility of related attitudes. To investigate this hypothesis, participants in an experimental condition repeatedly expressed their attitudes towards exemplars of several semantic categories during an evaluative categorization task. Participants in a control condition performed a non‐evaluative task with the same exemplars and evaluated unrelated attitude objects. After a 30‐minute interval, participants in the experimental condition were faster than controls to evaluate not only the original exemplars but also novel exemplars of the same categories. This finding suggests that the effect of attitude rehearsal on accessibility generalizes to attitudes towards untrained but semantically related attitude objects. © 2016 The Authors. European Journal of Social Psychology published by John Wiley & Sons, Ltd. PMID:28701803

A qualitative quantum rate model for hydrogen transfer in soybean lipoxygenase

NASA Astrophysics Data System (ADS)

Jevtic, S.; Anders, J.

2017-09-01

The hydrogen transfer reaction catalysed by soybean lipoxygenase (SLO) has been the focus of intense study following observations of a high kinetic isotope effect (KIE). Today high KIEs are generally thought to indicate departure from classical rate theory and are seen as a strong signature of tunnelling of the transferring particle, hydrogen or one of its isotopes, through the reaction energy barrier. In this paper, we build a qualitative quantum rate model with few free parameters that describes the dynamics of the transferring particle when it is exposed to energetic potentials exerted by the donor and the acceptor. The enzyme's impact on the dynamics is modelled by an additional energetic term, an oscillatory contribution known as "gating." By varying two key parameters, the gating frequency and the mean donor-acceptor separation, the model is able to reproduce well the KIE data for SLO wild-type and a variety of SLO mutants over the experimentally accessible temperature range. While SLO-specific constants have been considered here, it is possible to adapt these for other enzymes.

Implementation of EPICS based vacuum control system for variable energy cyclotron centre, Kolkata

NASA Astrophysics Data System (ADS)

Roy, Anindya; Bhole, R. B.; Nandy, Partha P.; Yadav, R. C.; Pal, Sarbajit; Roy, Amitava

2015-03-01

The vacuum system of the Room Temperature (K = 130) Cyclotron of Variable Energy Cyclotron Centre is comprised of vacuum systems of main machine and Beam Transport System. The vacuum control system is upgraded to a PLC based Automated system from the initial relay based Manual system. The supervisory control of the vacuum system is implemented in Experimental Physics and Industrial Control System (EPICS). An EPICS embedded ARM based vacuum gauge controller is developed to mitigate the requirement of vendor specific gauge controller for gauges and also for seamless integration of the gauge controllers with the control system. A set of MS-Windows ActiveX components with embedded EPICS Channel Access interface are developed to build operator interfaces with less complex programming and to incorporate typical Windows feature, e.g., user authentication, file handling, better fonts, colors, mouse actions etc. into the operator interfaces. The control parameters, monitoring parameters, and system interlocks of the system are archived in MySQL based EPICS MySQL Archiver developed indigenously. In this paper, we describe the architecture, the implementation details, and the performance of the system.

Development of a rotating electric field conductance sensor for measurement of water holdup in vertical oil–gas–water flows

NASA Astrophysics Data System (ADS)

Wang, Da-Yang; Jin, Ning-De; Zhuang, Lian-Xin; Zhai, Lu-Sheng; Ren, Ying-Yu

2018-07-01

Three types of rotating electric field conductance sensors (REFCSs) with four, six, and eight electrodes are designed and optimized in this paper to measure the water holdup of oil–gas–water three-phase flow in vertical upward 20 mm inner diameter pipe. The geometric parameters of the REFCSs are optimized using finite element method to access highly sensitive and homogeneous detection fields. The performance of the REFCSs in the water holdup measurement of three-phase flows is experimentally evaluated by generalizing the Maxwell equation. Based on the measured water holdup from the REFCSs, the slippage behaviors in oil–gas–water are uncovered and the superficial velocity of the water phase is determined. The results show that the REFCSs present a high resolution in the water holdup measurement. The REFCS with eight electrodes has better performance than those with four- and six-electrodes, which indicates that its configuration and geometric parameters are more suitable for vertical oil–gas–water three-phase flow measurement in 20 mm inner diameter pipe.

A study of single and binary ion plasma expansion into laboratory-generated plasma wakes

NASA Technical Reports Server (NTRS)

Wright, Kenneth Herbert, Jr.

1988-01-01

Plasma expansion into the wake of a large rectangular plate immersed in a collisionless, supersonic plasma was investigated in laboratory experiments. The experimental conditions address both single ion and binary ion plasma flows for the case of a body whose size is large in comparison with the Debye length, when the potential difference between the body and the plasma is relatively small. A new plasma source was developed to generate equi-velocity, binary ion plasma flows, which allows access to new parameter space that have previously been unavailable for laboratory studies. Specifically, the new parameters are the ionic mass ratio and the ionic component density ratio. In a series of experiments, a krypton-neon plasma is employed where the ambient density ratio of neon to krypton is varied more than an order of magnitude. The expansion in both the single ion and binary ion plasma cases is limited to early times, i.e., a few ion plasma periods, by the combination of plasma density, plasma drift speed, and vacuum chamber size, which prevented detailed comparison with self-similar theory.

Modeling the kinetics of bubble nucleation in champagne and carbonated beverages.

PubMed

Liger-Belair, Gérard; Parmentier, Maryline; Jeandet, Philippe

2006-10-26

In champagne and carbonated beverages, bubble nucleation was mostly found to take place from tiny Taylor-like bubbles trapped inside immersed cellulose fibers stuck on the glass wall. The present paper complements a previous paper about the thorough examination of the bubble nucleation process in a flute poured with champagne (Liger-Belair et al. J. Phys. Chem. B 2005, 109, 14573). In this previous paper, a model was built that accurately reproduces the dynamics of these tiny Taylor-like bubbles that grow inside the fiber's lumen by diffusion of CO(2)-dissolved molecules. In the present paper, by use of the model recently developed, the frequency of bubble formation from cellulose fibers is accessed and linked with various liquid and fiber parameters, namely, the concentration c(L) of CO(2)-dissolved molecules, the liquid temperature theta, its viscosity eta, the ambient pressure P, the course of the gas pocket growing trapped inside the fiber's lumen before releasing a bubble, and the radius r of the fiber's lumen. The relative influence of the latter parameters on the bubbling frequency is discussed and supported with recent experimental observations and data.

Metallic coatings of microelectromechanical structures at low temperatures: Stress, elasticity, and nonlinear dissipation

NASA Astrophysics Data System (ADS)

Collin, E.; Kofler, J.; Lakhloufi, S.; Pairis, S.; Bunkov, Yu. M.; Godfrin, H.

2010-06-01

We present mechanical measurements performed at low temperatures on cantilever-based microelectromechanical structures coated with a metallic layer. Two very different coatings are presented in order to illustrate the capabilities of the present approach, namely (soft) aluminum and (hard) niobium oxide. The temperature is used as a control parameter to access materials properties. We benefit from low temperature techniques to extract a phase-resolved measurement of the first mechanical resonance mode in cryogenic vacuum. By repeating the experiment on the same samples, after multiple metallic depositions, we can determine accurately the contribution of the coating layers to the mechanical properties in terms of surface stress, additional mass, additional elasticity, and damping. Analytic theoretical expressions are derived and used to fit the data. Taking advantage of the extremely broad dynamic range provided by the technique, we can measure the anelasticity of the thin metallic film. The key parameters describing the metals' dynamics are analyzed in an original way in order to provide new experimental grounds for future theoretical modelings of the underlying mechanisms.

Implementation of EPICS based vacuum control system for variable energy cyclotron centre, Kolkata.

PubMed

Roy, Anindya; Bhole, R B; Nandy, Partha P; Yadav, R C; Pal, Sarbajit; Roy, Amitava

2015-03-01

The vacuum system of the Room Temperature (K = 130) Cyclotron of Variable Energy Cyclotron Centre is comprised of vacuum systems of main machine and Beam Transport System. The vacuum control system is upgraded to a PLC based Automated system from the initial relay based Manual system. The supervisory control of the vacuum system is implemented in Experimental Physics and Industrial Control System (EPICS). An EPICS embedded ARM based vacuum gauge controller is developed to mitigate the requirement of vendor specific gauge controller for gauges and also for seamless integration of the gauge controllers with the control system. A set of MS-Windows ActiveX components with embedded EPICS Channel Access interface are developed to build operator interfaces with less complex programming and to incorporate typical Windows feature, e.g., user authentication, file handling, better fonts, colors, mouse actions etc. into the operator interfaces. The control parameters, monitoring parameters, and system interlocks of the system are archived in MySQL based EPICS MySQL Archiver developed indigenously. In this paper, we describe the architecture, the implementation details, and the performance of the system.

Controlling the opto-mechanics of a cantilever in an interferometer via cavity loss

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

Schmidsfeld, A. von, E-mail: avonschm@uos.de; Reichling, M., E-mail: reichling@uos.de

2015-09-21

In a non-contact atomic force microscope, based on interferometric cantilever displacement detection, the optical return loss of the system is tunable via the distance between the fiber end and the cantilever. We utilize this for tuning the interferometer from a predominant Michelson to a predominant Fabry-Pérot characteristics and introduce the Fabry-Pérot enhancement factor as a quantitative measure for multibeam interference in the cavity. This experimentally easily accessible and adjustable parameter provides a control of the opto-mechanical interaction between the cavity light field and the cantilever. The quantitative assessment of the light pressure acting on the cantilever oscillating in the cavitymore » via the frequency shift allows an in-situ measurement of the cantilever stiffness with remarkable precision.« less

Interpreting Microbial Biosynthesis in the Genomic Age: Biological and Practical Considerations

PubMed Central

Miller, Ian J.; Chevrette, Marc G.; Kwan, Jason C.

2017-01-01

Genome mining has become an increasingly powerful, scalable, and economically accessible tool for the study of natural product biosynthesis and drug discovery. However, there remain important biological and practical problems that can complicate or obscure biosynthetic analysis in genomic and metagenomic sequencing projects. Here, we focus on limitations of available technology as well as computational and experimental strategies to overcome them. We review the unique challenges and approaches in the study of symbiotic and uncultured systems, as well as those associated with biosynthetic gene cluster (BGC) assembly and product prediction. Finally, to explore sequencing parameters that affect the recovery and contiguity of large and repetitive BGCs assembled de novo, we simulate Illumina and PacBio sequencing of the Salinispora tropica genome focusing on assembly of the salinilactam (slm) BGC. PMID:28587290

Exact results relating spin-orbit interactions in two-dimensional strongly correlated systems

NASA Astrophysics Data System (ADS)

Kucska, Nóra; Gulácsi, Zsolt

2018-06-01

A 2D square, two-bands, strongly correlated and non-integrable system is analysed exactly in the presence of many-body spin-orbit interactions via the method of Positive Semidefinite Operators. The deduced exact ground states in the high concentration limit are strongly entangled, and given by the spin-orbit coupling are ferromagnetic and present an enhanced carrier mobility, which substantially differs for different spin projections. The described state emerges in a restricted parameter space region, which however is clearly accessible experimentally. The exact solutions are provided via the solution of a matching system of equations containing 74 coupled, non-linear and complex algebraic equations. In our knowledge, other exact results for 2D interacting systems with spin-orbit interactions are not present in the literature.

Controllable high-fidelity quantum state transfer and entanglement generation in circuit QED.

PubMed

Xu, Peng; Yang, Xu-Chen; Mei, Feng; Xue, Zheng-Yuan

2016-01-25

We propose a scheme to realize controllable quantum state transfer and entanglement generation among transmon qubits in the typical circuit QED setup based on adiabatic passage. Through designing the time-dependent driven pulses applied on the transmon qubits, we find that fast quantum sate transfer can be achieved between arbitrary two qubits and quantum entanglement among the qubits also can also be engineered. Furthermore, we numerically analyzed the influence of the decoherence on our scheme with the current experimental accessible systematical parameters. The result shows that our scheme is very robust against both the cavity decay and qubit relaxation, the fidelities of the state transfer and entanglement preparation process could be very high. In addition, our scheme is also shown to be insensitive to the inhomogeneous of qubit-resonator coupling strengths.

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

Zhang, Y. B.; Budai, J. D.; Tischler, J. Z.

How boundaries surrounding recrystallization grains migrate through the 3D network of dislocation boundaries in deformed crystalline materials is unknown and critical for the resulting recrystallized crystalline materials. Furthermore, by using X-ray Laue diffraction microscopy, we show for the first time the migration pattern of a typical recrystallization boundary through a well-characterized deformation matrix. The data provide a unique possibility to investigate effects of both boundary misorientation and plane normal on the migration, information which cannot be accessed with any other techniques. Our results show that neither of these two parameters can explain the observed migration behavior. Instead we suggest thatmore » the subdivision of the deformed microstructure ahead of the boundary plays the dominant role. Our experimental observations challenge the assumptions of existing recrystallization theories, and set the stage for determination of mobilities of recrystallization boundaries.« less

Motility-Driven Glass and Jamming Transitions in Biological Tissues

NASA Astrophysics Data System (ADS)

Bi, Dapeng; Yang, Xingbo; Marchetti, M. Cristina; Manning, M. Lisa

2016-04-01

Cell motion inside dense tissues governs many biological processes, including embryonic development and cancer metastasis, and recent experiments suggest that these tissues exhibit collective glassy behavior. To make quantitative predictions about glass transitions in tissues, we study a self-propelled Voronoi model that simultaneously captures polarized cell motility and multibody cell-cell interactions in a confluent tissue, where there are no gaps between cells. We demonstrate that the model exhibits a jamming transition from a solidlike state to a fluidlike state that is controlled by three parameters: the single-cell motile speed, the persistence time of single-cell tracks, and a target shape index that characterizes the competition between cell-cell adhesion and cortical tension. In contrast to traditional particulate glasses, we are able to identify an experimentally accessible structural order parameter that specifies the entire jamming surface as a function of model parameters. We demonstrate that a continuum soft glassy rheology model precisely captures this transition in the limit of small persistence times and explain how it fails in the limit of large persistence times. These results provide a framework for understanding the collective solid-to-liquid transitions that have been observed in embryonic development and cancer progression, which may be associated with epithelial-to-mesenchymal transition in these tissues.

Toward Understanding Drug Incorporation and Delivery from Biocompatible Metal-Organic Frameworks in View of Cutaneous Administration.

PubMed

Rojas, Sara; Colinet, Isabel; Cunha, Denise; Hidalgo, Tania; Salles, Fabrice; Serre, Christian; Guillou, Nathalie; Horcajada, Patricia

2018-03-31

Although metal-organic frameworks (MOFs) have widely demonstrated their convenient performances as drug-delivery systems, there is still work to do to fully understand the drug incorporation/delivery processes from these materials. In this work, a combined experimental and computational investigation of the main structural and physicochemical parameters driving drug adsorption/desorption kinetics was carried out. Two model drugs (aspirin and ibuprofen) and three water-stable, biocompatible MOFs (MIL-100(Fe), UiO-66(Zr), and MIL-127(Fe)) have been selected to obtain a variety of drug-matrix couples with different structural and physicochemical characteristics. This study evidenced that the drug-loading and drug-delivery processes are mainly governed by structural parameters (accessibility of the framework and drug volume) as well as the MOF/drug hydrophobic/hydrophilic balance. As a result, the delivery of the drug under simulated cutaneous conditions (aqueous media at 37 °C) demonstrated that these systems fulfill the requirements to be used as topical drug-delivery systems, such as released payload between 1 and 7 days. These results highlight the importance of the rational selection of MOFs, evidencing the effect of geometrical and chemical parameters of both the MOF and the drug on the drug adsorption and release.

Toward Understanding Drug Incorporation and Delivery from Biocompatible Metal–Organic Frameworks in View of Cutaneous Administration

PubMed Central

2018-01-01

Although metal–organic frameworks (MOFs) have widely demonstrated their convenient performances as drug-delivery systems, there is still work to do to fully understand the drug incorporation/delivery processes from these materials. In this work, a combined experimental and computational investigation of the main structural and physicochemical parameters driving drug adsorption/desorption kinetics was carried out. Two model drugs (aspirin and ibuprofen) and three water-stable, biocompatible MOFs (MIL-100(Fe), UiO-66(Zr), and MIL-127(Fe)) have been selected to obtain a variety of drug–matrix couples with different structural and physicochemical characteristics. This study evidenced that the drug-loading and drug-delivery processes are mainly governed by structural parameters (accessibility of the framework and drug volume) as well as the MOF/drug hydrophobic/hydrophilic balance. As a result, the delivery of the drug under simulated cutaneous conditions (aqueous media at 37 °C) demonstrated that these systems fulfill the requirements to be used as topical drug-delivery systems, such as released payload between 1 and 7 days. These results highlight the importance of the rational selection of MOFs, evidencing the effect of geometrical and chemical parameters of both the MOF and the drug on the drug adsorption and release. PMID:29623304

Optimization of Recycled Glass Fibre-Reinforced Plastics Gear via Integration of the Taguchi Method and Grey Relational Analysis

NASA Astrophysics Data System (ADS)

Mizamzul Mehat, Nik; Syuhada Zakarria, Noor; Kamaruddin, Shahrul

2018-03-01

The increase in demand for industrial gears has resulted in the increase in usage of plastic-matrix composites particularly glass fibre-reinforced plastics as the gear materials. The usage of these synthetic fibers is to enhance the mechanical strength and the thermal resistance of the plastic gears. Nevertheless, the production of large quantities of these synthetic fibre-reinforced composites poses a serious threat to the ecosystem. Comprehending to this fact, the present work aimed at investigating the effects of incorporating recycled glass fibre-reinforced plastics in various compositions particularly on dimensional stability and mechanical properties of gear produced with diverse injection moulding processing parameters setting. The integration of Grey relational analysis (GRA) and Taguchi method was adopted to evaluate the influence of recycled glass fibre-reinforced plastics and variation in processing parameters on gear quality. From the experimental results, the blending ratio was found as the most influential parameter of 56.0% contribution in both improving tensile properties as well as in minimizing shrinkage, followed by mould temperature of 24.1% contribution and cooling time of 10.6% contribution. The results obtained from the aforementioned work are expected to contribute to accessing the feasibility of using recycled glass fibre-reinforced plastics especially for gear application.

Experimental benchmark of the NINJA code for application to the Linac4 H- ion source plasma

NASA Astrophysics Data System (ADS)

Briefi, S.; Mattei, S.; Rauner, D.; Lettry, J.; Tran, M. Q.; Fantz, U.

2017-10-01

For a dedicated performance optimization of negative hydrogen ion sources applied at particle accelerators, a detailed assessment of the plasma processes is required. Due to the compact design of these sources, diagnostic access is typically limited to optical emission spectroscopy yielding only line-of-sight integrated results. In order to allow for a spatially resolved investigation, the electromagnetic particle-in-cell Monte Carlo collision code NINJA has been developed for the Linac4 ion source at CERN. This code considers the RF field generated by the ICP coil as well as the external static magnetic fields and calculates self-consistently the resulting discharge properties. NINJA is benchmarked at the diagnostically well accessible lab experiment CHARLIE (Concept studies for Helicon Assisted RF Low pressure Ion sourcEs) at varying RF power and gas pressure. A good general agreement is observed between experiment and simulation although the simulated electron density trends for varying pressure and power as well as the absolute electron temperature values deviate slightly from the measured ones. This can be explained by the assumption of strong inductive coupling in NINJA, whereas the CHARLIE discharges show the characteristics of loosely coupled plasmas. For the Linac4 plasma, this assumption is valid. Accordingly, both the absolute values of the accessible plasma parameters and their trends for varying RF power agree well in measurement and simulation. At varying RF power, the H- current extracted from the Linac4 source peaks at 40 kW. For volume operation, this is perfectly reflected by assessing the processes in front of the extraction aperture based on the simulation results where the highest H- density is obtained for the same power level. In surface operation, the production of negative hydrogen ions at the converter surface can only be considered by specialized beam formation codes, which require plasma parameters as input. It has been demonstrated that this input can be provided reliably by the NINJA code.

Three-particle annihilation in a 2D heterostructure revealed through data-hypercubic photoresponse microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Gabor, Nathaniel M.

2017-05-01

Van de Waals (vdW) heterostructures - which consist of precisely assembled atomically thin electronic materials - exhibit unusual quantum behavior. These quantum materials-by-design are of fundamental interest in basic scientific research and hold tremendous potential in advanced technological applications. Problematically, the fundamental optoelectronic response in these heterostructures is difficult to access using the standard techniques within the traditions of materials science and condensed matter physics. In the standard approach, characterization is based on the measurement of a small amount of one-dimensional data, which is used to gain a precise picture of the material properties of the sample. However, these techniques are fundamentally lacking in describing the complex interdependency of experimental degrees of freedom in vdW heterostructures. In this talk, I will present our recent experiments that utilize a highly data-intensive approach to gain deep understanding of the infrared photoresponse in vdW heterostructure photodetectors. These measurements, which combine state-of-the-art data analytics and measurement design with fundamentally new device structures and experimental parameters, give a clear picture of electron-hole pair interactions at ultrafast time scales.

Mathematical modelling of metabolic pathways affected by an enzyme deficiency. Energy and redox metabolism of glucose-6-phosphate-dehydrogenase-deficient erythrocytes.

PubMed

Schuster, R; Jacobasch, G; Holzhütter, H G

1989-07-01

The effects of various forms of glucose-6-phosphate dehydrogenase deficiency on erythrocyte metabolism have been studied on the basis of a complex mathematical model which comprises the main pathways of this cell: glycolysis, pentose pathway, reactions of the glutathione and adenine nucleotide metabolism. The calculated flux rates through the oxidative pentose pathway with and without methylene blue are in good accord with experimental results. The degree of deficiency as predicted by the model on the basis of calculated upper oxidative load boundaries, as well as of maximal methylene blue stimulation, correlates with the individual clinical manifestation of the metabolic disease. Therefore, the model allows one to judge the degree of metabolic disorder in the presence of glucose-6-phosphate dehydrogenase enzymopathies if the kinetic properties of the defect enzyme are known. Experimentally accessible parameters for an assessment of the oxidative load capacity of cells in vivo are proposed. It is pointed out that the threshold of tolerance as to energetic load is drastically reduced in the case of severe glucose-6-phosphate dehydrogenase deficiency.

Beam-Plasma Interaction Experiments on the Princeton Advanced Test Stand

NASA Astrophysics Data System (ADS)

Stepanov, A.; Gilson, E. P.; Grisham, L.; Kaganovich, I. D.; Davidson, R. C.

2011-10-01

The Princeton Advanced Test Stand (PATS) is a compact experimental facility for studying the fundamental physics of intense beam-plasma interactions relevant to the Neutralized Drift Compression Experiment - II (NDCX-II). The PATS facility consists of a 100 keV ion beam source mounted on a six-foot-long vacuum chamber with numerous ports for diagnostic access. A 100 keV Ar+ beam is launched into a volumetric plasma, which is produced by a ferroelectric plasma source (FEPS). Beam diagnostics upstream and downstream of the FEPS allow for detailed studies of the effects that the plasma has on the beam. This setup is designed for studying the dependence of charge and current neutralization and beam emittance growth on the beam and plasma parameters. This work reports initial measurements of beam quality produced by the extraction electrodes that were recently installed on the PATS device. The transverse beam phase space is measured with double-slit emittance scanners, and the experimental results are compared to WARP simulations of the extraction system. This research is supported by the U.S. Department of Energy.

Thermal conductivity of thin insulating films determined by tunnel magneto-Seebeck effect measurements and finite-element modeling

NASA Astrophysics Data System (ADS)

Huebner, Torsten; Martens, Ulrike; Walowski, Jakob; Münzenberg, Markus; Thomas, Andy; Reiss, Günter; Kuschel, Timo

2018-06-01

In general, it is difficult to access the thermal conductivity of thin insulating films experimentally by electrical means. Here, we present a new approach utilizing the tunnel magneto-Seebeck effect (TMS) in combination with finite-element modeling (FEM). We detect the laser-induced TMS and the absolute thermovoltage of laser-heated magnetic tunnel junctions with 2.6 nm thin barriers of MgAl2O4 (MAO) and MgO, respectively. A second measurement of the absolute thermovoltage after a dielectric breakdown of the barrier grants insight into the remaining thermovoltage of the stack. Thus, the pure TMS without any parasitic Nernst contributions from the leads can be identified. In combination with FEM via COMSOL, we are able to extract values for the thermal conductivity of MAO (0.7 W (K · m)‑1) and MgO (5.8 W (K · m)‑1), which are in very good agreement with theoretical predictions. Our method provides a new promising way to extract the experimentally challenging parameter of the thermal conductivity of thin insulating films.

Combinatorial Characterization of TiO2 Chemical Vapor Deposition Utilizing Titanium Isopropoxide.

PubMed

Reinke, Michael; Ponomarev, Evgeniy; Kuzminykh, Yury; Hoffmann, Patrik

2015-07-13

The combinatorial characterization of the growth kinetics in chemical vapor deposition processes is challenging because precise information about the local precursor flow is usually difficult to access. In consequence, combinatorial chemical vapor deposition techniques are utilized more to study functional properties of thin films as a function of chemical composition, growth rate or crystallinity than to study the growth process itself. We present an experimental procedure which allows the combinatorial study of precursor surface kinetics during the film growth using high vacuum chemical vapor deposition. As consequence of the high vacuum environment, the precursor transport takes place in the molecular flow regime, which allows predicting and modifying precursor impinging rates on the substrate with comparatively little experimental effort. In this contribution, we study the surface kinetics of titanium dioxide formation using titanium tetraisopropoxide as precursor molecule over a large parameter range. We discuss precursor flux and temperature dependent morphology, crystallinity, growth rates, and precursor deposition efficiency. We conclude that the surface reaction of the adsorbed precursor molecules comprises a higher order reaction component with respect to precursor surface coverage.

Spatially Localized Chemical Patterns around an A + B → Oscillator Front.

PubMed

Budroni, M A; Lemaigre, L; Escala, D M; Muñuzuri, A P; De Wit, A

2016-02-18

When two gels, each loaded with a different set of reactants A and B of an oscillatory reaction, are brought into contact, reaction-diffusion patterns such as waves or Turing patterns can develop in the reactive contact zone. The initial condition which separates the reactants at the beginning leads to a localization in space of the different dynamical regimes accessible to the chemical oscillator. We study here both numerically and experimentally the composite traveling structures resulting from the interaction between chemical fronts and localized waves in the case in which the reactants of such an A + B → oscillator system are those of the canonical Belousov-Zhabotinsky (BZ) oscillating reaction. A transition between different dynamics is obtained by varying the initial concentration of the organic substrate of the BZ reactants, which is one of the parameters controlling the local excitability. We show that the dynamical regime (excitable or oscillatory) characterizing the BZ oscillator in the initial contact area is the key feature which determines the spatiotemporal evolution of the system. The experimental results are in qualitative agreement with the theoretical predictions.

Magnetized Collisionless Shock Studies Using High Velocity Plasmoids

NASA Astrophysics Data System (ADS)

Weber, Thomas; Intrator, T.

2013-04-01

Magnetized collisionless shocks are ubiquitous throughout the cosmos and are observed to accelerate particles to relativistic velocities, amplify magnetic fields, transport energy, and create non-thermal distributions. They exhibit transitional scale lengths much shorter than the collisional mean free path and are mediated by collective interactions rather than Coulomb collisions. The Magnetized Shock Experiment (MSX) leverages advances in Field Reversed Configuration (FRC) plasmoid formation and acceleration to produce highly supersonic and super-Alfvénic supercritical shocks with pre-existing magnetic field at perpendicular, parallel or oblique angles to the direction of propagation. Adjustable shock speed, density, and magnetic field provide unique access to a range of parameter space relevant to a variety of naturally occurring shocks. This effort examines experimentally, analytically, and numerically the physics of collisionless shock formation, structure, and kinetic effects in a laboratory setting and draw comparisons between experimental data and astronomical observations. Supported by DOE Office of Fusion Energy Sciences and National Nuclear Security Administration under LANS contract DE-AC52-06NA25369 Approved for Public Release: LA-UR-12-22886

MLACP: machine-learning-based prediction of anticancer peptides

PubMed Central

Manavalan, Balachandran; Basith, Shaherin; Shin, Tae Hwan; Choi, Sun; Kim, Myeong Ok; Lee, Gwang

2017-01-01

Cancer is the second leading cause of death globally, and use of therapeutic peptides to target and kill cancer cells has received considerable attention in recent years. Identification of anticancer peptides (ACPs) through wet-lab experimentation is expensive and often time consuming; therefore, development of an efficient computational method is essential to identify potential ACP candidates prior to in vitro experimentation. In this study, we developed support vector machine- and random forest-based machine-learning methods for the prediction of ACPs using the features calculated from the amino acid sequence, including amino acid composition, dipeptide composition, atomic composition, and physicochemical properties. We trained our methods using the Tyagi-B dataset and determined the machine parameters by 10-fold cross-validation. Furthermore, we evaluated the performance of our methods on two benchmarking datasets, with our results showing that the random forest-based method outperformed the existing methods with an average accuracy and Matthews correlation coefficient value of 88.7% and 0.78, respectively. To assist the scientific community, we also developed a publicly accessible web server at www.thegleelab.org/MLACP.html. PMID:29100375

The Impact of Electronic Patient Portals on Patient Care: A Systematic Review of Controlled Trials

PubMed Central

Ammenwerth, Elske; Schnell-Inderst, Petra

2012-01-01

Background Modern information technology is changing and provides new challenges to health care. The emergence of the Internet and the electronic health record (EHR) has brought new opportunities for patients to play a more active role in his/her care. Although in many countries patients have the right to access their clinical information, access to clinical records electronically is not common. Patient portals consist of provider-tethered applications that allow patients to electronically access health information that are documented and managed by a health care institution. Although patient portals are already being implemented, it is still unclear in which ways these technologies can influence patient care. Objective To systematically review the available evidence on the impact of electronic patient portals on patient care. Methods A systematic search was conducted using PubMed and other sources to identify controlled experimental or quasi-experimental studies on the impact of patient portals that were published between 1990 and 2011. A total of 1,306 references from all the publication hits were screened, and 13 papers were retrieved for full text analysis. Results We identified 5 papers presenting 4 distinct studies. There were no statistically significant changes between intervention and control group in the 2 randomized controlled trials investigating the effect of patient portals on health outcomes. Significant changes in the patient portal group, compared to a control group, could be observed for the following parameters: quicker decrease in office visit rates and slower increase in telephone contacts; increase in number of messages sent; changes of the medication regimen; and better adherence to treatment. Conclusions The number of available controlled studies with regard to patient portals is low. Even when patient portals are often discussed as a way to empower patients and improve quality of care, there is insufficient evidence to support this assumption. PMID:23183044

Physiological Parameters Database for PBPK Modeling (External Review Draft)

EPA Science Inventory

EPA released for public comment a physiological parameters database (created using Microsoft ACCESS) intended to be used in PBPK modeling. The database contains physiological parameter values for humans from early childhood through senescence. It also contains similar data for an...

IsoDesign: a software for optimizing the design of 13C-metabolic flux analysis experiments.

PubMed

Millard, Pierre; Sokol, Serguei; Letisse, Fabien; Portais, Jean-Charles

2014-01-01

The growing demand for (13) C-metabolic flux analysis ((13) C-MFA) in the field of metabolic engineering and systems biology is driving the need to rationalize expensive and time-consuming (13) C-labeling experiments. Experimental design is a key step in improving both the number of fluxes that can be calculated from a set of isotopic data and the precision of flux values. We present IsoDesign, a software that enables these parameters to be maximized by optimizing the isotopic composition of the label input. It can be applied to (13) C-MFA investigations using a broad panel of analytical tools (MS, MS/MS, (1) H NMR, (13) C NMR, etc.) individually or in combination. It includes a visualization module to intuitively select the optimal label input depending on the biological question to be addressed. Applications of IsoDesign are described, with an example of the entire (13) C-MFA workflow from the experimental design to the flux map including important practical considerations. IsoDesign makes the experimental design of (13) C-MFA experiments more accessible to a wider biological community. IsoDesign is distributed under an open source license at http://metasys.insa-toulouse.fr/software/isodes/ © 2013 Wiley Periodicals, Inc.

Software-Defined Architectures for Spectrally Efficient Cognitive Networking in Extreme Environments

NASA Astrophysics Data System (ADS)

Sklivanitis, Georgios

The objective of this dissertation is the design, development, and experimental evaluation of novel algorithms and reconfigurable radio architectures for spectrally efficient cognitive networking in terrestrial, airborne, and underwater environments. Next-generation wireless communication architectures and networking protocols that maximize spectrum utilization efficiency in congested/contested or low-spectral availability (extreme) communication environments can enable a rich body of applications with unprecedented societal impact. In recent years, underwater wireless networks have attracted significant attention for military and commercial applications including oceanographic data collection, disaster prevention, tactical surveillance, offshore exploration, and pollution monitoring. Unmanned aerial systems that are autonomously networked and fully mobile can assist humans in extreme or difficult-to-reach environments and provide cost-effective wireless connectivity for devices without infrastructure coverage. Cognitive radio (CR) has emerged as a promising technology to maximize spectral efficiency in dynamically changing communication environments by adaptively reconfiguring radio communication parameters. At the same time, the fast developing technology of software-defined radio (SDR) platforms has enabled hardware realization of cognitive radio algorithms for opportunistic spectrum access. However, existing algorithmic designs and protocols for shared spectrum access do not effectively capture the interdependencies between radio parameters at the physical (PHY), medium-access control (MAC), and network (NET) layers of the network protocol stack. In addition, existing off-the-shelf radio platforms and SDR programmable architectures are far from fulfilling runtime adaptation and reconfiguration across PHY, MAC, and NET layers. Spectrum allocation in cognitive networks with multi-hop communication requirements depends on the location, network traffic load, and interference profile at each network node. As a result, the development and implementation of algorithms and cross-layer reconfigurable radio platforms that can jointly treat space, time, and frequency as a unified resource to be dynamically optimized according to inter- and intra-network interference constraints is of fundamental importance. In the next chapters, we present novel algorithmic and software/hardware implementation developments toward the deployment of spectrally efficient terrestrial, airborne, and underwater wireless networks. In Chapter 1 we review the state-of-art in commercially available SDR platforms, describe their software and hardware capabilities, and classify them based on their ability to enable rapid prototyping and advance experimental research in wireless networks. Chapter 2 discusses system design and implementation details toward real-time evaluation of a software-radio platform for all-spectrum cognitive channelization in the presence of narrowband or wideband primary stations. All-spectrum channelization is achieved by designing maximum signal-to-interference-plus-noise ratio (SINR) waveforms that span the whole continuum of the device-accessible spectrum, while satisfying peak power and interference temperature (IT) constraints for the secondary and primary users, respectively. In Chapter 3, we introduce the concept of all-spectrum channelization based on max-SINR optimized sparse-binary waveforms, we propose optimal and suboptimal waveform design algorithms, and evaluate their SINR and bit-error-rate (BER) performance in an SDR testbed. Chapter 4 considers the problem of channel estimation with minimal pilot signaling in multi-cell multi-user multi-input multi-output (MIMO) systems with very large antenna arrays at the base station, and proposes a least-squares (LS)-type algorithm that iteratively extracts channel and data estimates from a short record of data measurements. Our algorithmic developments toward spectrally-efficient cognitive networking through joint optimization of channel access code-waveforms and routes in a multi-hop network are described in Chapter 5. Algorithmic designs are software optimized on heterogeneous multi-core general-purpose processor (GPP)-based SDR architectures by leveraging a novel software-radio framework that offers self-optimization and real-time adaptation capabilities at the PHY, MAC, and NET layers of the network protocol stack. Our system design approach is experimentally validated under realistic conditions in a large-scale hybrid ground-air testbed deployment. Chapter 6 reviews the state-of-art in software and hardware platforms for underwater wireless networking and proposes a software-defined acoustic modem prototype that enables (i) cognitive reconfiguration of PHY/MAC parameters, and (ii) cross-technology communication adaptation. The proposed modem design is evaluated in terms of effective communication data rate in both water tank and lake testbed setups. In Chapter 7, we present a novel receiver configuration for code-waveform-based multiple-access underwater communications. The proposed receiver is fully reconfigurable and executes (i) all-spectrum cognitive channelization, and (ii) combined synchronization, channel estimation, and demodulation. Experimental evaluation in terms of SINR and BER show that all-spectrum channelization is a powerful proposition for underwater communications. At the same time, the proposed receiver design can significantly enhance bandwidth utilization. Finally, in Chapter 8, we focus on challenging practical issues that arise in underwater acoustic sensor network setups where co-located multi-antenna sensor deployment is not feasible due to power, computation, and hardware limitations, and design, implement, and evaluate an underwater receiver structure that accounts for multiple carrier frequency and timing offsets in virtual (distributed) MIMO underwater systems.

Experimental realization of a multiplexed quantum memory with 225 individually accessible memory cells

PubMed Central

Pu, Y-F; Jiang, N.; Chang, W.; Yang, H-X; Li, C.; Duan, L-M

2017-01-01

To realize long-distance quantum communication and quantum network, it is required to have multiplexed quantum memory with many memory cells. Each memory cell needs to be individually addressable and independently accessible. Here we report an experiment that realizes a multiplexed DLCZ-type quantum memory with 225 individually accessible memory cells in a macroscopic atomic ensemble. As a key element for quantum repeaters, we demonstrate that entanglement with flying optical qubits can be stored into any neighboring memory cells and read out after a programmable time with high fidelity. Experimental realization of a multiplexed quantum memory with many individually accessible memory cells and programmable control of its addressing and readout makes an important step for its application in quantum information technology. PMID:28480891

TAMEE: data management and analysis for tissue microarrays.

PubMed

Thallinger, Gerhard G; Baumgartner, Kerstin; Pirklbauer, Martin; Uray, Martina; Pauritsch, Elke; Mehes, Gabor; Buck, Charles R; Zatloukal, Kurt; Trajanoski, Zlatko

2007-03-07

With the introduction of tissue microarrays (TMAs) researchers can investigate gene and protein expression in tissues on a high-throughput scale. TMAs generate a wealth of data calling for extended, high level data management. Enhanced data analysis and systematic data management are required for traceability and reproducibility of experiments and provision of results in a timely and reliable fashion. Robust and scalable applications have to be utilized, which allow secure data access, manipulation and evaluation for researchers from different laboratories. TAMEE (Tissue Array Management and Evaluation Environment) is a web-based database application for the management and analysis of data resulting from the production and application of TMAs. It facilitates storage of production and experimental parameters, of images generated throughout the TMA workflow, and of results from core evaluation. Database content consistency is achieved using structured classifications of parameters. This allows the extraction of high quality results for subsequent biologically-relevant data analyses. Tissue cores in the images of stained tissue sections are automatically located and extracted and can be evaluated using a set of predefined analysis algorithms. Additional evaluation algorithms can be easily integrated into the application via a plug-in interface. Downstream analysis of results is facilitated via a flexible query generator. We have developed an integrated system tailored to the specific needs of research projects using high density TMAs. It covers the complete workflow of TMA production, experimental use and subsequent analysis. The system is freely available for academic and non-profit institutions from http://genome.tugraz.at/Software/TAMEE.

Free energy simulations of amylin I26P mutation in a lipid bilayer.

PubMed

Jalili, Seifollah; Maleki, Afsaneh; Akhavan, Mojdeh; Najafi, Bijan; Schofield, Jeremy

2015-02-01

The amylin peptide in a dioleoylphosphatidylcholine (DOPC) bilayer is studied using united atom molecular dynamics (MD) simulations. Dynamics and transport properties of the peptide and the phospholipid bilayer are investigated. The lateral diffusion of DOPC is in the order of 10(-8) cm(2) s(-1), which is in agreement with the experimental results. The order parameter and density profile for phospholipid molecules in the bilayer are calculated. The secondary structure of amylin peptide shows that the amino acids in two terminals are structureless and two α-helical segments in the peptide are connected through an unstructured link. This structure is similar to the experimental structure in the membrane-mimicking media. Free energy calculations of the Ile26 → Pro mutation in the amylin peptide are performed in the bilayer and in aqueous solution using molecular dynamics simulations and a thermodynamic cycle. It is shown that in the mutated peptide in aqueous solution, the α-helix structure changes to a 5-helix, whereas this configuration is preserved in the bilayer environment. It is interesting that the accessible surface area increases for hydrophobic residues in the bilayer and for hydrophilic residues in aqueous solution as the coupling parameter changes from 0 to 1. These results are significant to understanding the aggregation mechanism of human amylin monomers in membranes to the dimers, trimers, oligomers, and fibrils associated with the type 2 diabetes at the atomic level.

40 CFR 63.2990 - Can I conduct short-term experimental production runs that cause parameters to deviate from...

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 12 2011-07-01 2009-07-01 true Can I conduct short-term experimental... I conduct short-term experimental production runs that cause parameters to deviate from operating limits? With the approval of the Administrator, you may conduct short-term experimental production runs...

40 CFR 63.2990 - Can I conduct short-term experimental production runs that cause parameters to deviate from...

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 12 2010-07-01 2010-07-01 true Can I conduct short-term experimental... I conduct short-term experimental production runs that cause parameters to deviate from operating limits? With the approval of the Administrator, you may conduct short-term experimental production runs...

Access to Space Interactive Design Web Site

NASA Technical Reports Server (NTRS)

Leon, John; Cutlip, William; Hametz, Mark

2000-01-01

The Access To Space (ATS) Group at NASA's Goddard Space Flight Center (GSFC) supports the science and technology community at GSFC by facilitating frequent and affordable opportunities for access to space. Through partnerships established with access mode suppliers, the ATS Group has developed an interactive Mission Design web site. The ATS web site provides both the information and the tools necessary to assist mission planners in selecting and planning their ride to space. This includes the evaluation of single payloads vs. ride-sharing opportunities to reduce the cost of access to space. Features of this site include the following: (1) Mission Database. Our mission database contains a listing of missions ranging from proposed missions to manifested. Missions can be entered by our user community through data input tools. Data is then accessed by users through various search engines: orbit parameters, ride-share opportunities, spacecraft parameters, other mission notes, launch vehicle, and contact information. (2) Launch Vehicle Toolboxes. The launch vehicle toolboxes provide the user a full range of information on vehicle classes and individual configurations. Topics include: general information, environments, performance, payload interface, available volume, and launch sites.

The effects of natural and induced short-term floods on four sugarcane accessions

USDA-ARS?s Scientific Manuscript database

A study was initiated at the USDA/ARS Subtropical Horticulture Research Station, Miami, FL to evaluate the potential for flood tolerance in several accessions from Saccharum barberi (Jeswiet) and S. sinense (Roxb. Amend. Jeswiet) sugarcane genera. The experimental design included 4 accessions, Kewal...

High School Student Information Access and Engineering Design Performance

ERIC Educational Resources Information Center

Mentzer, Nathan

2014-01-01

Developing solutions to engineering design problems requires access to information. Research has shown that appropriately accessing and using information in the design process improves solution quality. This quasi-experimental study provides two groups of high school students with a design problem in a three hour design experience. One group has…

Accessibility of Nitroxide Side Chains: Absolute Heisenberg Exchange Rates from Power Saturation EPR

PubMed Central

Altenbach, Christian; Froncisz, Wojciech; Hemker, Roy; Mchaourab, Hassane; Hubbell, Wayne L.

2005-01-01

In site-directed spin labeling, the relative solvent accessibility of spin-labeled side chains is taken to be proportional to the Heisenberg exchange rate (Wex) of the nitroxide with a paramagnetic reagent in solution. In turn, relative values of Wex are determined by continuous wave power saturation methods and expressed as a proportional and dimensionless parameter Π. In the experiments presented here, NiEDDA is characterized as a paramagnetic reagent for solvent accessibility studies, and it is shown that absolute values of Wex can be determined from Π, and that the proportionality constant relating them is independent of the paramagnetic reagent and mobility of the nitroxide. Based on absolute exchange rates, an accessibility factor is defined (0 < ρ < 1) that serves as a quantitative measure of side-chain solvent accessibility. The accessibility factors for a nitroxide side chain at 14 different sites in T4 lysozyme are shown to correlate with a structure-based accessibility parameter derived from the crystal structure of the protein. These results provide a useful means for relating crystallographic and site-directed spin labeling data, and hence comparing crystal and solution structures. PMID:15994891

Flushing ports of totally implantable venous access devices, and impact of the Huber point needle bevel orientation: experimental tests and numerical computation.

PubMed

Guiffant, Gérard; Durussel, Jean Jacques; Flaud, Patrice; Vigier, Jean Pierre; Merckx, Jacques

2012-01-01

The use of totally implantable venous access devices developed as a medical device allowing mid- and long-term, frequent, repeated, or continuous injection of therapeutic products, by vascular, cavitary, or perineural access. The effective flushing of these devices is a central element to assure long-lasting use. Our experimental work demonstrates that directing the Huber point needle opening in the diametrically opposite direction of the implantable port exit channel increases the flushing efficiency. These results are consolidated by numerical computations, which support recommendations not only for their maintenance, but also for their use.

Flushing ports of totally implantable venous access devices, and impact of the Huber point needle bevel orientation: experimental tests and numerical computation

PubMed Central

Guiffant, Gérard; Durussel, Jean Jacques; Flaud, Patrice; Vigier, Jean Pierre; Merckx, Jacques

2012-01-01

The use of totally implantable venous access devices developed as a medical device allowing mid- and long-term, frequent, repeated, or continuous injection of therapeutic products, by vascular, cavitary, or perineural access. The effective flushing of these devices is a central element to assure long-lasting use. Our experimental work demonstrates that directing the Huber point needle opening in the diametrically opposite direction of the implantable port exit channel increases the flushing efficiency. These results are consolidated by numerical computations, which support recommendations not only for their maintenance, but also for their use. PMID:23166455

Parametric study of the swimming performance of a fish robot propelled by a flexible caudal fin.

PubMed

Low, K H; Chong, C W

2010-12-01

In this paper, we aim to study the swimming performance of fish robots by using a statistical approach. A fish robot employing a carangiform swimming mode had been used as an experimental platform for the performance study. The experiments conducted aim to investigate the effect of various design parameters on the thrust capability of the fish robot with a flexible caudal fin. The controllable parameters associated with the fin include frequency, amplitude of oscillation, aspect ratio and the rigidity of the caudal fin. The significance of these parameters was determined in the first set of experiments by using a statistical approach. A more detailed parametric experimental study was then conducted with only those significant parameters. As a result, the parametric study could be completed with a reduced number of experiments and time spent. With the obtained experimental result, we were able to understand the relationship between various parameters and a possible adjustment of parameters to obtain a higher thrust. The proposed statistical method for experimentation provides an objective and thorough analysis of the effects of individual or combinations of parameters on the swimming performance. Such an efficient experimental design helps to optimize the process and determine factors that influence variability.

Analyzing the effect of routing protocols on media access control protocols in radio networks

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

Barrett, C. L.; Drozda, M.; Marathe, A.

2002-01-01

We study the effect of routing protocols on the performance of media access control (MAC) protocols in wireless radio networks. Three well known MAC protocols: 802.11, CSMA, and MACA are considered. Similarly three recently proposed routing protocols: AODV, DSR and LAR scheme 1 are considered. The experimental analysis was carried out using GloMoSim: a tool for simulating wireless networks. The main focus of our experiments was to study how the routing protocols affect the performance of the MAC protocols when the underlying network and traffic parameters are varied. The performance of the protocols was measured w.r.t. five important parameters: (i)more » number of received packets, (ii) average latency of each packet, (iii) throughput (iv) long term fairness and (v) number of control packets at the MAC layer level. Our results show that combinations of routing and MAC protocols yield varying performance under varying network topology and traffic situations. The result has an important implication; no combination of routing protocol and MAC protocol is the best over all situations. Also, the performance analysis of protocols at a given level in the protocol stack needs to be studied not locally in isolation but as a part of the complete protocol stack. A novel aspect of our work is the use of statistical technique, ANOVA (Analysis of Variance) to characterize the effect of routing protocols on MAC protocols. This technique is of independent interest and can be utilized in several other simulation and empirical studies.« less

Lower hybrid accessibility in a large, hot reversed field pinch

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

Dziubek, R.A.; Harvey, R.W.; Hokin, S.A.

1995-11-01

Accessibility and damping of the slow wave in a reversed field pinch (RFP) plasma is investigated theoretically, using projected Reversed Field Experiment (RFX) plasma parameters. By numerically solving the hot plasma dispersion relation, regions of propagation are found and the possibility of mode conversion is analyzed. If the parallel index of refraction of the wave is chosen judiciously at the edge of the plasma, the slow wave is accessible to a target region located just inside the reversal surface without mode conversion. Landau damping is also optimized in this region. A representative fast electron population is then added in ordermore » to determine its effect on accessibility and damping. The presence of these electrons, whose parameters were estimated by extrapolation of Madison Symmetric Torus (MST) data, does not affect the accessibility of the wave. However, the initial phase velocity of the wave needs to be increased somewhat in order to maintain optimal damping in the target zone.« less

Design of experiments for identification of complex biochemical systems with applications to mitochondrial bioenergetics.

PubMed

Vinnakota, Kalyan C; Beard, Daniel A; Dash, Ranjan K

2009-01-01

Identification of a complex biochemical system model requires appropriate experimental data. Models constructed on the basis of data from the literature often contain parameters that are not identifiable with high sensitivity and therefore require additional experimental data to identify those parameters. Here we report the application of a local sensitivity analysis to design experiments that will improve the identifiability of previously unidentifiable model parameters in a model of mitochondrial oxidative phosphorylation and tricaboxylic acid cycle. Experiments were designed based on measurable biochemical reactants in a dilute suspension of purified cardiac mitochondria with experimentally feasible perturbations to this system. Experimental perturbations and variables yielding the most number of parameters above a 5% sensitivity level are presented and discussed.

Precision calculations for h → WW/ZZ → 4 fermions in the Two-Higgs-Doublet Model with Prophecy4f

NASA Astrophysics Data System (ADS)

Altenkamp, Lukas; Dittmaier, Stefan; Rzehak, Heidi

2018-03-01

We have calculated the next-to-leading-order electroweak and QCD corrections to the decay processes h → WW/ZZ → 4 fermions of the light CP-even Higgs boson h of various types of Two-Higgs-Doublet Models (Types I and II, "lepton-specific" and "flipped" models). The input parameters are defined in four different renormalization schemes, where parameters that are not directly accessible by experiments are defined in the \\overline{MS} scheme. Numerical results are presented for the corrections to partial decay widths for various benchmark scenarios previously motivated in the literature, where we investigate the dependence on the \\overline{MS} renormalization scale and on the choice of the renormalization scheme in detail. We find that it is crucial to be precise with these issues in parameter analyses, since parameter conversions between different schemes can involve sizeable or large corrections, especially in scenarios that are close to experimental exclusion limits or theoretical bounds. It even turns out that some renormalization schemes are not applicable in specific regions of parameter space. Our investigation of differential distributions shows that corrections beyond the Standard Model are mostly constant offsets induced by the mixing between the light and heavy CP-even Higgs bosons, so that differential analyses of h→4 f decay observables do not help to identify Two-Higgs-Doublet Models. Moreover, the decay widths do not significantly depend on the specific type of those models. The calculations are implemented in the public Monte Carlo generator Prophecy4f and ready for application.

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

PubMed

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

2016-09-26

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

Accessing the band alignment in high efficiency Cu(In,Ga)(Se,S)2 (CIGSSe) solar cells with an InxSy:Na buffer based on temperature dependent measurements and simulations

NASA Astrophysics Data System (ADS)

Schoneberg, Johannes; Ohland, Jörg; Eraerds, Patrick; Dalibor, Thomas; Parisi, Jürgen; Richter, Michael

2018-04-01

We present a one-dimensional simulation model for high efficiency Cu(In,Ga)(Se,S)2 solar cells with a novel band alignment at the hetero-junction. The simulation study is based on new findings about the doping concentration of the InxSy:Na buffer and i-ZnO layers as well as comprehensive solar cell characterization by means of capacitance, current voltage, and external quantum efficiency measurements. The simulation results show good agreement with the experimental data over a broad temperature range, suggesting the simulation model with an interface-near region (INR) of approximately 100 nm around the buffer/absorber interface that is of great importance for the solar cell performance. The INR exhibits an inhomogeneous doping and defect density profile as well as interface traps at the i-layer/buffer and buffer/absorber interfaces. These crucial parameters could be accessed via their opposing behavior on the simulative reconstruction of different measurement characteristics. In this work, we emphasize the necessity to reconstruct the results of a set of experimental methods by means of simulation to find the most appropriate model for the solar cell. Lowly doped buffer and intrinsic window layers in combination with a high space charge at the front of the absorber lead to a novel band alignment in the simulated band structure of the solar cell. The presented insights may guide the strategy of further solar cell optimization including (alkali-) post deposition treatments.

An anisotropic, hyperelastic model for skin: experimental measurements, finite element modelling and identification of parameters for human and murine skin.

PubMed

Groves, Rachel B; Coulman, Sion A; Birchall, James C; Evans, Sam L

2013-02-01

The mechanical characteristics of skin are extremely complex and have not been satisfactorily simulated by conventional engineering models. The ability to predict human skin behaviour and to evaluate changes in the mechanical properties of the tissue would inform engineering design and would prove valuable in a diversity of disciplines, for example the pharmaceutical and cosmetic industries, which currently rely upon experiments performed in animal models. The aim of this study was to develop a predictive anisotropic, hyperelastic constitutive model of human skin and to validate this model using laboratory data. As a corollary, the mechanical characteristics of human and murine skin have been compared. A novel experimental design, using tensile tests on circular skin specimens, and an optimisation procedure were adopted for laboratory experiments to identify the material parameters of the tissue. Uniaxial tensile tests were performed along three load axes on excised murine and human skin samples, using a single set of material parameters for each skin sample. A finite element model was developed using the transversely isotropic, hyperelastic constitutive model of Weiss et al. (1996) and was embedded within a Veronda-Westmann isotropic material matrix, using three fibre families to create anisotropic behaviour. The model was able to represent the nonlinear, anisotropic behaviour of the skin well. Additionally, examination of the optimal material coefficients and the experimental data permitted quantification of the mechanical differences between human and murine skin. Differences between the skin types, most notably the extension of the skin at low load, have highlighted some of the limitations of murine skin as a biomechanical model of the human tissue. The development of accurate, predictive computational models of human tissue, such as skin, to reduce, refine or replace animal models and to inform developments in the medical, engineering and cosmetic fields, is a significant challenge but is highly desirable. Concurrent advances in computer technology and our understanding of human physiology must be utilised to produce more accurate and accessible predictive models, such as the finite element model described in this study. Copyright © 2012 Elsevier Ltd. All rights reserved.

Mining high-throughput experimental data to link gene and function

PubMed Central

Blaby-Haas, Crysten E.; de Crécy-Lagard, Valérie

2011-01-01

Nearly 2200 genomes encoding some 6 million proteins have now been sequenced. Around 40% of these proteins are of unknown function even when function is loosely and minimally defined as “belonging to a superfamily”. In addition to in silico methods, the swelling stream of high-throughput experimental data can give valuable clues for linking these “unknowns” with precise biological roles. The goal is to develop integrative data-mining platforms that allow the scientific community at large to access and utilize this rich source of experimental knowledge. To this end, we review recent advances in generating whole-genome experimental datasets, where this data can be accessed, and how it can be used to drive prediction of gene function. PMID:21310501

Experimental investigation of effective parameters on signal enhancement in spark assisted laser induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

Hassanimatin, M. M.; Tavassoli, S. H.

2018-05-01

A combination of electrical spark and laser induced breakdown spectroscopy (LIBS), which is called spark assisted LIBS (SA-LIBS), has shown its capability in plasma spectral emission enhancement. The aim of this paper is a detailed study of plasma emission to determine the effect of plasma and experimental parameters on increasing the spectral signal. An enhancement ratio of SA-LIBS spectral lines compared with LIBS is theoretically introduced. The parameters affecting the spectral enhancement ratio including ablated mass, plasma temperature, the lifetime of neutral and ionic spectral lines, plasma volume, and electron density are experimentally investigated and discussed. By substitution of the effective parameters, the theoretical spectral enhancement ratio is calculated and compared with the experimental one. Two samples of granite as a dielectric and aluminum as a metal at different laser pulse energies are studied. There is a good agreement between the calculated and the experimental enhancement ratio.

Kalai-Smorodinsky bargaining solution for optimal resource allocation over wireless DS-CDMA visual sensor networks

NASA Astrophysics Data System (ADS)

Pandremmenou, Katerina; Kondi, Lisimachos P.; Parsopoulos, Konstantinos E.

2012-01-01

Surveillance applications usually require high levels of video quality, resulting in high power consumption. The existence of a well-behaved scheme to balance video quality and power consumption is crucial for the system's performance. In the present work, we adopt the game-theoretic approach of Kalai-Smorodinsky Bargaining Solution (KSBS) to deal with the problem of optimal resource allocation in a multi-node wireless visual sensor network (VSN). In our setting, the Direct Sequence Code Division Multiple Access (DS-CDMA) method is used for channel access, while a cross-layer optimization design, which employs a central processing server, accounts for the overall system efficacy through all network layers. The task assigned to the central server is the communication with the nodes and the joint determination of their transmission parameters. The KSBS is applied to non-convex utility spaces, efficiently distributing the source coding rate, channel coding rate and transmission powers among the nodes. In the underlying model, the transmission powers assume continuous values, whereas the source and channel coding rates can take only discrete values. Experimental results are reported and discussed to demonstrate the merits of KSBS over competing policies.

Optical design of a robotic TV camera probe for minimally invasive abdominal surgery

NASA Astrophysics Data System (ADS)

Todaro, Susanna; He, Weiyi; Killinger, Dennis

2011-03-01

Minimally invasive techniques are a promising new field of surgery; however, they limit the surgeon's access points and maneuverability. In order to increase the number of access points in minimally invasive abdominal surgery, a proposed implantable medical probe braces to the abdominal wall and provides illumination and video signal. The probe is cylindrical, about 25 mm long and 10 mm in diameter. A ring of LEDs on the end of the probe illuminates the tissue, and the resulting image is focused onto an HD video detector. It was necessary to apply beam-shaping reflectors to collimate the light onto a small target area, to avoid illuminating areas not picked up by the video. These reflectors were designed and simulated using the optical ray tracing software TracePro. Two LED chip geometries and three types of reflector geometries were analyzed, and the parameters for each geometry were optimized. For the straight-edged reflectors, the intensity patterns and optimization were compared to experimental results. Although parabolic reflectors produced the best collimation, cone reflectors with a 20-degree half-angle produced significant collimation at a much cheaper price. This work was supported by NSF REU program (award No DMR-1004873).

Effects of simultaneous combined exposure to CDMA and WCDMA electromagnetic fields on serum hormone levels in rats

PubMed Central

Jin, Yeung Bae; Choi, Hyung-Do; Kim, Byung Chan; Pack, Jeong-Ki; Kim, Nam; Lee, Yun-Sil

2013-01-01

Despite more than a decade of research on the endocrine system, there have been no published studies about the effects of concurrent exposure of radiofrequency electromagnetic fields (RF-EMF) on this system. The present study investigated the several parameters of the endocrine system including melatonin, thyroid stimulating hormone, stress hormone and sex hormone after code division multiple access (CDMA, 849 MHz) and wideband code division multiple access (WCDMA, 1.95 GHz) signals for simultaneous exposure in rats. Sprague-Dawley rats were exposed to RF-EMF signals for 45 min/day, 5 days/week for up to 8 weeks. The whole-body average specific absorption rate (SAR) of CDMA or WCDMA was 2.0 W/kg (total 4.0 W/kg). At 4 and 8 weeks after the experiment began, each experimental group's 40 rats (male 20, female 20) were autopsied. Exposure for 8 weeks to simultaneous CDMA and WCDMA RF did not affect serum levels in rats of melatonin, thyroid stimulating hormone (TSH), triiodothyronine (T3) and thyroxin (T4), adrenocorticotropic hormone (ACTH) and sex hormones (testosterone and estrogen) as assessed by the ELISA method. PMID:23239176

Detection of Spoofed MAC Addresses in 802.11 Wireless Networks

NASA Astrophysics Data System (ADS)

Tao, Kai; Li, Jing; Sampalli, Srinivas

Medium Access Control (MAC) address spoofing is considered as an important first step in a hacker's attempt to launch a variety of attacks on 802.11 wireless networks. Unfortunately, MAC address spoofing is hard to detect. Most current spoofing detection systems mainly use the sequence number (SN) tracking technique, which has drawbacks. Firstly, it may lead to an increase in the number of false positives. Secondly, such techniques cannot be used in systems with wireless cards that do not follow standard 802.11 sequence number patterns. Thirdly, attackers can forge sequence numbers, thereby causing the attacks to go undetected. We present a new architecture called WISE GUARD (Wireless Security Guard) for detection of MAC address spoofing on 802.11 wireless LANs. It integrates three detection techniques - SN tracking, Operating System (OS) fingerprinting & tracking and Received Signal Strength (RSS) fingerprinting & tracking. It also includes the fingerprinting of Access Point (AP) parameters as an extension to the OS fingerprinting for detection of AP address spoofing. We have implemented WISE GUARD on a test bed using off-the-shelf wireless devices and open source drivers. Experimental results show that the new design enhances the detection effectiveness and reduces the number of false positives in comparison with current approaches.

40 CFR 63.2990 - Can I conduct short-term experimental production runs that cause parameters to deviate from...

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 13 2013-07-01 2012-07-01 true Can I conduct short-term experimental... Plan § 63.2990 Can I conduct short-term experimental production runs that cause parameters to deviate from operating limits? With the approval of the Administrator, you may conduct short-term experimental...

Experimental and analytical determination of stability parameters for a balloon tethered in a wind

NASA Technical Reports Server (NTRS)

Redd, L. T.; Bennett, R. M.; Bland, S. R.

1973-01-01

Experimental and analytical techniques for determining stability parameters for a balloon tethered in a steady wind are described. These techniques are applied to a particular 7.64-meter-long balloon, and the results are presented. The stability parameters of interest appear as coefficients in linearized stability equations and are derived from the various forces and moments acting on the balloon. In several cases the results from the experimental and analytical techniques are compared and suggestions are given as to which techniques are the most practical means of determining values for the stability parameters.

Theoretical and experimental determination of K - and L -shell x-ray relaxation parameters in Ni

NASA Astrophysics Data System (ADS)

Guerra, M.; Sampaio, J. M.; Parente, F.; Indelicato, P.; Hönicke, P.; Müller, M.; Beckhoff, B.; Marques, J. P.; Santos, J. P.

2018-04-01

Fluorescence yields (FY) for the Ni K and L shells were determined by a theoretical and an experimental group within the framework of the International Initiative on X-ray Fundamental Parameters (FPs) collaboration. Coster-Kronig (CK) parameters were also measured for the L shell of Ni. Theoretical calculations of the same parameters were performed using the Dirac-Fock method, including relativistic and QED corrections. The experimental values for the FY and CK were determined at the PTB laboratory in the synchrotron radiation facility BESSY II, Berlin, Germany, and are compared to the corresponding calculated values.

Langmuir probe analysis in electronegative plasmas

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

Bredin, Jerome, E-mail: jerome.bredin@lpp.polytechnique.fr; Chabert, Pascal; Aanesland, Ane

2014-12-15

This paper compares two methods to analyze Langmuir probe data obtained in electronegative plasmas. The techniques are developed to allow investigations in plasmas, where the electronegativity α{sub 0} = n{sub –}/n{sub e} (the ratio between the negative ion and electron densities) varies strongly. The first technique uses an analytical model to express the Langmuir probe current-voltage (I-V) characteristic and its second derivative as a function of the electron and ion densities (n{sub e}, n{sub +}, n{sub –}), temperatures (T{sub e}, T{sub +}, T{sub –}), and masses (m{sub e}, m{sub +}, m{sub –}). The analytical curves are fitted to the experimental data bymore » adjusting these variables and parameters. To reduce the number of fitted parameters, the ion masses are assumed constant within the source volume, and quasi-neutrality is assumed everywhere. In this theory, Maxwellian distributions are assumed for all charged species. We show that this data analysis can predict the various plasma parameters within 5–10%, including the ion temperatures when α{sub 0} > 100. However, the method is tedious, time consuming, and requires a precise measurement of the energy distribution function. A second technique is therefore developed for easier access to the electron and ion densities, but does not give access to the ion temperatures. Here, only the measured I-V characteristic is needed. The electron density, temperature, and ion saturation current for positive ions are determined by classical probe techniques. The electronegativity α{sub 0} and the ion densities are deduced via an iterative method since these variables are coupled via the modified Bohm velocity. For both techniques, a Child-Law sheath model for cylindrical probes has been developed and is presented to emphasize the importance of this model for small cylindrical Langmuir probes.« less

An improved swarm optimization for parameter estimation and biological model selection.

PubMed

Abdullah, Afnizanfaizal; Deris, Safaai; Mohamad, Mohd Saberi; Anwar, Sohail

2013-01-01

One of the key aspects of computational systems biology is the investigation on the dynamic biological processes within cells. Computational models are often required to elucidate the mechanisms and principles driving the processes because of the nonlinearity and complexity. The models usually incorporate a set of parameters that signify the physical properties of the actual biological systems. In most cases, these parameters are estimated by fitting the model outputs with the corresponding experimental data. However, this is a challenging task because the available experimental data are frequently noisy and incomplete. In this paper, a new hybrid optimization method is proposed to estimate these parameters from the noisy and incomplete experimental data. The proposed method, called Swarm-based Chemical Reaction Optimization, integrates the evolutionary searching strategy employed by the Chemical Reaction Optimization, into the neighbouring searching strategy of the Firefly Algorithm method. The effectiveness of the method was evaluated using a simulated nonlinear model and two biological models: synthetic transcriptional oscillators, and extracellular protease production models. The results showed that the accuracy and computational speed of the proposed method were better than the existing Differential Evolution, Firefly Algorithm and Chemical Reaction Optimization methods. The reliability of the estimated parameters was statistically validated, which suggests that the model outputs produced by these parameters were valid even when noisy and incomplete experimental data were used. Additionally, Akaike Information Criterion was employed to evaluate the model selection, which highlighted the capability of the proposed method in choosing a plausible model based on the experimental data. In conclusion, this paper presents the effectiveness of the proposed method for parameter estimation and model selection problems using noisy and incomplete experimental data. This study is hoped to provide a new insight in developing more accurate and reliable biological models based on limited and low quality experimental data.

Multiple Phase Transitions in the Culture Dissemination

NASA Astrophysics Data System (ADS)

Wang, Bing; Han, Yuexing; Chen, Luonan; Aihara, Kazuyuki

We study the coevolution process in the Axelrod’s model with the consideration of agents’ abilities to access to the information. With a parameter to control the ability of communication, we observe two kinds of phase transitions both for cultural domains and network fragments, respectively. With the simulation results, we find the relationship between the critical value and the controlled parameter. The results indicate that the powerful ability to access to the information benefits the dissemination of culture in the system.

Aerothermal modeling, phase 1. Volume 2: Experimental data

NASA Technical Reports Server (NTRS)

Kenworthy, M. J.; Correa, S. M.; Burrus, D. L.

1983-01-01

The experimental test effort is discussed. The test data are presented. The compilation is divided into sets representing each of the 18 experimental configurations tested. A detailed description of each configuration, and plots of the temperature difference ratio parameter or pattern factor parameter calculated from the test data are also provided.

KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems

PubMed Central

2014-01-01

Background The kinetic modeling of biological systems is mainly composed of three steps that proceed iteratively: model building, simulation and analysis. In the first step, it is usually required to set initial metabolite concentrations, and to assign kinetic rate laws, along with estimating parameter values using kinetic data through optimization when these are not known. Although the rapid development of high-throughput methods has generated much omics data, experimentalists present only a summary of obtained results for publication, the experimental data files are not usually submitted to any public repository, or simply not available at all. In order to automatize as much as possible the steps of building kinetic models, there is a growing requirement in the systems biology community for easily exchanging data in combination with models, which represents the main motivation of KiMoSys development. Description KiMoSys is a user-friendly platform that includes a public data repository of published experimental data, containing concentration data of metabolites and enzymes and flux data. It was designed to ensure data management, storage and sharing for a wider systems biology community. This community repository offers a web-based interface and upload facility to turn available data into publicly accessible, centralized and structured-format data files. Moreover, it compiles and integrates available kinetic models associated with the data. KiMoSys also integrates some tools to facilitate the kinetic model construction process of large-scale metabolic networks, especially when the systems biologists perform computational research. Conclusions KiMoSys is a web-based system that integrates a public data and associated model(s) repository with computational tools, providing the systems biology community with a novel application facilitating data storage and sharing, thus supporting construction of ODE-based kinetic models and collaborative research projects. The web application implemented using Ruby on Rails framework is freely available for web access at http://kimosys.org, along with its full documentation. PMID:25115331

Predicting the performance of a power amplifier using large-signal circuit simulations of an AlGaN/GaN HFET model

NASA Astrophysics Data System (ADS)

Bilbro, Griff L.; Hou, Danqiong; Yin, Hong; Trew, Robert J.

2009-02-01

We have quantitatively modeled the conduction current and charge storage of an HFET in terms its physical dimensions and material properties. For DC or small-signal RF operation, no adjustable parameters are necessary to predict the terminal characteristics of the device. Linear performance measures such as small-signal gain and input admittance can be predicted directly from the geometric structure and material properties assumed for the device design. We have validated our model at low-frequency against experimental I-V measurements and against two-dimensional device simulations. We discuss our recent extension of our model to include a larger class of electron velocity-field curves. We also discuss the recent reformulation of our model to facilitate its implementation in commercial large-signal high-frequency circuit simulators. Large signal RF operation is more complex. First, the highest CW microwave power is fundamentally bounded by a brief, reversible channel breakdown in each RF cycle. Second, the highest experimental measurements of efficiency, power, or linearity always require harmonic load pull and possibly also harmonic source pull. Presently, our model accounts for these facts with an adjustable breakdown voltage and with adjustable load impedances and source impedances for the fundamental frequency and its harmonics. This has allowed us to validate our model for large signal RF conditions by simultaneously fitting experimental measurements of output power, gain, and power added efficiency of real devices. We show that the resulting model can be used to compare alternative device designs in terms of their large signal performance, such as their output power at 1dB gain compression or their third order intercept points. In addition, the model provides insight into new device physics features enabled by the unprecedented current and voltage levels of AlGaN/GaN HFETs, including non-ohmic resistance in the source access regions and partial depletion of the 2DEG in the drain access region.

Combining novel technologies with improved logistics to reduce hemodialysis vascular access dysfunction.

PubMed

Roy-Chaudhury, P; Lee, T; Duncan, H; El-Khatib, M

2009-01-01

Hemodialysis (HD) vascular access dysfunction is currently a huge clinical problem for which there are no effective therapies. There are, however, a number of promising technologies that are currently at the experimental or clinical trial stage. We believe that the application of these novel technologies in combination with better clinical protocols for vascular access care could significantly reduce the current problems associated with HD vascular access.

Variation in cassava germplasm for tolerance to post-harvest physiological deterioration.

PubMed

Venturini, M T; Santos, L R; Vildoso, C I A; Santos, V S; Oliveira, E J

2016-05-06

Tolerant varieties can effectively control post-harvest physiological deterioration (PPD) of cassava, although knowledge on the genetic variability and inheritance of this trait is needed. The objective of this study was to estimate genetic parameters and identify sources of tolerance to PPD and their stability in cassava accessions. Roots from 418 cassava accessions, grown in four independent experiments, were evaluated for PPD tolerance 0, 2, 5, and 10 days post-harvest. Data were transformed into area under the PPD-progress curve (AUP-PPD) to quantify tolerance. Genetic parameters, stability (Si), adaptability (Ai), and the joint analysis of stability and adaptability (Zi) were obtained via residual maximum likelihood (REML) and best linear unbiased prediction (BLUP) methods. Variance in the genotype (G) x environment (E) interaction and genotypic variance were important for PPD tolerance. Individual broad-sense heritability (hg(2)= 0.38 ± 0.04) and average heritability in accessions (hmg(2)= 0.52) showed high genetic control of PPD tolerance. Genotypic correlation of AUP-PPD in different experiments was of medium magnitude (ȓgA = 0.42), indicating significant G x E interaction. The predicted genotypic values o f G x E free of interaction (û + ĝi) showed high variation. Of the 30 accessions with high Zi, 19 were common to û + ĝi, Si, and Ai parameters. The genetic gain with selection of these 19 cassava accessions was -55.94, -466.86, -397.72, and -444.03% for û + ĝi, Si, Ai, and Zi, respectively, compared with the overall mean for each parameter. These results demonstrate the variability and potential of cassava germplasm to introduce PPD tolerance in commercial varieties.

Parametric study of closed wet cooling tower thermal performance

NASA Astrophysics Data System (ADS)

Qasim, S. M.; Hayder, M. J.

2017-08-01

The present study involves experimental and theoretical analysis to evaluate the thermal performance of modified Closed Wet Cooling Tower (CWCT). The experimental study includes: design, manufacture and testing prototype of a modified counter flow forced draft CWCT. The modification based on addition packing to the conventional CWCT. A series of experiments was carried out at different operational parameters. In view of energy analysis, the thermal performance parameters of the tower are: cooling range, tower approach, cooling capacity, thermal efficiency, heat and mass transfer coefficients. The theoretical study included develops Artificial Neural Network (ANN) models to predicting various thermal performance parameters of the tower. Utilizing experimental data for training and testing, the models simulated by multi-layer back propagation algorithm for varying all operational parameters stated in experimental test.

Optimal experimental design for parameter estimation of a cell signaling model.

PubMed

Bandara, Samuel; Schlöder, Johannes P; Eils, Roland; Bock, Hans Georg; Meyer, Tobias

2009-11-01

Differential equation models that describe the dynamic changes of biochemical signaling states are important tools to understand cellular behavior. An essential task in building such representations is to infer the affinities, rate constants, and other parameters of a model from actual measurement data. However, intuitive measurement protocols often fail to generate data that restrict the range of possible parameter values. Here we utilized a numerical method to iteratively design optimal live-cell fluorescence microscopy experiments in order to reveal pharmacological and kinetic parameters of a phosphatidylinositol 3,4,5-trisphosphate (PIP(3)) second messenger signaling process that is deregulated in many tumors. The experimental approach included the activation of endogenous phosphoinositide 3-kinase (PI3K) by chemically induced recruitment of a regulatory peptide, reversible inhibition of PI3K using a kinase inhibitor, and monitoring of the PI3K-mediated production of PIP(3) lipids using the pleckstrin homology (PH) domain of Akt. We found that an intuitively planned and established experimental protocol did not yield data from which relevant parameters could be inferred. Starting from a set of poorly defined model parameters derived from the intuitively planned experiment, we calculated concentration-time profiles for both the inducing and the inhibitory compound that would minimize the predicted uncertainty of parameter estimates. Two cycles of optimization and experimentation were sufficient to narrowly confine the model parameters, with the mean variance of estimates dropping more than sixty-fold. Thus, optimal experimental design proved to be a powerful strategy to minimize the number of experiments needed to infer biological parameters from a cell signaling assay.

DoSSiER: Database of scientific simulation and experimental results

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

Wenzel, Hans; Yarba, Julia; Genser, Krzystof

The Geant4, GeantV and GENIE collaborations regularly perform validation and regression tests for simulation results. DoSSiER (Database of Scientific Simulation and Experimental Results) is being developed as a central repository to store the simulation results as well as the experimental data used for validation. DoSSiER can be easily accessed via a web application. In addition, a web service allows for programmatic access to the repository to extract records in json or xml exchange formats. In this paper, we describe the functionality and the current status of various components of DoSSiER as well as the technology choices we made.

DoSSiER: Database of scientific simulation and experimental results

DOE PAGES

Wenzel, Hans; Yarba, Julia; Genser, Krzystof; ...

2016-08-01

The Geant4, GeantV and GENIE collaborations regularly perform validation and regression tests for simulation results. DoSSiER (Database of Scientific Simulation and Experimental Results) is being developed as a central repository to store the simulation results as well as the experimental data used for validation. DoSSiER can be easily accessed via a web application. In addition, a web service allows for programmatic access to the repository to extract records in json or xml exchange formats. In this paper, we describe the functionality and the current status of various components of DoSSiER as well as the technology choices we made.

Breeding of Acrocomia aculeata using genetic diversity parameters and correlations to select accessions based on vegetative, phenological, and reproductive characteristics.

PubMed

Coser, S M; Motoike, S Y; Corrêa, T R; Pires, T P; Resende, M D V

2016-10-17

Macaw palm (Acrocomia aculeata) is a promising species for use in biofuel production, and establishing breeding programs is important for the development of commercial plantations. The aim of the present study was to analyze genetic diversity, verify correlations between traits, estimate genetic parameters, and select different accessions of A. aculeata in the Macaw Palm Germplasm Bank located in Universidade Federal de Viçosa, to develop a breeding program for this species. Accessions were selected based on precocity (PREC), total spathe (TS), diameter at breast height (DBH), height of the first spathe (HFS), and canopy area (CA). The traits were evaluated in 52 accessions during the 2012/2013 season and analyzed by restricted estimation maximum likelihood/best linear unbiased predictor procedures. Genetic diversity resulted in the formation of four groups by Tocher's clustering method. The correlation analysis showed it was possible to have indirect and early selection for the traits PREC and DBH. Estimated genetic parameters strengthened the genetic variability verified by cluster analysis. Narrow-sense heritability was classified as moderate (PREC, TS, and CA) to high (HFS and DBH), resulting in strong genetic control of the traits and success in obtaining genetic gains by selection. Accuracy values were classified as moderate (PREC and CA) to high (TS, HFS, and DBH), reinforcing the success of the selection process. Selection of accessions for PREC, TS, and HFS by the rank-average method permits selection gains of over 100%, emphasizing the successful use of the accessions in breeding programs and obtaining superior genotypes for commercial plantations.

Confocal fluorescence techniques in industrial application

NASA Astrophysics Data System (ADS)

Eggeling, Christian; Gall, Karsten; Palo, Kaupo; Kask, Peet; Brand, Leif

2003-06-01

The FCS+plus family of evaluation tools for confocal fluorescence spectroscopy, which was developed during recent years, offers a comprehensive view to a series of fluorescence properties. Originating in fluorescence correlation spectroscopy (FCS) and using similar experimental equipment, a system of signal processing methods such as fluorescence intensity distribution analysis (FIDA) was created to analyze in detail the fluctuation behavior of fluorescent particles within a small area of detection. Giving simultaneous access to molecular parameters like concentration, translational and rotational diffusion, molecular brightness, and multicolor coincidence, this portfolio was enhanced by more traditional techniques of fluorescence lifetime as well as time-resolved anisotropy determination. The cornerstones of the FCS+plus methodology will be shortly described. The inhibition of a phosphatase enzyme activity gives a comprehensive industrial application that demonstrates FCS+plus' versatility and its potential for pharmaceutical drug discovery.

Quantum Glass of Interacting Bosons with Off-Diagonal Disorder

NASA Astrophysics Data System (ADS)

Piekarska, A. M.; Kopeć, T. K.

2018-04-01

We study disordered interacting bosons described by the Bose-Hubbard model with Gaussian-distributed random tunneling amplitudes. It is shown that the off-diagonal disorder induces a spin-glass-like ground state, characterized by randomly frozen quantum-mechanical U(1) phases of bosons. To access criticality, we employ the "n -replica trick," as in the spin-glass theory, and the Trotter-Suzuki method for decomposition of the statistical density operator, along with numerical calculations. The interplay between disorder, quantum, and thermal fluctuations leads to phase diagrams exhibiting a glassy state of bosons, which are studied as a function of model parameters. The considered system may be relevant for quantum simulators of optical-lattice bosons, where the randomness can be introduced in a controlled way. The latter is supported by a proposition of experimental realization of the system in question.

Toward Accurate and Quantitative Comparative Metagenomics

PubMed Central

Nayfach, Stephen; Pollard, Katherine S.

2016-01-01

Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341

Controllable high-fidelity quantum state transfer and entanglement generation in circuit QED

PubMed Central

Xu, Peng; Yang, Xu-Chen; Mei, Feng; Xue, Zheng-Yuan

2016-01-01

We propose a scheme to realize controllable quantum state transfer and entanglement generation among transmon qubits in the typical circuit QED setup based on adiabatic passage. Through designing the time-dependent driven pulses applied on the transmon qubits, we find that fast quantum sate transfer can be achieved between arbitrary two qubits and quantum entanglement among the qubits also can also be engineered. Furthermore, we numerically analyzed the influence of the decoherence on our scheme with the current experimental accessible systematical parameters. The result shows that our scheme is very robust against both the cavity decay and qubit relaxation, the fidelities of the state transfer and entanglement preparation process could be very high. In addition, our scheme is also shown to be insensitive to the inhomogeneous of qubit-resonator coupling strengths. PMID:26804326

Toward Accurate and Quantitative Comparative Metagenomics.

PubMed

Nayfach, Stephen; Pollard, Katherine S

2016-08-25

Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. Copyright © 2016 Elsevier Inc. All rights reserved.

Quantum Monte Carlo calculations of two neutrons in finite volume

DOE PAGES

Klos, P.; Lynn, J. E.; Tews, I.; ...

2016-11-18

Ab initio calculations provide direct access to the properties of pure neutron systems that are challenging to study experimentally. In addition to their importance for fundamental physics, their properties are required as input for effective field theories of the strong interaction. In this work, we perform auxiliary-field diffusion Monte Carlo calculations of the ground state and first excited state of two neutrons in a finite box, considering a simple contact potential as well as chiral effective field theory interactions. We compare the results against exact diagonalizations and present a detailed analysis of the finite-volume effects, whose understanding is crucial formore » determining observables from the calculated energies. Finally, using the Lüscher formula, we extract the low-energy S-wave scattering parameters from ground- and excited-state energies for different box sizes.« less

Terahertz thickness determination with interferometric vibration correction for industrial applications.

PubMed

Pfeiffer, Tobias; Weber, Stefan; Klier, Jens; Bachtler, Sebastian; Molter, Daniel; Jonuscheit, Joachim; Von Freymann, Georg

2018-05-14

In many industrial fields, like automotive and painting industry, the thickness of thin layers is a crucial parameter for quality control. Hence, the demand for thickness measurement techniques continuously grows. In particular, non-destructive and contact-free terahertz techniques access a wide range of thickness determination applications. However, terahertz time-domain spectroscopy based systems perform the measurement in a sampling manner, requiring fixed distances between measurement head and sample. In harsh industrial environments vibrations of sample and measurement head distort the time-base and decrease measurement accuracy. We present an interferometer-based vibration correction for terahertz time-domain measurements, able to reduce thickness distortion by one order of magnitude for vibrations with frequencies up to 100 Hz and amplitudes up to 100 µm. We further verify the experimental results by numerical calculations and find very good agreement.

Mechanical Characterization of Partially Crystallized Sphere Packings

NASA Astrophysics Data System (ADS)

Hanifpour, M.; Francois, N.; Vaez Allaei, S. M.; Senden, T.; Saadatfar, M.

2014-10-01

We study grain-scale mechanical and geometrical features of partially crystallized packings of frictional spheres, produced experimentally by a vibrational protocol. By combining x-ray computed tomography, 3D image analysis, and discrete element method simulations, we have access to the 3D structure of internal forces. We investigate how the network of mechanical contacts and intergranular forces change when the packing structure evolves from amorphous to near perfect crystalline arrangements. We compare the behavior of the geometrical neighbors (quasicontracts) of a grain to the evolution of the mechanical contacts. The mechanical coordination number Zm is a key parameter characterizing the crystallization onset. The high fluctuation level of Zm and of the force distribution in highly crystallized packings reveals that a geometrically ordered structure still possesses a highly random mechanical backbone similar to that of amorphous packings.

Matching experimental and three dimensional numerical models for structural vibration problems with uncertainties

NASA Astrophysics Data System (ADS)

Langer, P.; Sepahvand, K.; Guist, C.; Bär, J.; Peplow, A.; Marburg, S.

2018-03-01

The simulation model which examines the dynamic behavior of real structures needs to address the impact of uncertainty in both geometry and material parameters. This article investigates three-dimensional finite element models for structural dynamics problems with respect to both model and parameter uncertainties. The parameter uncertainties are determined via laboratory measurements on several beam-like samples. The parameters are then considered as random variables to the finite element model for exploring the uncertainty effects on the quality of the model outputs, i.e. natural frequencies. The accuracy of the output predictions from the model is compared with the experimental results. To this end, the non-contact experimental modal analysis is conducted to identify the natural frequency of the samples. The results show a good agreement compared with experimental data. Furthermore, it is demonstrated that geometrical uncertainties have more influence on the natural frequencies compared to material parameters and material uncertainties are about two times higher than geometrical uncertainties. This gives valuable insights for improving the finite element model due to various parameter ranges required in a modeling process involving uncertainty.

Limited ability driven phase transitions in the coevolution process in Axelrod's model

NASA Astrophysics Data System (ADS)

Wang, Bing; Han, Yuexing; Chen, Luonan; Aihara, Kazuyuki

2009-04-01

We study the coevolution process in Axelrod's model by taking into account of agents' abilities to access information, which is described by a parameter α to control the geographical range of communication. We observe two kinds of phase transitions in both cultural domains and network fragments, which depend on the parameter α. By simulation, we find that not all rewiring processes pervade the dissemination of culture, that is, a very limited ability to access information constrains the cultural dissemination, while an exceptional ability to access information aids the dissemination of culture. Furthermore, by analyzing the network characteristics at the frozen states, we find that there exists a stage at which the network develops to be a small-world network with community structures.

Mining high-throughput experimental data to link gene and function.

PubMed

Blaby-Haas, Crysten E; de Crécy-Lagard, Valérie

2011-04-01

Nearly 2200 genomes that encode around 6 million proteins have now been sequenced. Around 40% of these proteins are of unknown function, even when function is loosely and minimally defined as 'belonging to a superfamily'. In addition to in silico methods, the swelling stream of high-throughput experimental data can give valuable clues for linking these unknowns with precise biological roles. The goal is to develop integrative data-mining platforms that allow the scientific community at large to access and utilize this rich source of experimental knowledge. To this end, we review recent advances in generating whole-genome experimental datasets, where this data can be accessed, and how it can be used to drive prediction of gene function. Copyright © 2011 Elsevier Ltd. All rights reserved.

Composite multi-parameter ranking of real and virtual compounds for design of MC4R agonists: renaissance of the Free-Wilson methodology.

PubMed

Nilsson, Ingemar; Polla, Magnus O

2012-10-01

Drug design is a multi-parameter task present in the analysis of experimental data for synthesized compounds and in the prediction of new compounds with desired properties. This article describes the implementation of a binned scoring and composite ranking scheme for 11 experimental parameters that were identified as key drivers in the MC4R project. The composite ranking scheme was implemented in an AstraZeneca tool for analysis of project data, thereby providing an immediate re-ranking as new experimental data was added. The automated ranking also highlighted compounds overlooked by the project team. The successful implementation of a composite ranking on experimental data led to the development of an equivalent virtual score, which was based on Free-Wilson models of the parameters from the experimental ranking. The individual Free-Wilson models showed good to high predictive power with a correlation coefficient between 0.45 and 0.97 based on the external test set. The virtual ranking adds value to the selection of compounds for synthesis but error propagation must be controlled. The experimental ranking approach adds significant value, is parameter independent and can be tuned and applied to any drug discovery project.

Traffic management mechanism for intranets with available-bit-rate access to the Internet

NASA Astrophysics Data System (ADS)

Hassan, Mahbub; Sirisena, Harsha R.; Atiquzzaman, Mohammed

1997-10-01

The design of a traffic management mechanism for intranets connected to the Internet via an available bit rate access- link is presented. Selection of control parameters for this mechanism for optimum performance is shown through analysis. An estimate for packet loss probability at the access- gateway is derived for random fluctuation of available bit rate of the access-link. Some implementation strategies of this mechanism in the standard intranet protocol stack are also suggested.

Experimental apparatus with full optical access for combustion experiments with laminar flames from a single circular nozzle at elevated pressures.

PubMed

Joo, Peter H; Gao, Jinlong; Li, Zhongshan; Aldén, Marcus

2015-03-01

The design and features of a high pressure chamber and burner that is suitable for combustion experiments at elevated pressures are presented. The high pressure combustion apparatus utilizes a high pressure burner that is comprised of a chamber burner module and an easily accessible interchangeable burner module to add to its flexibility. The burner is well suited to study both premixed and non-premixed flames. The optical access to the chamber is provided through four viewports for direct visual observations and optical-based diagnostic techniques. Auxiliary features include numerous access ports and electrical connections and as a result, the combustion apparatus is also suitable to work with plasmas and liquid fuels. Images of methane flames at elevated pressures up to 25 atm and preliminary results of optical-based measurements demonstrate the suitability of the high pressure experimental apparatus for combustion experiments.

Explosive decomposition of ethylene oxide at elevated condition: effect of ignition energy, nitrogen dilution, and turbulence.

PubMed

Pekalski, A A; Zevenbergen, J F; Braithwaite, M; Lemkowitz, S M; Pasman, H J

2005-02-14

Experimental and theoretical investigation of explosive decomposition of ethylene oxide (EO) at fixed initial experimental parameters (T=100 degrees C, P=4 bar) in a 20-l sphere was conducted. Safety-related parameters, namely the maximum explosion pressure, the maximum rate of pressure rise, and the Kd values, were experimentally determined for pure ethylene oxide and ethylene oxide diluted with nitrogen. The influence of the ignition energy on the explosion parameters was also studied. All these dependencies are quantified in empirical formulas. Additionally, the effect of turbulence on explosive decomposition of ethylene oxide was investigated. In contrast to previous studies, it is found that turbulence significantly influences the explosion severity parameters, mostly the rate of pressure rise. Thermodynamic models are used to calculate the maximum explosion pressure of pure and of nitrogen-diluted ethylene oxide, at different initial temperatures. Soot formation was experimentally observed. Relation between the amounts of soot formed and the explosion pressure was experimentally observed and was calculated.

Assessing the accuracy of subject-specific, muscle-model parameters determined by optimizing to match isometric strength.

PubMed

DeSmitt, Holly J; Domire, Zachary J

2016-12-01

Biomechanical models are sensitive to the choice of model parameters. Therefore, determination of accurate subject specific model parameters is important. One approach to generate these parameters is to optimize the values such that the model output will match experimentally measured strength curves. This approach is attractive as it is inexpensive and should provide an excellent match to experimentally measured strength. However, given the problem of muscle redundancy, it is not clear that this approach generates accurate individual muscle forces. The purpose of this investigation is to evaluate this approach using simulated data to enable a direct comparison. It is hypothesized that the optimization approach will be able to recreate accurate muscle model parameters when information from measurable parameters is given. A model of isometric knee extension was developed to simulate a strength curve across a range of knee angles. In order to realistically recreate experimentally measured strength, random noise was added to the modeled strength. Parameters were solved for using a genetic search algorithm. When noise was added to the measurements the strength curve was reasonably recreated. However, the individual muscle model parameters and force curves were far less accurate. Based upon this examination, it is clear that very different sets of model parameters can recreate similar strength curves. Therefore, experimental variation in strength measurements has a significant influence on the results. Given the difficulty in accurately recreating individual muscle parameters, it may be more appropriate to perform simulations with lumped actuators representing similar muscles.

Using Geographic Information Systems and Spatial Analysis Methods to Assess Household Water Access and Sanitation Coverage in the SHINE Trial.

PubMed

Ntozini, Robert; Marks, Sara J; Mangwadu, Goldberg; Mbuya, Mduduzi N N; Gerema, Grace; Mutasa, Batsirai; Julian, Timothy R; Schwab, Kellogg J; Humphrey, Jean H; Zungu, Lindiwe I

2015-12-15

Access to water and sanitation are important determinants of behavioral responses to hygiene and sanitation interventions. We estimated cluster-specific water access and sanitation coverage to inform a constrained randomization technique in the SHINE trial. Technicians and engineers inspected all public access water sources to ascertain seasonality, function, and geospatial coordinates. Households and water sources were mapped using open-source geospatial software. The distance from each household to the nearest perennial, functional, protected water source was calculated, and for each cluster, the median distance and the proportion of households within <500 m and >1500 m of such a water source. Cluster-specific sanitation coverage was ascertained using a random sample of 13 households per cluster. These parameters were included as covariates in randomization to optimize balance in water and sanitation access across treatment arms at the start of the trial. The observed high variability between clusters in both parameters suggests that constraining on these factors was needed to reduce risk of bias. © The Author 2015. Published by Oxford University Press for the Infectious Diseases Society of America.

SBML-PET: a Systems Biology Markup Language-based parameter estimation tool.

PubMed

Zi, Zhike; Klipp, Edda

2006-11-01

The estimation of model parameters from experimental data remains a bottleneck for a major breakthrough in systems biology. We present a Systems Biology Markup Language (SBML) based Parameter Estimation Tool (SBML-PET). The tool is designed to enable parameter estimation for biological models including signaling pathways, gene regulation networks and metabolic pathways. SBML-PET supports import and export of the models in the SBML format. It can estimate the parameters by fitting a variety of experimental data from different experimental conditions. SBML-PET has a unique feature of supporting event definition in the SMBL model. SBML models can also be simulated in SBML-PET. Stochastic Ranking Evolution Strategy (SRES) is incorporated in SBML-PET for parameter estimation jobs. A classic ODE Solver called ODEPACK is used to solve the Ordinary Differential Equation (ODE) system. http://sysbio.molgen.mpg.de/SBML-PET/. The website also contains detailed documentation for SBML-PET.

With-in host dynamics of L. monocytogenes and thresholds for distinct infection scenarios.

PubMed

Rahman, Ashrafur; Munther, Daniel; Fazil, Aamir; Smith, Ben; Wu, Jianhong

2018-05-26

The case fatality and illness rates associated with L. monocytogenes continue to pose a serious public health burden despite the significant efforts and control protocol administered by private and public sectors. Due to the advance in surveillance and improvement in detection methodology, the knowledge of sources, transmission routes, growth potential in food process units and storage, effect of pH and temperature are well understood. However, the with-in host growth and transmission mechanisms of L. monocytogenes, particularly within the human host, remain unclear, largely due to the limited access to scientific experimentation on the human population. In order to provide insight towards the human immune response to the infection caused by L. monocytogenes, we develop a with-in host mathematical model. The model explains, in terms of biological parameters, the states of asymptomatic infection, mild infection and systemic infection leading to listeriosis. The activation and proliferation of T-cells are found to be critical for the susceptibility of the infection. Utilizing stability analysis and numerical simulation, the ranges of the critical parameters relative to infection states are established. Bifurcation analysis shows the impact of the differences of these parameters on the dynamics of the model. Finally, we present model applications in regards to predicting the risk potential of listeriosis relative to the susceptible human population. Copyright © 2018. Published by Elsevier Ltd.

Mean field analysis of a spatial stochastic model of a gene regulatory network.

PubMed

Sturrock, M; Murray, P J; Matzavinos, A; Chaplain, M A J

2015-10-01

A gene regulatory network may be defined as a collection of DNA segments which interact with each other indirectly through their RNA and protein products. Such a network is said to contain a negative feedback loop if its products inhibit gene transcription, and a positive feedback loop if a gene product promotes its own production. Negative feedback loops can create oscillations in mRNA and protein levels while positive feedback loops are primarily responsible for signal amplification. It is often the case in real biological systems that both negative and positive feedback loops operate in parameter regimes that result in low copy numbers of gene products. In this paper we investigate the spatio-temporal dynamics of a single feedback loop in a eukaryotic cell. We first develop a simplified spatial stochastic model of a canonical feedback system (either positive or negative). Using a Gillespie's algorithm, we compute sample trajectories and analyse their corresponding statistics. We then derive a system of equations that describe the spatio-temporal evolution of the stochastic means. Subsequently, we examine the spatially homogeneous case and compare the results of numerical simulations with the spatially explicit case. Finally, using a combination of steady-state analysis and data clustering techniques, we explore model behaviour across a subregion of the parameter space that is difficult to access experimentally and compare the parameter landscape of our spatio-temporal and spatially-homogeneous models.

Comparative Assessment of Torso and Seat Mounted Restraint Systems using Manikins on the Vertical Deceleration Tower

DTIC Science & Technology

2017-03-01

experimental effort involving a series of +z-axis impact tests was conducted on the 711th Human Performance Wing’s Vertical Deceleration Tower (VDT...parameters) and a JSF-styled ejection seat configuration (combined non -baseline test parameters) produced similar biodynamic response parameters for the LOIS...Photography .............................................................................. 12 6.0 EXPERIMENTAL DESIGN

50 CFR 223.301 - Special rules-marine and anadromous fishes.

Code of Federal Regulations, 2014 CFR

2014-10-01

... section comprise a nonessential, experimental population (NEP). (2) Take of this species that is allowed... 50 CFR 223.203(a). (4) Geographic extent of the nonessential experimental population of Middle Columbia River steelhead. (i) The geographic range of this experimental population is all accessible...

Preoperative ultrasound still valuable for radio-cephalic arteriovenous fistula creation?

PubMed

Pajek, Jernej; Malovrh, Marko

2017-03-06

Radio-cephalic arteriovenous fistula is a prototype hemodialysis access with small incidences of infection and distal ischemia, it spares proximal veins for future access use and it helps in the maturation of veins that may be used for more proximal access creations. This access type is prone to higher early failure rates compared to more proximal fistulas and there are unsolved uncertainties regarding exact ultrasound parameters predictive of fistula outcome. Evolution of ultrasound use has yielded several functional parameters that can be measured in addition to anatomical lumen sizes, which remain core parameters on which the decision to construct fistula in radio-cephalic forearm position is based. We propose to use arterial hyperemic response and wall morphology to aid in this decision when radial artery diameter falls in the interval with predictive uncertainty of 1.6-1.9 mm and to use venous flow pattern, respiratory variation, radial artery status and possibly venous distensibility when cephalic vein augmented diameter lies in the borderline interval of 2-2.4 mm. Ultrasound preoperative mapping and planning should be followed by expert surgical technique and several technique modifications of the classical end-to-side approach are possible to enhance operation outcome and diminish the incidence of stenosis most often present at juxta-anastomotic location. In our experience radio-cephalic arteriovenous fistula remains the golden standard for hemodialysis access and preoperative ultrasound the single best imaging modality to plan the operation and predict its success.

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

Levin, Barnaby D. A.; Padgett, Elliot; Chen, Chien-Chun

Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co 2 P nanocrystal, platinum nanoparticles on a carbonmore » nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data.« less

A synopsis of the EVA training conducted on EASE/ACCESS for STS-61-B

NASA Technical Reports Server (NTRS)

Havens, Kathryn A.

1987-01-01

Experimental Assembly of Structure in EVA (EASE)/Assembly Concept for Construction of Erectable Space Structures (ACCESS) training problems; photography/television coverage; training schedules; flight data file (FDF), and flight rules production are summarized.

The Numerical Calculation and Experimental Measurement of the Inductance Parameters for Permanent Magnet Synchronous Motor in Electric Vehicle

NASA Astrophysics Data System (ADS)

Jiang, Chao; Qiao, Mingzhong; Zhu, Peng

2017-12-01

A permanent magnet synchronous motor with radial magnetic circuit and built-in permanent magnet is designed for the electric vehicle. Finite element numerical calculation and experimental measurement are adopted to obtain the direct axis and quadrature axis inductance parameters of the motor which are vital important for the motor control. The calculation method is simple, the measuring principle is clear, the results of numerical calculation and experimental measurement are mutual confirmation. A quick and effective method is provided to obtain the direct axis and quadrature axis inductance parameters of the motor, and then improve the design of motor or adjust the control parameters of the motor controller.

Comparison of three nondestructive and contactless techniques for investigations of recombination parameters on an example of silicon samples

NASA Astrophysics Data System (ADS)

Chrobak, Ł.; Maliński, M.

2018-06-01

This paper presents a comparison of three nondestructive and contactless techniques used for determination of recombination parameters of silicon samples. They are: photoacoustic method, modulated free carriers absorption method and the photothermal radiometry method. In the paper the experimental set-ups used for measurements of the recombination parameters in these methods as also theoretical models used for interpretation of obtained experimental data have been presented and described. The experimental results and their respective fits obtained with these nondestructive techniques are shown and discussed. The values of the recombination parameters obtained with these methods are also presented and compared. Main advantages and disadvantages of presented methods have been discussed.

Initial experiments to understand the interaction of stellar radiation with molecular clouds

NASA Astrophysics Data System (ADS)

Vandervort, Robert; Davis, Josh; Trantham, Matt; Klein, Sallee; Shvarts, Dov; Keiter, Paul; Drake, R. Paul

2017-10-01

Enhanced star formation triggered by local O and B type stars is an astrophysical problem of interest. O and B type stars are massive, hot stars that emit an enormous amount of radiation. This radiation acts to either compress or blow apart gas clumps in the interstellar media. For example, in the optically thick limit, when the radiation in the gas clump has a short mean free path, radiation is absorbed near the clump edge and compresses the clump. In the optically thin limit, when the mean free path is long, the radiation is absorbed throughout, acting to heat the clump. This heating explodes the gas clump. Careful selection of parameters, such as foam density or source temperature, allow the experimental platform to access different hydrodynamic regimes. 2D CRASH simulations guide our parameter selection. A stellar radiation source is mimicked by a laser-irradiated, thin, gold foil, providing a source of thermal x-rays around 100 eV. The gas clump is mimicked by low-density CRF foam. We plan to show the preliminary experimental results of this platform in the optically thick limit, from experiments scheduled in August. This work is funded by the U.S. DOE, through the NNSA-DS and SC-OFES Joint Program in HEDPLP, Grant No. DE-NA0002956, and the NLUF Program, Grant No. DE-NA0002719, and through LLE, University of Rochester by the NNSA/OICF under Cooperative Agreement No. DE-NA0001944. This work is funded by the Lawrence Livermore National Laboratory under subcontract B614207.

Implementation of EPICS based vacuum control system for variable energy cyclotron centre, Kolkata

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

Roy, Anindya, E-mail: r-ani@vecc.gov.in; Bhole, R. B.; Nandy, Partha P.

2015-03-15

The vacuum system of the Room Temperature (K = 130) Cyclotron of Variable Energy Cyclotron Centre is comprised of vacuum systems of main machine and Beam Transport System. The vacuum control system is upgraded to a PLC based Automated system from the initial relay based Manual system. The supervisory control of the vacuum system is implemented in Experimental Physics and Industrial Control System (EPICS). An EPICS embedded ARM based vacuum gauge controller is developed to mitigate the requirement of vendor specific gauge controller for gauges and also for seamless integration of the gauge controllers with the control system. A setmore » of MS-Windows ActiveX components with embedded EPICS Channel Access interface are developed to build operator interfaces with less complex programming and to incorporate typical Windows feature, e.g., user authentication, file handling, better fonts, colors, mouse actions etc. into the operator interfaces. The control parameters, monitoring parameters, and system interlocks of the system are archived in MySQL based EPICS MySQL Archiver developed indigenously. In this paper, we describe the architecture, the implementation details, and the performance of the system.« less

Prediction of anaerobic biodegradability and bioaccessibility of municipal sludge by coupling sequential extractions with fluorescence spectroscopy: towards ADM1 variables characterization.

PubMed

Jimenez, Julie; Gonidec, Estelle; Cacho Rivero, Jesús Andrés; Latrille, Eric; Vedrenne, Fabien; Steyer, Jean-Philippe

2014-03-01

Advanced dynamic anaerobic digestion models, such as ADM1, require both detailed organic matter characterisation and intimate knowledge of the involved metabolic pathways. In the current study, a methodology for municipal sludge characterization is investigated to describe two key parameters: biodegradability and bioaccessibility of organic matter. The methodology is based on coupling sequential chemical extractions with 3D fluorescence spectroscopy. The use of increasingly strong solvents reveals different levels of organic matter accessibility and the spectroscopy measurement leads to a detailed characterisation of the organic matter. The results obtained from testing 52 municipal sludge samples (primary, secondary, digested and thermally treated) showed a successful correlation with sludge biodegradability and bioaccessibility. The two parameters, traditionally obtained through the biochemical methane potential (BMP) lab tests, are now obtain in only 5 days compared to the 30-60 days usually required. Experimental data, obtained from two different laboratory scale reactors, were used to validate the ADM1 model. The proposed approach showed a strong application potential for reactor design and advanced control of anaerobic digestion processes. Copyright © 2013 Elsevier Ltd. All rights reserved.

DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs.

PubMed

Chodkiewicz, Michał L; Migacz, Szymon; Rudnicki, Witold; Makal, Anna; Kalinowski, Jarosław A; Moriarty, Nigel W; Grosse-Kunstleve, Ralf W; Afonine, Pavel V; Adams, Paul D; Dominiak, Paulina Maria

2018-02-01

It has been recently established that the accuracy of structural parameters from X-ray refinement of crystal structures can be improved by using a bank of aspherical pseudoatoms instead of the classical spherical model of atomic form factors. This comes, however, at the cost of increased complexity of the underlying calculations. In order to facilitate the adoption of this more advanced electron density model by the broader community of crystallographers, a new software implementation called DiSCaMB , 'densities in structural chemistry and molecular biology', has been developed. It addresses the challenge of providing for high performance on modern computing architectures. With parallelization options for both multi-core processors and graphics processing units (using CUDA), the library features calculation of X-ray scattering factors and their derivatives with respect to structural parameters, gives access to intermediate steps of the scattering factor calculations (thus allowing for experimentation with modifications of the underlying electron density model), and provides tools for basic structural crystallographic operations. Permissively (MIT) licensed, DiSCaMB is an open-source C++ library that can be embedded in both academic and commercial tools for X-ray structure refinement.

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

Fertig, Fabian, E-mail: fabian.fertig@ise.fraunhofer.de; Greulich, Johannes; Rein, Stefan

Spatially resolved determination of solar cell parameters is beneficial for loss analysis and optimization of conversion efficiency. One key parameter that has been challenging to access by an imaging technique on solar cell level is short-circuit current density. This work discusses the robustness of a recently suggested approach to determine short-circuit current density spatially resolved based on a series of lock-in thermography images and options for a simplified image acquisition procedure. For an accurate result, one or two emissivity-corrected illuminated lock-in thermography images and one dark lock-in thermography image have to be recorded. The dark lock-in thermography image can bemore » omitted if local shunts are negligible. Furthermore, it is shown that omitting the correction of lock-in thermography images for local emissivity variations only leads to minor distortions for standard silicon solar cells. Hence, adequate acquisition of one image only is sufficient to generate a meaningful map of short-circuit current density. Beyond that, this work illustrates the underlying physics of the recently proposed method and demonstrates its robustness concerning varying excitation conditions and locally increased series resistance. Experimentally gained short-circuit current density images are validated for monochromatic illumination in comparison to the reference method of light-beam induced current.« less

Kinetic operational models of agonism for G-protein-coupled receptors.

PubMed

Hoare, Samuel R J; Pierre, Nicolas; Moya, Arturo Gonzalez; Larson, Brad

2018-06-07

The application of kinetics to research and therapeutic development of G-protein-coupled receptors has become increasingly valuable. Pharmacological models provide the foundation of pharmacology, providing concepts and measurable parameters such as efficacy and potency that have underlain decades of successful drug discovery. Currently there are few pharmacological models that incorporate kinetic activity in such a way as to yield experimentally-accessible drug parameters. In this study, a kinetic model of pharmacological response was developed that provides a kinetic descriptor of efficacy (the transduction rate constant, k τ ) and allows measurement of receptor-ligand binding kinetics from functional data. The model assumes: (1) receptor interacts with a precursor of the response ("Transduction potential") and converts it to the response. (2) The response can decay. Familiar response vs time plots emerge, depending on whether transduction potential is depleted and/or response decays. These are the straight line, the "association" exponential curve, and the rise-and-fall curve. Convenient, familiar methods are described for measuring the model parameters and files are provided for the curve-fitting program Prism (GraphPad Software) that can be used as a guide. The efficacy parameter k τ is straightforward to measure and accounts for receptor reserve; all that is required is measurement of response over time at a maximally-stimulating concentration of agonist. The modular nature of the model framework allows it to be extended. Here this is done to incorporate antagonist-receptor binding kinetics and slow agonist-receptor equilibration. In principle, the modular framework can incorporate other cellular processes, such as receptor desensitization. The kinetic response model described here can be applied to measure kinetic pharmacological parameters than can be used to advance the understanding of GPCR pharmacology and optimize new and improved therapeutics. Copyright © 2018 Elsevier Ltd. All rights reserved.

Experimental investigation of efficient locomotion of underwater snake robots for lateral undulation and eel-like motion patterns.

PubMed

Kelasidi, Eleni; Liljebäck, Pål; Pettersen, Kristin Y; Gravdahl, Jan T

2015-01-01

Underwater snake robots offer many interesting capabilities for underwater operations. The long and slender structure of such robots provide superior capabilities for access through narrow openings and within confined areas. This is interesting for inspection and monitoring operations, for instance within the subsea oil and gas industry and within marine archeology. In addition, underwater snake robots can provide both inspection and intervention capabilities and are thus interesting candidates for the next generation inspection and intervention AUVs. Furthermore, bioinspired locomotion through oscillatory gaits, like lateral undulation and eel-like motion, is interesting from an energy efficiency point of view. Increasing the motion efficiency in terms of the achieved forward speed by improving the method of propulsion is a key issue for underwater robots. Moreover, energy efficiency is one of the main challenges for long-term autonomy of these systems. In this study, we will consider both these two aspects of efficiency. This paper considers the energy efficiency of swimming snake robots by presenting and experimentally investigating fundamental properties of the velocity and the power consumption of an underwater snake robot for both lateral undulation and eel-like motion patterns. In particular, we investigate the relationship between the parameters of the gait patterns, the forward velocity and the energy consumption for different motion patterns. The simulation and experimental results are seen to support the theoretical findings.

Hydrogen Donor-Acceptor Fluctuations from Kinetic Isotope Effects: A Phenomenological Model

PubMed Central

Roston, Daniel; Cheatum, Christopher M.; Kohen, Amnon

2012-01-01

Kinetic isotope effects (KIEs) and their temperature dependence can probe the structural and dynamic nature of enzyme-catalyzed proton or hydride transfers. The molecular interpretation of their temperature dependence requires expensive and specialized QM/MM calculations to provide a quantitative molecular understanding. Currently available phenomenological models use a non-adiabatic assumption that is not appropriate for most hydride and proton-transfer reactions, while others require more parameters than the experimental data justify. Here we propose a phenomenological interpretation of KIEs based on a simple method to quantitatively link the size and temperature dependence of KIEs to a conformational distribution of the catalyzed reaction. The present model assumes adiabatic hydrogen tunneling, and by fitting experimental KIE data, the model yields a population distribution for fluctuations of the distance between donor and acceptor atoms. Fits to data from a variety of proton and hydride transfers catalyzed by enzymes and their mutants, as well as non-enzymatic reactions, reveal that steeply temperature-dependent KIEs indicate the presence of at least two distinct conformational populations, each with different kinetic behaviors. We present the results of these calculations for several published cases and discuss how the predictions of the calculations might be experimentally tested. The current analysis does not replace molecular quantum mechanics/molecular mechanics (QM/MM) investigations, but it provides a fast and accessible way to quantitatively interpret KIEs in the context of a Marcus-like model. PMID:22857146

An Improved Swarm Optimization for Parameter Estimation and Biological Model Selection

PubMed Central

Abdullah, Afnizanfaizal; Deris, Safaai; Mohamad, Mohd Saberi; Anwar, Sohail

2013-01-01

One of the key aspects of computational systems biology is the investigation on the dynamic biological processes within cells. Computational models are often required to elucidate the mechanisms and principles driving the processes because of the nonlinearity and complexity. The models usually incorporate a set of parameters that signify the physical properties of the actual biological systems. In most cases, these parameters are estimated by fitting the model outputs with the corresponding experimental data. However, this is a challenging task because the available experimental data are frequently noisy and incomplete. In this paper, a new hybrid optimization method is proposed to estimate these parameters from the noisy and incomplete experimental data. The proposed method, called Swarm-based Chemical Reaction Optimization, integrates the evolutionary searching strategy employed by the Chemical Reaction Optimization, into the neighbouring searching strategy of the Firefly Algorithm method. The effectiveness of the method was evaluated using a simulated nonlinear model and two biological models: synthetic transcriptional oscillators, and extracellular protease production models. The results showed that the accuracy and computational speed of the proposed method were better than the existing Differential Evolution, Firefly Algorithm and Chemical Reaction Optimization methods. The reliability of the estimated parameters was statistically validated, which suggests that the model outputs produced by these parameters were valid even when noisy and incomplete experimental data were used. Additionally, Akaike Information Criterion was employed to evaluate the model selection, which highlighted the capability of the proposed method in choosing a plausible model based on the experimental data. In conclusion, this paper presents the effectiveness of the proposed method for parameter estimation and model selection problems using noisy and incomplete experimental data. This study is hoped to provide a new insight in developing more accurate and reliable biological models based on limited and low quality experimental data. PMID:23593445

The patient's safety and access to experimental drugs after the termination of clinical trials: regulations and trends.

PubMed

da Silva, Ricardo Eccard; Amato, Angélica Amorim; Sousa, Thiago do Rego; de Carvalho, Marta Rodrigues; Novaes, Maria Rita Carvalho Garbi

2018-05-12

Participants' rights and safety must be guaranteed not only while a clinical trial is being conducted but also when a clinical trial finishes. The criteria for post-trial access to experimental drugs, however, are unclear in various countries. The objectives of this study were (i) to ascertain if there were regulations or guidelines related to patients' access to drugs after the end of clinical trials in the countries selected in the study and (ii) to analyze trends in post-trial access in countries classified by their level of economic development. This study is a retrospective review. The data are from the records of clinical trials from 2014 registered in the World Health Organization's International Clinical Trials Registry Platform (ICTRP) database. Among the countries selected, provision of drugs post-trial is mandatory only in Argentina, Brazil, Chile, Finland, and Peru. The plans for post-trial access tend to be more present in low- and middle-income and upper middle-income countries, in comparison with high-income countries. Studies involving vulnerable populations are 2.53 times more likely to have plans for post-trial access than studies which do not. The guaranteeing of post-trial access remains mandatory in few countries. Considering that individuals seen as vulnerable have been included in clinical trials without plans for post-trial access, stakeholders must discuss the need to develop regulations mandating the guaranteeing of post-trial access in specified situations.

Highly Sensitive Refractive Index Sensors with Plasmonic Nanoantennas-Utilization of Optimal Spectral Detuning of Fano Resonances.

PubMed

Mesch, Martin; Weiss, Thomas; Schäferling, Martin; Hentschel, Mario; Hegde, Ravi S; Giessen, Harald

2018-05-25

We analyze and optimize the performance of coupled plasmonic nanoantennas for refractive index sensing. The investigated structure supports a sub- and super-radiant mode that originates from the weak coupling of a dipolar and quadrupolar mode, resulting in a Fano-type spectral line shape. In our study, we vary the near-field coupling of the two modes and particularly examine the influence of the spectral detuning between them on the sensing performance. Surprisingly, the case of matched resonance frequencies does not provide the best sensor. Instead, we find that the right amount of coupling strength and spectral detuning allows for achieving the ideal combination of narrow line width and sufficient excitation strength of the subradiant mode, and therefore results in optimized sensor performance. Our findings are confirmed by experimental results and first-order perturbation theory. The latter is based on the resonant state expansion and provides direct access to resonance frequency shifts and line width changes as well as the excitation strength of the modes. Based on these parameters, we define a figure of merit that can be easily calculated for different sensing geometries and agrees well with the numerical and experimental results.

Far-from-Equilibrium Route to Superthermal Light in Bimodal Nanolasers

NASA Astrophysics Data System (ADS)

Marconi, Mathias; Javaloyes, Julien; Hamel, Philippe; Raineri, Fabrice; Levenson, Ariel; Yacomotti, Alejandro M.

2018-02-01

Microscale and nanoscale lasers inherently exhibit rich photon statistics due to complex light-matter interaction in a strong spontaneous emission noise background. It is well known that they may display superthermal fluctuations—photon superbunching—in specific situations due to either gain competition, leading to mode-switching instabilities, or carrier-carrier coupling in superradiant microcavities. Here we show a generic route to superbunching in bimodal nanolasers by preparing the system far from equilibrium through a parameter quench. We demonstrate, both theoretically and experimentally, that transient dynamics after a short-pump-pulse-induced quench leads to heavy-tailed superthermal statistics when projected onto the weak mode. We implement a simple experimental technique to access the probability density functions that further enables quantifying the distance from thermal equilibrium via the thermodynamic entropy. The universality of this mechanism relies on the far-from-equilibrium dynamical scenario, which can be mapped to a fast cooling process of a suspension of Brownian particles in a liquid. Our results open up new avenues to mold photon statistics in multimode optical systems and may constitute a test bed to investigate out-of-equilibrium thermodynamics using micro or nanocavity arrays.

Dynamic behavior of the weld pool in stationary GMAW

NASA Astrophysics Data System (ADS)

Chapuis, J.; Romero, E.; Bordreuil, C.; Soulié, F.; Fras, G.

2010-06-01

Because hump formation limits welding productivity, better understanding of the humping phenomena during the welding process is needed to access to process modifications that decrease the tendency for hump formation and then allow higher productivity welding. From a physical point of view, the mechanism identified is the Rayleigh instability initiated by strong surface tension gradient which induces a variation of kinetic flow. But the causes of the appearance of this instability are not yet well explained. Because of the phenomena complex and multi-physics, we chose in first step to conduct an analysis of the characteristic times involved in weld pool in pulsed stationary GMAW. The goal is to study the dynamic behavior of the weld pool, using our experimental multi physics approach. The experimental tool and methodology developed to understand these fast phenomena are presented first: frames acquisition with high speed digital camera and specific optical devices, numerical library. The analysis of geometric parameters of the weld pool during welding operation are presented in the last part: we observe the variations of wetting angles (or contact lines angles), the base and the height of the weld pool (macro-drop) versus weld time.

Residual stress analysis of welded joints by the variational eigenstrain approach

NASA Astrophysics Data System (ADS)

Korsunsky, Alexander M.; Regino, Gabriel; Nowell, David

2005-04-01

We present the formulation for finding the distribution of eigenstrains, i.e. the sources of residual stress, from a set of measurements of residual elastic strain (e.g. by diffraction), or residual stress, or stress redistribution, or distortion. The variational formulation employed seeks to achieve the best agreement between the model prediction and some measured parameters in the sense of a minimum of a functional given by a sum over the entire set of measurements. The advantage of this approach lies in its flexibility: different sets of measurements and information about different components of the stress-strain state can be incorporated. We demonstrate the power of the technique by analysing experimental data for welds in thin sheet of a nickel superalloy aerospace material. Very good agreement can be achieved between the prediction and the measurement results without the necessity of using iterative solution. In practice complete characterisation of residual stress states is often very difficult, due to limitations of facility access, measurement time or specimen dimensions. Implications of the new technique for experimental analysis are all the more significant, since it allows the reconstruction of the entire stress state from incomplete sets of data.

Predicting the Types of Ion Channel-Targeted Conotoxins Based on AVC-SVM Model.

PubMed

Xianfang, Wang; Junmei, Wang; Xiaolei, Wang; Yue, Zhang

2017-01-01

The conotoxin proteins are disulfide-rich small peptides. Predicting the types of ion channel-targeted conotoxins has great value in the treatment of chronic diseases, epilepsy, and cardiovascular diseases. To solve the problem of information redundancy existing when using current methods, a new model is presented to predict the types of ion channel-targeted conotoxins based on AVC (Analysis of Variance and Correlation) and SVM (Support Vector Machine). First, the F value is used to measure the significance level of the feature for the result, and the attribute with smaller F value is filtered by rough selection. Secondly, redundancy degree is calculated by Pearson Correlation Coefficient. And the threshold is set to filter attributes with weak independence to get the result of the refinement. Finally, SVM is used to predict the types of ion channel-targeted conotoxins. The experimental results show the proposed AVC-SVM model reaches an overall accuracy of 91.98%, an average accuracy of 92.17%, and the total number of parameters of 68. The proposed model provides highly useful information for further experimental research. The prediction model will be accessed free of charge at our web server.

Predicting the Types of Ion Channel-Targeted Conotoxins Based on AVC-SVM Model

PubMed Central

Xiaolei, Wang

2017-01-01

The conotoxin proteins are disulfide-rich small peptides. Predicting the types of ion channel-targeted conotoxins has great value in the treatment of chronic diseases, epilepsy, and cardiovascular diseases. To solve the problem of information redundancy existing when using current methods, a new model is presented to predict the types of ion channel-targeted conotoxins based on AVC (Analysis of Variance and Correlation) and SVM (Support Vector Machine). First, the F value is used to measure the significance level of the feature for the result, and the attribute with smaller F value is filtered by rough selection. Secondly, redundancy degree is calculated by Pearson Correlation Coefficient. And the threshold is set to filter attributes with weak independence to get the result of the refinement. Finally, SVM is used to predict the types of ion channel-targeted conotoxins. The experimental results show the proposed AVC-SVM model reaches an overall accuracy of 91.98%, an average accuracy of 92.17%, and the total number of parameters of 68. The proposed model provides highly useful information for further experimental research. The prediction model will be accessed free of charge at our web server. PMID:28497044

UV-Vis reflection spectroscopy under variable angle incidence at the air-liquid interface.

PubMed

Roldán-Carmona, Cristina; Rubia-Payá, Carlos; Pérez-Morales, Marta; Martín-Romero, María T; Giner-Casares, Juan J; Camacho, Luis

2014-03-07

The UV-Vis reflection spectroscopy (UV-Vis-RS) in situ at the air-liquid interface provides information about tilt and aggregation of chromophores in Langmuir monolayers. This information is particularly important given in most cases the chromophore is located at the polar region of the Langmuir monolayer. This region of the Langmuir monolayers has been hardly accessible by other experimental techniques. In spite of its enormous potential, the application of UV-Vis-RS has been limited mainly to reflection measurements under light normal incidence or at lower incidence angles than the Brewster angle. Remarkably, this technique is quite sensitive to the tilt of the chromophores at values of incidence angles close to or larger than the Brewster angle. Therefore, a novel method to obtain the order parameter of the chromophores at the air-liquid interface by using s- and p-polarized radiation at different incidence angles is proposed. This method allowed for the first time the experimental observation of the two components with different polarization properties of a single UV-Vis band at the air-liquid interface. The method of UV-Vis spectroscopy under variable angle incidence is presented as a new tool for obtaining rich detailed information on Langmuir monolayers.

Electrocutaneous stimulation system for Braille reading.

PubMed

Echenique, Ana Maria; Graffigna, Juan Pablo; Mut, Vicente

2010-01-01

This work is an assistive technology for people with visual disabilities and aims to facilitate access to written information in order to achieve better social inclusion and integration into work and educational activities. Two methods of electrical stimulation (by current and voltage) of the mechanoreceptors was tested to obtain tactile sensations on the fingertip. Current and voltage stimulation were tested in a Braille cell and line prototype, respectively. These prototypes are evaluated in 33 blind and visually impaired subjects. The result of experimentation with both methods showed that electrical stimulation causes sensations of touch defined in the fingertip. Better results in the Braille characters reading were obtained with current stimulation (85% accuracy). However this form of stimulation causes uncomfortable sensations. The latter feeling was minimized with the method of voltage stimulation, but with low efficiency (50% accuracy) in terms of identification of the characters. We concluded that electrical stimulation is a promising method for the development of a simple and unexpensive Braille reading system for blind people. We observed that voltage stimulation is preferred by the users. However, more experimental tests must be carry out in order to find the optimum values of the stimulus parameters and increase the accuracy the Braille characters reading.

Accessing the dynamics of end-grafted flexible polymer chains by atomic force-electrochemical microscopy. Theoretical modeling of the approach curves by the elastic bounded diffusion model and Monte Carlo simulations. Evidence for compression-induced lateral chain escape.

PubMed

Abbou, Jeremy; Anne, Agnès; Demaille, Christophe

2006-11-16

The dynamics of a molecular layer of linear poly(ethylene glycol) (PEG) chains of molecular weight 3400, bearing at one end a ferrocene (Fc) label and thiol end-grafted at a low surface coverage onto a gold substrate, is probed using combined atomic force-electrochemical microscopy (AFM-SECM), at the scale of approximately 100 molecules. Force and current approach curves are simultaneously recorded as a force-sensing microelectrode (tip) is inserted within the approximately 10 nm thick, redox labeled, PEG chain layer. Whereas the force approach curve gives access to the structure of the compressed PEG layer, the tip-current, resulting from tip-to-substrate redox cycling of the Fc head of the chain, is controlled by chain dynamics. The elastic bounded diffusion model, which considers the motion of the Fc head as diffusion in a conformational field, complemented by Monte Carlo (MC) simulations, from which the chain conformation can be derived for any degree of confinement, allows the theoretical tip-current approach curve to be calculated. The experimental current approach curve can then be very satisfyingly reproduced by theory, down to a tip-substrate separation of approximately 2 nm, using only one adjustable parameter characterizing the chain dynamics: the effective diffusion coefficient of the chain head. At closer tip-substrate separations, an unpredicted peak is observed in the experimental current approach curve, which is shown to find its origin in a compression-induced escape of the chain from within the narrowing tip-substrate gap. MC simulations provide quantitative support for lateral chain elongation as the escape mechanism.

Development of solid-state NMR techniques for the characterisation of pharmaceutical compounds

NASA Astrophysics Data System (ADS)

Tatton, Andrew S.

Structural characterisation in the solid state is an important step in understanding the physical and chemical properties of a material. Solid-state NMR techniques applied to solid delivery forms are presented as an alternative to more established structural characterisation methods. The effect of homonuclear decoupling upon heteronuclear couplings is investigated using a combination of experimental and density-matrix simulation results acquired from a 13C-1H spinecho pulse sequence, modulated by scalar couplings. It is found that third-order cross terms under MAS and homonuclear decoupling contribute to strong dephasing effects in the NMR signal. Density-matrix simulations allow access to parameters currently unattainable in experiment, and demonstrate that higher homonuclear decoupling rf nutation frequencies reduce the magnitude of third-order cross terms. 15N-1H spinecho experiments were applied to pharmaceutically relevant samples to differentiate between the number of directly attached protons. Using this method, proton transfer in an acid-base reaction is proven in pharmaceutical salts. The indirect detection of 14N lineshapes via protons obtained using 2D 14N-1H HMQC experiments is presented, where coherence transfer is achieved via heteronuclear through-space dipolar couplings. The importance of fast MAS frequencies is demonstrated, and it is found that increasing the recoupling duration reveals longer range NH proximities. The 2D 14N-1H HMQC method is used to demonstrate the presence of specific hydrogen bonding interactions, and thus aid in identifying molecular association in a cocrystal and an amorphous dispersion. In addition, hydrogen bonding motifs were identified by observing the changes in the 14N quadrupolar parameters between individual molecular components relative to the respective solid delivery form. First-principles calculations of NMR chemical shifts and quadrupolar parameters using the GIPAW method were combined with 14N-1H experimental results to assist with spectral assignment and the identification of the hydrogen bonding interactions.

Thermodynamic properties of rhodium at high temperature and pressure by using mean field potential approach

NASA Astrophysics Data System (ADS)

Kumar, Priyank; Bhatt, Nisarg K.; Vyas, Pulastya R.; Gohel, Vinod B.

2016-10-01

The thermophysical properties of rhodium are studied up to melting temperature by incorporating anharmonic effects due to lattice ions and thermally excited electrons. In order to account anharmonic effects due to lattice vibrations, we have employed mean field potential (MFP) approach and for thermally excited electrons Mermin functional. The local form of the pseudopotential with only one effective adjustable parameter rc is used to construct MFP and hence vibrational free energy due to ions - Fion. We have studied equation of state at 300 K and further, to access the applicability of present conjunction scheme, we have also estimated shock-Hugoniot and temperature along principle Hugoniot. We have carried out the study of temperature variation of several thermophysical properties like thermal expansion (βP), enthalpy (EH), specific heats at constant pressure and volume (CP and CV), specific heats due to lattice ions and thermally excited electrons ( and , isothermal and adiabatic bulk moduli (BT and Bs) and thermodynamic Gruneisen parameter (γth) in order to examine the inclusion of anharmonic effects in the present study. The computed results are compared with available experimental results measured by using different methods and previously obtained theoretical results using different theoretical philosophy. Our computed results are in good agreement with experimental findings and for some physical quantities better or comparable with other theoretical results. We conclude that local form of the pseudopotential used accounts s-p-d hybridization properly and found to be transferable at extreme environment without changing the values of the parameter. Thus, even the behavior of transition metals having complexity in electronic structure can be well understood with local pseudopotential without any modification in the potential at extreme environment. Looking to the success of present scheme (MFP + pseudopotential) we would like to extend it further for the study of liquid state properties as well as thermophysical properties of d and f block metals.

Advanced optical simulation of scintillation detectors in GATE V8.0: first implementation of a reflectance model based on measured data

NASA Astrophysics Data System (ADS)

Stockhoff, Mariele; Jan, Sebastien; Dubois, Albertine; Cherry, Simon R.; Roncali, Emilie

2017-06-01

Typical PET detectors are composed of a scintillator coupled to a photodetector that detects scintillation photons produced when high energy gamma photons interact with the crystal. A critical performance factor is the collection efficiency of these scintillation photons, which can be optimized through simulation. Accurate modelling of photon interactions with crystal surfaces is essential in optical simulations, but the existing UNIFIED model in GATE is often inaccurate, especially for rough surfaces. Previously a new approach for modelling surface reflections based on measured surfaces was validated using custom Monte Carlo code. In this work, the LUT Davis model is implemented and validated in GATE and GEANT4, and is made accessible for all users in the nuclear imaging research community. Look-up-tables (LUTs) from various crystal surfaces are calculated based on measured surfaces obtained by atomic force microscopy. The LUTs include photon reflection probabilities and directions depending on incidence angle. We provide LUTs for rough and polished surfaces with different reflectors and coupling media. Validation parameters include light output measured at different depths of interaction in the crystal and photon track lengths, as both parameters are strongly dependent on reflector characteristics and distinguish between models. Results from the GATE/GEANT4 beta version are compared to those from our custom code and experimental data, as well as the UNIFIED model. GATE simulations with the LUT Davis model show average variations in light output of  <2% from the custom code and excellent agreement for track lengths with R 2  >  0.99. Experimental data agree within 9% for relative light output. The new model also simplifies surface definition, as no complex input parameters are needed. The LUT Davis model makes optical simulations for nuclear imaging detectors much more precise, especially for studies with rough crystal surfaces. It will be available in GATE V8.0.

Remote Internet access to advanced analytical facilities: a new approach with Web-based services.

PubMed

Sherry, N; Qin, J; Fuller, M Suominen; Xie, Y; Mola, O; Bauer, M; McIntyre, N S; Maxwell, D; Liu, D; Matias, E; Armstrong, C

2012-09-04

Over the past decade, the increasing availability of the World Wide Web has held out the possibility that the efficiency of scientific measurements could be enhanced in cases where experiments were being conducted at distant facilities. Examples of early successes have included X-ray diffraction (XRD) experimental measurements of protein crystal structures at synchrotrons and access to scanning electron microscopy (SEM) and NMR facilities by users from institutions that do not possess such advanced capabilities. Experimental control, visual contact, and receipt of results has used some form of X forwarding and/or VNC (virtual network computing) software that transfers the screen image of a server at the experimental site to that of the users' home site. A more recent development is a web services platform called Science Studio that provides teams of scientists with secure links to experiments at one or more advanced research facilities. The software provides a widely distributed team with a set of controls and screens to operate, observe, and record essential parts of the experiment. As well, Science Studio provides high speed network access to computing resources to process the large data sets that are often involved in complex experiments. The simple web browser and the rapid transfer of experimental data to a processing site allow efficient use of the facility and assist decision making during the acquisition of the experimental results. The software provides users with a comprehensive overview and record of all parts of the experimental process. A prototype network is described involving X-ray beamlines at two different synchrotrons and an SEM facility. An online parallel processing facility has been developed that analyzes the data in near-real time using stream processing. Science Studio and can be expanded to include many other analytical applications, providing teams of users with rapid access to processed results along with the means for detailed discussion of their significance.

Determinants of access to experimental antiretroviral drugs in an Italian cohort of patients with HIV: a multilevel analysis.

PubMed

Girardi, Enrico; Scognamiglio, Paola; Angeletti, Claudio; Gori, Andrea; Buonfrate, Dora; Arlotti, Massimo; Mazzarello, Giovanni; Castagna, Antonella; Andreoni, Massimo; d'Arminio Monforte, Antonella; Antinori, Andrea; Ippolito, Giuseppe

2012-02-15

Identification of the determinants of access to investigational drugs is important to promote equity and scientific validity in clinical research. We aimed to analyze factors associated with the use of experimental antiretrovirals in Italy. We studied participants in the Italian Cohort of Antiretroviral-Naive Patients (ICoNA). All patients 18 years or older who had started cART (≥ 3 drugs including at least two NRTI) after their enrolment and during 1997-2007 were included in this analysis. We performed a random effect logistic regression analysis to take into account clustering observations within clinical units. The outcome variable was the use of an experimental antiretroviral, defined as an antiretroviral started before commercial availability, in any episode of therapy initiation/change. Use of an experimental antiretroviral obtained through a clinical trial or an expanded access program (EAP) was also analyzed separately. A total of 9,441 episodes of therapy initiation/change were analyzed in 3,752 patients. 392 episodes (360 patients) involved an experimental antiretroviral. In multivariable analysis, factors associated with the overall use of experimental antiretrovirals were: number of experienced drugs (≥ 8 drugs versus "naive": adjusted odds ratio [AOR] = 3.71) or failed antiretrovirals(3-4 drugs and ≥ 5 drugs versus 0-2 drugs: AOR = 1.42 and 2.38 respectively); calendar year (AOR = 0.80 per year) and plasma HIV-RNA copies/ml at therapy change (≥ 4 log versus < 2 log: AOR = 1.55). The probability of taking an experimental antiretroviral through a trial was significantly lower for patients suffering from liver co-morbidity(AOR = 0.65) and for those who experienced 3-4 drugs (vs naive) (AOR = 0.55), while it increased for multi-treated patients(AOR = 2.60). The probability to start an experimental antiretroviral trough an EAP progressively increased with the increasing number of experienced and of failed drugs and also increased for patients with liver co-morbidity (AOR = 1.44; p = 0.053). and for male homosexuals (vs heterosexuals: AOR = 1.67). Variability of the random effect associated to clinical units was statistically significant (p < 0.001) although no association was found with specific characteristics of clinical unit examined. Among patients with HIV infection in Italy, access to experimental antiretrovirals seems to be influenced mainly by exhaustion of treatment options and not by socio-demographic factors.

Scaling of transient storage parameter estimates with increasing reach length in a mountain headwater stream

Treesearch

M. Briggs; M. N. Gooseff; B. McGlynn

2006-01-01

We performed two conservative tracer injections in a mountain stream in order to access the relationship between storage parameters on the short subreach scale to the longer reach which they comprise.

Dark matter and color octets beyond the Standard Model

NASA Astrophysics Data System (ADS)

Krnjaic, Gordan Z.

Although the Standard Model (SM) of particles and interactions has survived forty years of experimental tests, it does not provide a complete description of nature. From cosmological and astrophysical observations, it is now clear that the majority of matter in the universe is not baryonic and interacts very weakly (if at all) via non-gravitational forces. The SM does not provide a dark matter candidate, so new particles must be introduced. Furthermore, recent Tevatron results suggest that SM predictions for benchmark collider observables are in tension with experimental observations. In this thesis, we will propose extensions to the SM that address each of these issues. Although there is abundant indirect evidence for the existence of dark matter, terrestrial efforts to observe its interactions have yielded conflicting results. We address this situation with a simple model of dark matter that features hydrogen-like bound states that scatter off SM nuclei by undergoing inelastic hyperfine transitions. We explore the available parameter space that results from demanding that DM self-interactions satisfy experimental bounds and ameliorate the tension between positive and null signals at the DAMA and CDMS experiments respectively. However, this simple model does not explain the cosmological abundance of dark matter and also encounters a Landau pole at a low energy scale. We, therefore, extend the field content and gauge group of the dark sector to resolve these issues with a renormalizable UV completion. We also explore the galactic dynamics of unbound dark matter and find that "dark ions" settle into a diffuse isothermal halo that differs from that of the bound states. This suppresses the local dark-ion density and expands the model's viable parameter space. We also consider the > 3σ excess in W plus dijet events recently observed at the Tevatron collider. We show that decays of a color-octet, electroweak-triplet scalar particle ("octo-triplet") can yield the requisite final state to explain the data. We also find that octotriplets can induce mixing in the B - B¯ system and may give rise to additional CP violation. The model makes concrete predictions for several final states accessible at the LHC, so it can promptly be discovered or falsified. Finally we address the anomalous top forward-backward asymmetry observed the Tevatron. We find that a spin-1 color octet particle with flavor blind axial interactions can explain this anomaly if the mass is in the 50 - 90 GeV range. We explore the multitude of experimental constrains in this mass window and present the viable parameter space as a function of the axigluon mass and coupling constant.

Assessing the welfare of laboratory mice in their home environment using animal-based measures--a benchmarking tool.

PubMed

Spangenberg, Elin M F; Keeling, Linda J

2016-02-01

Welfare problems in laboratory mice can be a consequence of an ongoing experiment, or a characteristic of a particular genetic line, but in some cases, such as breeding animals, they are most likely to be a result of the design and management of the home cage. Assessment of the home cage environment is commonly performed using resource-based measures, like access to nesting material. However, animal-based measures (related to the health status and behaviour of the animals) can be used to assess the current welfare of animals regardless of the inputs applied (i.e. the resources or management). The aim of this study was to design a protocol for assessing the welfare of laboratory mice using only animal-based measures. The protocol, to be used as a benchmarking tool, assesses mouse welfare in the home cage and does not contain parameters related to experimental situations. It is based on parameters corresponding to the 12 welfare criteria established by the Welfare Quality® project. Selection of animal-based measures was performed by scanning existing published, web-based and informal protocols, and by choosing parameters that matched these criteria, were feasible in practice and, if possible, were already validated indicators of mouse welfare. The parameters should identify possible animal welfare problems and enable assessment directly in an animal room during cage cleaning procedures, without the need for extra equipment. Thermal comfort behaviours and positive emotional states are areas where more research is needed to find valid, reliable and feasible animal-based measures. © The Author(s) 2015.

An Architecture for Enabling Migration of Tactical Networks to Future Flexible Ad Hoc WBWF

DTIC Science & Technology

2010-09-01

Requirements Several multiple access schemes TDMA OFDMA SC-OFDMA, FH- CDMA , DS - CDMA , hybrid access schemes, transitions between them Dynamic...parameters algorithms depend on the multiple access scheme If DS - CDMA : handling of macro-diversity (linked to cooperative routing) TDMA and/of OFDMA...Transport format Ciphering @MAC/RLC level : SCM Physical layer (PHY) : signal processing (mod, FEC, etc) CDMA : macro-diversity CDMA , OFDMA

Theoretical and experimental investigation of the nonlinear dynamical trends of passively mode-locked quantum dot lasers

NASA Astrophysics Data System (ADS)

Raghunathan, Ravi

In recent years, passively mode-locked quantum dot lasers have shown great promise as compact, efficient and reliable pulsed sources of light for a range of precision and high performance applications, such as high bit-rate optical communications, diverse waveform generation, metrology, and clock distribution in high-performance computing (HPC) processors. For such applications, stable optical pulses with short picosecond pulse durations and multi-gigahertz repetition rates are required. In addition, a low pulse-to-pulse timing jitter is also necessary to prevent errors arising from the ambiguity between neighboring pulses. In order to optimize pulse quality in terms of optical characteristics such as pulse shape and pulse train behavior, as well as RF characteristics such as phase noise and timing jitter, understanding the nonlinear output dynamics of such devices is of critical importance, not only to get a sense of the regimes of operation where device output might be stable or unstable, but also to gain insight into the parameters that influence the output characteristics the most, and how they can be accessed and exploited to optimize design and performance for next generation applications. In this dissertation, theoretical and experimental studies have been combined to investigate the dynamical trends of two-section passively mode-locked quantum dot lasers. On the theoretical side, a novel numerical modeling scheme is presented as a powerful and versatile framework to study the nonlinear dynamics specific to a device, with device-specific parameters extracted over a range of operating conditions. The practical utility of this scheme is then demonstrated, first, in an analytical capability to interpret and explain dynamical trends observed in experiment, and subsequently, as a predictive tool to guide experiment to operate in a desired dynamical regime. Modeling results are compared to experimental findings where possible. Finally, optical feedback from an external reflector is experimentally studied as an additional control mechanism over the output dynamics of the device, and shown to enable invaluable insight into the behavior of the RF and optical spectra of the output. Together, the theoretical and experimental findings of this dissertation are shown to offer a systematic approach to understand, control and exploit the dynamical trends of passively mode-locked two-section quantum dot lasers.

Experimental analysis and simulation calculation of the inductances of loosely coupled transformer

NASA Astrophysics Data System (ADS)

Kerui, Chen; Yang, Han; Yan, Zhang; Nannan, Gao; Ying, Pei; Hongbo, Li; Pei, Li; Liangfeng, Guo

2017-11-01

The experimental design of iron-core wireless power transmission system is designed, and an experimental model of loosely coupled transformer is built. Measuring the air gap on both sides of the transformer 15mm inductor under the parameters. The feasibility and feasibility of using the finite element method to calculate the coil inductance parameters of the loosely coupled transformer are analyzed. The system was modeled by ANSYS, and the magnetic field was calculated by finite element method, and the inductance parameters were calculated. The finite element method is used to calculate the inductive parameters of the loosely coupled transformer, and the basis for the accurate compensation of the capacitance of the wireless power transmission system is established.

A measuring stick for other minds. Comment on 'Seeing mental states: An experimental strategy for measuring the observability of other minds' by Cristina Becchio et al.

NASA Astrophysics Data System (ADS)

Zillekens, Imme Christina; Schilbach, Leonhard

2018-03-01

In their compelling article 'Seeing mental states: An experimental strategy for measuring the observability of other minds' Becchio et al. [1] tackle a long-standing and controversial issue, namely the perennial question of whether we can access or even quite literally see other minds. Much of the relevant interdisciplinary literature is built on the premise that one's access to others' minds is indirect and inferential in nature [e.g. [4,5

Article processing charges, funding, and open access publishing at Journal of Experimental & Clinical Assisted Reproduction.

PubMed

Sills, Eric Scott; Vincent, Tina Thibault; Palermo, Gianpiero D

2005-01-13

Journal of Experimental & Clinical Assisted Reproduction is an Open Access, online, electronic journal published by BioMed Central with full contents available to the scientific and medical community free of charge to all readers. Authors maintain the copyright to their own work, a policy facilitating dissemination of data to the widest possible audience without requiring permission from the publisher. This Open Access publishing model is subsidized by authors (or their institutions/funding agencies) in the form of a single pound330 article processing charge (APC), due at the time of manuscript acceptance for publication. Payment of the APC is not a condition for formal peer review and does not apply to articles rejected after review. Additionally, this fee is waived for authors whose institutions are BioMed Central members or where genuine financial hardship exists. Considering ordinary publication fees related to page charges and reprints, the APC at Journal of Experimental & Clinical Assisted Reproduction is comparable to costs associated with publishing in some traditional print journals, and is less expensive than many. Implementation of the APC within this Open Access framework is envisioned as a modern research-friendly policy that supports networking among investigators, brings new research into reach rapidly, and empowers authors with greater control over their own scholarly publications.

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

Abdel-Khalek, S., E-mail: sayedquantum@yahoo.co.uk; The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, Miramare-Trieste; Berrada, K.

The dynamics of a superconducting (SC) qubit interacting with a field under decoherence with and without time-dependent coupling effect is analyzed. Quantum features like the collapse–revivals for the dynamics of population inversion, sudden birth and sudden death of entanglement, and statistical properties are investigated under the phase damping effect. Analytic results for certain parametric conditions are obtained. We analyze the influence of decoherence on the negativity and Wehrl entropy for different values of the physical parameters. We also explore an interesting relation between the SC-field entanglement and Wehrl entropy behavior during the time evolution. We show that the amount ofmore » SC-field entanglement can be enhanced as the field tends to be more classical. The studied model of SC-field system with the time-dependent coupling has high practical importance due to their experimental accessibility which may open new perspectives in different tasks of quantum formation processing.« less

Hidden in the light: Magnetically induced afterglow from trapped chameleon fields

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

Gies, Holger; Mota, David F.; Shaw, Douglas J.

2008-01-15

We propose an afterglow phenomenon as a unique trace of chameleon fields in optical experiments. The vacuum interaction of a laser pulse with a magnetic field can lead to a production and subsequent trapping of chameleons in the vacuum chamber, owing to their mass dependence on the ambient matter density. Magnetically induced reconversion of the trapped chameleons into photons creates an afterglow over macroscopic timescales that can conveniently be searched for by current optical experiments. We show that the chameleon parameter range accessible to available laboratory technology is comparable to scales familiar from astrophysical stellar energy-loss arguments. We analyze quantitativelymore » the afterglow properties for various experimental scenarios and discuss the role of potential background and systematic effects. We conclude that afterglow searches represent an ideal tool to aim at the production and detection of cosmologically relevant scalar fields in the laboratory.« less

Design and VNA-measurement of coplanar waveguide (CPW) on benzocyclobutene (BCB) at THz frequencies

NASA Astrophysics Data System (ADS)

Cao, Lei; Grimault-Jacquin, Anne-Sophie; Zerounian, Nicolas; Aniel, Frédéric

2014-03-01

The low permittivity and the low loss tangent of the benzocyclobutene polymer (BCB) offers to coplanar waveguides (CPW) a low dispersive propagation properties at THz frequency. These transmission lines have been designed, modeled with a three dimensional (3D) solver of Maxwell equations based on finite element method (FEM) from 20 to 1000 GHz at various characteristic impedances (Zc). Their dispersion and losses (radiation, conduction and dielectric) have been investigated separately versus the waveguide size, the nature of the substrate (dielectric or semiconductor) to optimize the THz signal propagation. Monomode CPW on BCB numerically designed for various Zc were realized and measured with vector network analyzer (VNA). S-parameters of CPW are de-embedded by optimization of the accesses' model. A good agreement is found between experimental and numerical results with low attenuation constants of 2.7 dB/mm and 3.5 dB/mm at 400 GHz and 500 GHz, respectively.

New method to evaluate the 7Li(p, n)7Be reaction near threshold

NASA Astrophysics Data System (ADS)

Herrera, María S.; Moreno, Gustavo A.; Kreiner, Andrés J.

2015-04-01

In this work a complete description of the 7Li(p, n)7Be reaction near threshold is given using center-of-mass and relative coordinates. It is shown that this standard approach, not used before in this context, leads to a simple mathematical representation which gives easy access to all relevant quantities in the reaction and allows a precise numerical implementation. It also allows in a simple way to include proton beam-energy spread affects. The method, implemented as a C++ code, was validated both with numerical and experimental data finding a good agreement. This tool is also used here to analyze scattered published measurements such as (p, n) cross sections, differential and total neutron yields for thick targets. Using these data we derive a consistent set of parameters to evaluate neutron production near threshold. Sensitivity of the results to data uncertainty and the possibility of incorporating new measurements are also discussed.

Performance of highly connected photonic switching lossless metro-access optical networks

NASA Astrophysics Data System (ADS)

Martins, Indayara Bertoldi; Martins, Yara; Barbosa, Felipe Rudge

2018-03-01

The present work analyzes the performance of photonic switching networks, optical packet switching (OPS) and optical burst switching (OBS), in mesh topology of different sizes and configurations. The "lossless" photonic switching node is based on a semiconductor optical amplifier, demonstrated and validated with experimental results on optical power gain, noise figure, and spectral range. The network performance was evaluated through computer simulations based on parameters such as average number of hops, optical packet loss fraction, and optical transport delay (Am). The combination of these elements leads to a consistent account of performance, in terms of network traffic and packet delivery for OPS and OBS metropolitan networks. Results show that a combination of highly connected mesh topologies having an ingress e-buffer present high efficiency and throughput, with very low packet loss and low latency, ensuring fast data delivery to the final receiver.

Boundary migration in a 3D deformed microstructure inside an opaque sample

DOE PAGES

Zhang, Y. B.; Budai, J. D.; Tischler, J. Z.; ...

2017-06-30

How boundaries surrounding recrystallization grains migrate through the 3D network of dislocation boundaries in deformed crystalline materials is unknown and critical for the resulting recrystallized crystalline materials. Furthermore, by using X-ray Laue diffraction microscopy, we show for the first time the migration pattern of a typical recrystallization boundary through a well-characterized deformation matrix. The data provide a unique possibility to investigate effects of both boundary misorientation and plane normal on the migration, information which cannot be accessed with any other techniques. Our results show that neither of these two parameters can explain the observed migration behavior. Instead we suggest thatmore » the subdivision of the deformed microstructure ahead of the boundary plays the dominant role. Our experimental observations challenge the assumptions of existing recrystallization theories, and set the stage for determination of mobilities of recrystallization boundaries.« less

Rapid generation of Mott insulators from arrays of noncondensed atoms

NASA Astrophysics Data System (ADS)

Sturm, M. R.; Schlosser, M.; Birkl, G.; Walser, R.

2018-06-01

We theoretically analyze a scheme for a fast adiabatic transfer of cold atoms from the atomic limit of isolated traps to a Mott insulator close to the superfluid phase. This gives access to the Bose-Hubbard physics without the need of a prior Bose-Einstein condensate. The initial state can be prepared by combining the deterministic assembly of atomic arrays with resolved Raman-sideband cooling. In the subsequent transfer the trap depth is reduced significantly. We derive conditions for the adiabaticity of this process and calculate optimal adiabatic ramp shapes. Using available experimental parameters, we estimate the impact of heating due to photon scattering and compute the fidelity of the transfer scheme. Finally, we discuss the particle number scaling behavior of the method for preparing low-entropy states. Our findings demonstrate the feasibility of the proposed scheme with state-of-the-art technology.

Contribution to the application of two-colour imaging to diesel combustion

NASA Astrophysics Data System (ADS)

Payri, F.; Pastor, J. V.; García, J. M.; Pastor, J. M.

2007-08-01

The two-colour method (2C) is a well-known methodology for the estimation of flame temperature and the soot-related KL factor. A 2C imaging system has been built with a single charge-coupled device (CCD) camera for visualization of the diesel flame in a single-cylinder 2-stroke engine with optical accesses. The work presented here focuses on methodological aspects. In that sense, the influence of calibration uncertainties on the measured temperature and KL factor has been analysed. Besides, a theoretical study is presented that tries to link the true flame temperature and soot distributions with those derived from the 2C images. Finally, an experimental study has been carried out in order to show the influence of injection pressure, air density and temperature on the 2C-derived parameters. Comparison with the expected results has shown the limitations of this methodology for diesel flame analysis.

Torque measurement at the single-molecule level.

PubMed

Forth, Scott; Sheinin, Maxim Y; Inman, James; Wang, Michelle D

2013-01-01

Methods for exerting and measuring forces on single molecules have revolutionized the study of the physics of biology. However, it is often the case that biological processes involve rotation or torque generation, and these parameters have been more difficult to access experimentally. Recent advances in the single-molecule field have led to the development of techniques that add the capability of torque measurement. By combining force, displacement, torque, and rotational data, a more comprehensive description of the mechanics of a biomolecule can be achieved. In this review, we highlight a number of biological processes for which torque plays a key mechanical role. We describe the various techniques that have been developed to directly probe the torque experienced by a single molecule, and detail a variety of measurements made to date using these new technologies. We conclude by discussing a number of open questions and propose systems of study that would be well suited for analysis with torsional measurement techniques.

Nonreciprocal dispersion of spin waves in ferromagnetic thin films covered with a finite-conductivity metal

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

Mruczkiewicz, M.; Krawczyk, M.

2014-03-21

We study the effect of one-side metallization of a uniform ferromagnetic thin film on its spin-wave dispersion relation in the Damon–Eshbach geometry. Due to the finite conductivity of the metallic cover layer on the ferromagnetic film, the spin-wave dispersion relation may be nonreciprocal only in a limited wave-vector range. We provide an approximate analytical solution for the spin-wave frequency, discuss its validity, and compare it with numerical results. The dispersion is analyzed systematically by varying the parameters of the ferromagnetic film, the metal cover layer and the value of the external magnetic field. The conclusions drawn from this analysis allowmore » us to define a structure based on a 30 nm thick CoFeB film with an experimentally accessible nonreciprocal dispersion relation in a relatively wide wave-vector range.« less

Features and selection of vascular access devices.

PubMed

Sansivero, Gail Egan

2010-05-01

To review venous anatomy and physiology, discuss assessment parameters before vascular access device (VAD) placement, and review VAD options. Journal articles, personal experience. A number of VAD options are available in clinical practice. Access planning should include comprehensive assessment, with attention to patient participation in the planning and selection process. Careful consideration should be given to long-term access needs and preservation of access sites. Oncology nurses are uniquely suited to perform a key role in VAD planning and placement. With knowledge of infusion therapy, anatomy and physiology, device options, and community resources, nurses can be key leaders in preserving vascular access and improving the safety and comfort of infusion therapy. Copyright 2010 Elsevier Inc. All rights reserved.

Remote Access to Earth Science Data by Content, Space and Time

NASA Technical Reports Server (NTRS)

Dobinson, E.; Raskin, G.

1998-01-01

This demo presents the combination on an http-based client/server application that facilitates internet access to Earth science data coupled with a Java applet GUI that allows the user to graphically select data based on spatial and temporal coverage plots and scientific parameters.

A pH-dependent conformational ensemble mediates proton transport through the influenza A/M2 protein†

PubMed Central

Polishchuk, Alexei L.; Lear, James D.; Ma, Chunlong; Lamb, Robert A.; Pinto, Lawrence H.; DeGrado, William F.

2010-01-01

The influenza A M2 protein exhibits inwardly rectifying, pH-activated proton transport that saturates at low pH. A comparison of high-resolution structures of the transmembrane domain at high and low pH suggests that pH-dependent conformational changes may facilitate proton conduction by alternately changing the accessibility of the N-terminal and C-terminal regions of the channel as a proton transits through the transmembrane domain. Here, we show that M2 functionally reconstituted in liposomes populates at least three different conformational states over a physiologically relevant pH range, with transition midpoints that are consistent with previously reported His37 pKas. We then develop and test two similar, quantitative mechanistic models of proton transport, where protonation shifts the equilibrium between structural states having different proton affinities and solvent accessibilities. The models account well for a collection of experimental data sets over a wide range of pHs and voltages and require only a small number of adjustable parameters to accurately describe the data. While the kinetic models do not require any specific conformation for the protein, they nevertheless are consistent with a large body of structural information based on high-resolution NMR and crystallographic structures, optical spectroscopy, and MD calculations. PMID:20968306

RatLab: an easy to use tool for place code simulations

PubMed Central

Schönfeld, Fabian; Wiskott, Laurenz

2013-01-01

In this paper we present the RatLab toolkit, a software framework designed to set up and simulate a wide range of studies targeting the encoding of space in rats. It provides open access to our modeling approach to establish place and head direction cells within unknown environments and it offers a set of parameters to allow for the easy construction of a variety of enclosures for a virtual rat as well as controlling its movement pattern over the course of experiments. Once a spatial code is formed RatLab can be used to modify aspects of the enclosure or movement pattern and plot the effect of such modifications on the spatial representation, i.e., place and head direction cell activity. The simulation is based on a hierarchical Slow Feature Analysis (SFA) network that has been shown before to establish a spatial encoding of new environments using visual input data only. RatLab encapsulates such a network, generates the visual training data, and performs all sampling automatically—with each of these stages being further configurable by the user. RatLab was written with the intention to make our SFA model more accessible to the community and to that end features a range of elements to allow for experimentation with the model without the need for specific programming skills. PMID:23908627

Real-Time Optical Monitoring of Flow Kinetics and Gas Phase Reactions Under High-Pressure OMCVD Conditions

NASA Technical Reports Server (NTRS)

Dietz, N.; McCall, S.; Bachmann, K. J.

2001-01-01

This contribution addresses the real-time optical characterization of gas flow and gas phase reactions as they play a crucial role for chemical vapor phase depositions utilizing elevated and high pressure chemical vapor deposition (HPCVD) conditions. The objectives of these experiments are to validate on the basis of results on real-time optical diagnostics process models simulation codes, and provide input parameter sets needed for analysis and control of chemical vapor deposition at elevated pressures. Access to microgravity is required to retain high pressure conditions of laminar flow, which is essential for successful acquisition and interpretation of the optical data. In this contribution, we describe the design and construction of the HPCVD system, which include access ports for various optical methods of real-time process monitoring and to analyze the initial stages of heteroepitaxy and steady-state growth in the different pressure ranges. To analyze the onset of turbulence, provisions are made for implementation of experimental methods for in-situ characterization of the nature of flow. This knowledge will be the basis for the design definition of experiments under microgravity, where gas flow conditions, gas phase and surface chemistry, might be analyzed by remote controlled real-time diagnostics tools, developed in this research project.

Real-Time Station Grouping under Dynamic Traffic for IEEE 802.11ah

PubMed Central

Tian, Le; Latré, Steven

2017-01-01

IEEE 802.11ah, marketed as Wi-Fi HaLow, extends Wi-Fi to the sub-1 GHz spectrum. Through a number of physical layer (PHY) and media access control (MAC) optimizations, it aims to bring greatly increased range, energy-efficiency, and scalability. This makes 802.11ah the perfect candidate for providing connectivity to Internet of Things (IoT) devices. One of these new features, referred to as the Restricted Access Window (RAW), focuses on improving scalability in highly dense deployments. RAW divides stations into groups and reduces contention and collisions by only allowing channel access to one group at a time. However, the standard does not dictate how to determine the optimal RAW grouping parameters. The optimal parameters depend on the current network conditions, and it has been shown that incorrect configuration severely impacts throughput, latency and energy efficiency. In this paper, we propose a traffic-adaptive RAW optimization algorithm (TAROA) to adapt the RAW parameters in real time based on the current traffic conditions, optimized for sensor networks in which each sensor transmits packets with a certain (predictable) frequency and may change the transmission frequency over time. The TAROA algorithm is executed at each target beacon transmission time (TBTT), and it first estimates the packet transmission interval of each station only based on packet transmission information obtained by access point (AP) during the last beacon interval. Then, TAROA determines the RAW parameters and assigns stations to RAW slots based on this estimated transmission frequency. The simulation results show that, compared to enhanced distributed channel access/distributed coordination function (EDCA/DCF), the TAROA algorithm can highly improve the performance of IEEE 802.11ah dense networks in terms of throughput, especially when hidden nodes exist, although it does not always achieve better latency performance. This paper contributes with a practical approach to optimizing RAW grouping under dynamic traffic in real time, which is a major leap towards applying RAW mechanism in real-life IoT networks. PMID:28677617

Real-Time Station Grouping under Dynamic Traffic for IEEE 802.11ah.

PubMed

Tian, Le; Khorov, Evgeny; Latré, Steven; Famaey, Jeroen

2017-07-04

IEEE 802.11ah, marketed as Wi-Fi HaLow, extends Wi-Fi to the sub-1 GHz spectrum. Through a number of physical layer (PHY) and media access control (MAC) optimizations, it aims to bring greatly increased range, energy-efficiency, and scalability. This makes 802.11ah the perfect candidate for providing connectivity to Internet of Things (IoT) devices. One of these new features, referred to as the Restricted Access Window (RAW), focuses on improving scalability in highly dense deployments. RAW divides stations into groups and reduces contention and collisions by only allowing channel access to one group at a time. However, the standard does not dictate how to determine the optimal RAW grouping parameters. The optimal parameters depend on the current network conditions, and it has been shown that incorrect configuration severely impacts throughput, latency and energy efficiency. In this paper, we propose a traffic-adaptive RAW optimization algorithm (TAROA) to adapt the RAW parameters in real time based on the current traffic conditions, optimized for sensor networks in which each sensor transmits packets with a certain (predictable) frequency and may change the transmission frequency over time. The TAROA algorithm is executed at each target beacon transmission time (TBTT), and it first estimates the packet transmission interval of each station only based on packet transmission information obtained by access point (AP) during the last beacon interval. Then, TAROA determines the RAW parameters and assigns stations to RAW slots based on this estimated transmission frequency. The simulation results show that, compared to enhanced distributed channel access/distributed coordination function (EDCA/DCF), the TAROA algorithm can highly improve the performance of IEEE 802.11ah dense networks in terms of throughput, especially when hidden nodes exist, although it does not always achieve better latency performance. This paper contributes with a practical approach to optimizing RAW grouping under dynamic traffic in real time, which is a major leap towards applying RAW mechanism in real-life IoT networks.

Power port contrast medium flushing and trapping: impact of temperature, an in vitro experimental study.

PubMed

Guiffant, Gérard; Durussel, Jean Jacques; Flaud, Patrice; Royon, Laurent; Marcy, Pierre Yves; Merckx, Jacques

2013-01-01

The use of totally implantable venous access devices (TIVADs) certified as "high pressure resistant" or "power port" has begun to spread worldwide as a safe procedure for power contrast injection. Owing to the thermo-rheological properties of the contrast media, the primary aim of this work is to present an in vitro experimental impact study concerning the impact of the temperature level on flushing efficiency after contrast medium injection. Moreover, we report experimental data that confirms the role of needle bevel orientation. The secondary aim is to answer the following questions: Is there significant device contrast medium trapping after contrast medium injection? Is saline flushing efficient? And, finally, is it safe to inject contrast medium through an indwelled port catheter? The experimental results show that in addition to hydrodynamics, temperature is a key parameter for the efficiency of device flushing after contrast medium injection. It appears that this is the case when the cavity is incompletely rinsed after three calibrated flushing volumes of 10 mL saline solution, even by using the Huber needle bevel opposite to the port exit. This leads to a potentially important trapped volume of contrast medium in the port, and consequently to the possibility of subsequent salt precipitates and long term trisubstituted benzene nuclei delivery that might impair the solute properties, which may be further injected via the power port later on. We thus suggest, in TIVADS patients, the use of a temporary supplementary intravenous line rather than the port to perform contrast medium injections in daily radiology routine practice.

Power port contrast medium flushing and trapping: impact of temperature, an in vitro experimental study

PubMed Central

Guiffant, Gérard; Durussel, Jean Jacques; Flaud, Patrice; Royon, Laurent; Marcy, Pierre Yves; Merckx, Jacques

2013-01-01

Purpose The use of totally implantable venous access devices (TIVADs) certified as “high pressure resistant” or “power port” has begun to spread worldwide as a safe procedure for power contrast injection. Owing to the thermo-rheological properties of the contrast media, the primary aim of this work is to present an in vitro experimental impact study concerning the impact of the temperature level on flushing efficiency after contrast medium injection. Moreover, we report experimental data that confirms the role of needle bevel orientation. The secondary aim is to answer the following questions: Is there significant device contrast medium trapping after contrast medium injection? Is saline flushing efficient? And, finally, is it safe to inject contrast medium through an indwelled port catheter? Results The experimental results show that in addition to hydrodynamics, temperature is a key parameter for the efficiency of device flushing after contrast medium injection. It appears that this is the case when the cavity is incompletely rinsed after three calibrated flushing volumes of 10 mL saline solution, even by using the Huber needle bevel opposite to the port exit. This leads to a potentially important trapped volume of contrast medium in the port, and consequently to the possibility of subsequent salt precipitates and long term trisubstituted benzene nuclei delivery that might impair the solute properties, which may be further injected via the power port later on. Conclusion We thus suggest, in TIVADS patients, the use of a temporary supplementary intravenous line rather than the port to perform contrast medium injections in daily radiology routine practice. PMID:24043959

Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting

PubMed Central

2016-01-01

Molecular dynamics simulations depend critically on the accuracy of the underlying force fields in properly representing biomolecules. Hence, it is crucial to validate the force-field parameter sets in this respect. In the context of the GROMOS force field, this is usually achieved by comparing simulation data to experimental observables for small molecules. In this study, we develop new amino acid backbone dihedral angle potential energy parameters based on the widely used 54A7 parameter set by matching to experimental J values and secondary structure propensity scales. In order to find the most appropriate backbone parameters, close to 100 000 different combinations of parameters have been screened. However, since the sheer number of combinations considered prohibits actual molecular dynamics simulations for each of them, we instead predicted the values for every combination using Hamiltonian reweighting. While the original 54A7 parameter set fails to reproduce the experimental data, we are able to provide parameters that match significantly better. However, to ensure applicability in the context of larger peptides and full proteins, further studies have to be undertaken. PMID:27559757

Work-Facilitating Information Visualization Techniques for Complex Wastewater Systems

NASA Astrophysics Data System (ADS)

Ebert, Achim; Einsfeld, Katja

The design and the operation of urban drainage systems and wastewater treatment plants (WWTP) have become increasingly complex. This complexity is due to increased requirements concerning process technology, technical, environmental, economical, and occupational safety aspects. The plant operator has access not only to some timeworn filers and measured parameters but also to numerous on-line and off-line parameters that characterize the current state of the plant in detail. Moreover, expert databases and specific support pages of plant manufactures are accessible through the World Wide Web. Thus, the operator is overwhelmed with predominantly unstructured data.

NEMAR plotting computer program

NASA Technical Reports Server (NTRS)

Myler, T. R.

1981-01-01

A FORTRAN coded computer program which generates CalComp plots of trajectory parameters is examined. The trajectory parameters are calculated and placed on a data file by the Near Earth Mission Analysis Routine computer program. The plot program accesses the data file and generates the plots as defined by inputs to the plot program. Program theory, user instructions, output definitions, subroutine descriptions and detailed FORTRAN coding information are included. Although this plot program utilizes a random access data file, a data file of the same type and formatted in 102 numbers per record could be generated by any computer program and used by this plot program.

Parameterization of an interfacial force field for accurate representation of peptide adsorption free energy on high-density polyethylene

PubMed Central

Abramyan, Tigran M.; Snyder, James A.; Yancey, Jeremy A.; Thyparambil, Aby A.; Wei, Yang; Stuart, Steven J.; Latour, Robert A.

2015-01-01

Interfacial force field (IFF) parameters for use with the CHARMM force field have been developed for interactions between peptides and high-density polyethylene (HDPE). Parameterization of the IFF was performed to achieve agreement between experimental and calculated adsorption free energies of small TGTG–X–GTGT host–guest peptides (T = threonine, G = glycine, and X = variable amino-acid residue) on HDPE, with ±0.5 kcal/mol agreement. This IFF parameter set consists of tuned nonbonded parameters (i.e., partial charges and Lennard–Jones parameters) for use with an in-house-modified CHARMM molecular dynamic program that enables the use of an independent set of force field parameters to control molecular behavior at a solid–liquid interface. The R correlation coefficient between the simulated and experimental peptide adsorption free energies increased from 0.00 for the standard CHARMM force field parameters to 0.88 for the tuned IFF parameters. Subsequent studies are planned to apply the tuned IFF parameter set for the simulation of protein adsorption behavior on an HDPE surface for comparison with experimental values of adsorbed protein orientation and conformation. PMID:25818122

Characterizing Computer Access Using a One-Channel EEG Wireless Sensor

PubMed Central

Guerrero-Cubero, Jaime; Gómez-González, Isabel M.; Merino-Monge, Manuel; Silva-Silva, Juan I.

2017-01-01

This work studies the feasibility of using mental attention to access a computer. Brain activity was measured with an electrode placed at the Fp1 position and the reference on the left ear; seven normally developed people and three subjects with cerebral palsy (CP) took part in the experimentation. They were asked to keep their attention high and low for as long as possible during several trials. We recorded attention levels and power bands conveyed by the sensor, but only the first was used for feedback purposes. All of the information was statistically analyzed to find the most significant parameters and a classifier based on linear discriminant analysis (LDA) was also set up. In addition, 60% of the participants were potential users of this technology with an accuracy of over 70%. Including power bands in the classifier did not improve the accuracy in discriminating between the two attentional states. For most people, the best results were obtained by using only the attention indicator in classification. Tiredness was higher in the group with disabilities (2.7 in a scale of 3) than in the other (1.5 in the same scale); and modulating the attention to access a communication board requires that it does not contain many pictograms (between 4 and 7) on screen and has a scanning period of a relatively high tscan≈ 10 s. The information transfer rate (ITR) is similar to the one obtained by other brain computer interfaces (BCI), like those based on sensorimotor rhythms (SMR) or slow cortical potentials (SCP), and makes it suitable as an eye-gaze independent BCI. PMID:28661425

Characterizing Computer Access Using a One-Channel EEG Wireless Sensor.

PubMed

Molina-Cantero, Alberto J; Guerrero-Cubero, Jaime; Gómez-González, Isabel M; Merino-Monge, Manuel; Silva-Silva, Juan I

2017-06-29

This work studies the feasibility of using mental attention to access a computer. Brain activity was measured with an electrode placed at the Fp1 position and the reference on the left ear; seven normally developed people and three subjects with cerebral palsy (CP) took part in the experimentation. They were asked to keep their attention high and low for as long as possible during several trials. We recorded attention levels and power bands conveyed by the sensor, but only the first was used for feedback purposes. All of the information was statistically analyzed to find the most significant parameters and a classifier based on linear discriminant analysis (LDA) was also set up. In addition, 60% of the participants were potential users of this technology with an accuracy of over 70%. Including power bands in the classifier did not improve the accuracy in discriminating between the two attentional states. For most people, the best results were obtained by using only the attention indicator in classification. Tiredness was higher in the group with disabilities (2.7 in a scale of 3) than in the other (1.5 in the same scale); and modulating the attention to access a communication board requires that it does not contain many pictograms (between 4 and 7) on screen and has a scanning period of a relatively high t s c a n ≈ 10 s. The information transfer rate (ITR) is similar to the one obtained by other brain computer interfaces (BCI), like those based on sensorimotor rhythms (SMR) or slow cortical potentials (SCP), and makes it suitable as an eye-gaze independent BCI.

Optically-gated Non-latched High Gain Power Device

DTIC Science & Technology

2008-11-21

parameters such as power conversion efficiency, dv/dt and di/dt stress on PSD and electromagnetic noise emission spectrum, which depend directly on the...4. EXPERIMENTAL STUDIES ON OTPT AND OPTICAL INTENSITY MODULATION OF OTPT PARAMETERS 33 4.1 Optical source, driver, and fiber details 33 4.2...off dynamics characterizations 36 4.5. Optical intensity modulation of OTPT parameters 37 5. EXPERIMENTAL STUDIES ON HYBRID OTPT-PSD AND OPTICAL

Dual Extended Kalman Filter for the Identification of Time-Varying Human Manual Control Behavior

NASA Technical Reports Server (NTRS)

Popovici, Alexandru; Zaal, Peter M. T.; Pool, Daan M.

2017-01-01

A Dual Extended Kalman Filter was implemented for the identification of time-varying human manual control behavior. Two filters that run concurrently were used, a state filter that estimates the equalization dynamics, and a parameter filter that estimates the neuromuscular parameters and time delay. Time-varying parameters were modeled as a random walk. The filter successfully estimated time-varying human control behavior in both simulated and experimental data. Simple guidelines are proposed for the tuning of the process and measurement covariance matrices and the initial parameter estimates. The tuning was performed on simulation data, and when applied on experimental data, only an increase in measurement process noise power was required in order for the filter to converge and estimate all parameters. A sensitivity analysis to initial parameter estimates showed that the filter is more sensitive to poor initial choices of neuromuscular parameters than equalization parameters, and bad choices for initial parameters can result in divergence, slow convergence, or parameter estimates that do not have a real physical interpretation. The promising results when applied to experimental data, together with its simple tuning and low dimension of the state-space, make the use of the Dual Extended Kalman Filter a viable option for identifying time-varying human control parameters in manual tracking tasks, which could be used in real-time human state monitoring and adaptive human-vehicle haptic interfaces.

Adaptive timing of detachment in a tick parasitizing hole-nesting birds.

PubMed

White, J; Heylen, D J A; Matthysen, E

2012-02-01

In non-permanent parasites with low intrinsic mobility such as ticks, dispersal is highly dependent on host movements as well as the timing of separation from the hosts. Optimal detachment behaviour is all the more crucial in nidicolous ticks as the risk of detaching in non-suitable habitat is high. In this study, we experimentally investigated the detachment behaviour of Ixodes arboricola, a nidicolous tick that primarily infests birds roosting in tree-holes. We infested great tits with I. arboricola larvae or nymphs, and submitted the birds to 2 experimental treatments, a control treatment in which birds had normal access to nest boxes and an experimental treatment, in which the birds were prevented access to their nest boxes for varying lengths of time. In the control group, most ticks detached within 5 days, whereas in the experimental group, ticks remained on the bird for as long as the bird was prevented access (up to 14 days). This prolonged attachment caused a decrease in survival and engorgement weight in nymphs, but not in larvae. The capacity of I. arboricola larvae to extend the duration of attachment in non-suitable environments with no apparent costs, may be an adaptation to unpredictable use of cavities by roosting hosts during winter, and at the same time may facilitate dispersal of the larval instars.

From microjoules to megajoules and kilobars to gigabars: Probing matter at extreme states of deformation

NASA Astrophysics Data System (ADS)

Remington, Bruce A.; Rudd, Robert E.; Wark, Justin S.

2015-09-01

Over the past 3 decades, there has been an exponential increase in work done in the newly emerging field of matter at extreme states of deformation and compression. This accelerating progress is due to the confluence of new experimental facilities, experimental techniques, theory, and simulations. Regimes of science hitherto thought out of reach in terrestrial settings are now being accessed routinely. High-pressure macroscopic states of matter are being experimentally studied on high-power lasers and pulsed power facilities, and next-generation light sources are probing the quantum response of matter at the atomic level. Combined, this gives experimental access to the properties and dynamics of matter from femtoseconds to microseconds in time scale and from kilobars to gigabars in pressure. There are a multitude of new regimes of science that are now accessible in laboratory settings. Examples include planetary formation dynamics, asteroid and meteor impact dynamics, space hardware response to hypervelocity dust and debris impacts, nuclear reactor component response to prolonged exposure to radiation damage, advanced research into light weight armor, capsule dynamics in inertial confinement fusion research, and the basic high energy density properties of matter. We review highlights and advances in this rapidly developing area of science and research.

The multistate impact parameter method for molecular charge exchange in nitrogen

NASA Technical Reports Server (NTRS)

Ioup, J. W.

1980-01-01

The multistate impact parameter method is applied to the calculation of total cross sections for low energy change transfer between nitrogen ions and nitrogen molecules. Experimental data showing the relationships between total cross section and ion energy for various pressures and electron ionization energies were obtained. Calculated and experimental cross section values from the work are compared with the experimental and theoretical results of other investigators.

Experimental equipment for measuring of rotary air motors parameters

NASA Astrophysics Data System (ADS)

Dvořák, Lukáš; Fojtášek, Kamil; Řeháček, Vojtěch

In the article the construction of an experimental device for measuring the parameters of small rotary air motors is described. Further a measurement methodology and measured data processing are described. At the end of the article characteristics of the chosen air motor are presented.

Nanomaterial datasets to advance tomography in scanning transmission electron microscopy

DOE PAGES

Levin, Barnaby D. A.; Padgett, Elliot; Chen, Chien-Chun; ...

2016-06-07

Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co 2 P nanocrystal, platinum nanoparticles on a carbonmore » nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data.« less

A remote laboratory for USRP-based software defined radio

NASA Astrophysics Data System (ADS)

Gandhinagar Ekanthappa, Rudresh; Escobar, Rodrigo; Matevossian, Achot; Akopian, David

2014-02-01

Electrical and computer engineering graduates need practical working skills with real-world electronic devices, which are addressed to some extent by hands-on laboratories. Deployment capacity of hands-on laboratories is typically constrained due to insufficient equipment availability, facility shortages, and lack of human resources for in-class support and maintenance. At the same time, at many sites, existing experimental systems are usually underutilized due to class scheduling bottlenecks. Nowadays, online education gains popularity and remote laboratories have been suggested to broaden access to experimentation resources. Remote laboratories resolve many problems as various costs can be shared, and student access to instrumentation is facilitated in terms of access time and locations. Labs are converted to homeworks that can be done without physical presence in laboratories. Even though they are not providing full sense of hands-on experimentation, remote labs are a viable alternatives for underserved educational sites. This paper studies remote modality of USRP-based radio-communication labs offered by National Instruments (NI). The labs are offered to graduate and undergraduate students and tentative assessments support feasibility of remote deployments.

Nanomaterial datasets to advance tomography in scanning transmission electron microscopy.

PubMed

Levin, Barnaby D A; Padgett, Elliot; Chen, Chien-Chun; Scott, M C; Xu, Rui; Theis, Wolfgang; Jiang, Yi; Yang, Yongsoo; Ophus, Colin; Zhang, Haitao; Ha, Don-Hyung; Wang, Deli; Yu, Yingchao; Abruña, Hector D; Robinson, Richard D; Ercius, Peter; Kourkoutis, Lena F; Miao, Jianwei; Muller, David A; Hovden, Robert

2016-06-07

Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co2P nanocrystal, platinum nanoparticles on a carbon nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data.

Nanomaterial datasets to advance tomography in scanning transmission electron microscopy

PubMed Central

Levin, Barnaby D.A.; Padgett, Elliot; Chen, Chien-Chun; Scott, M.C.; Xu, Rui; Theis, Wolfgang; Jiang, Yi; Yang, Yongsoo; Ophus, Colin; Zhang, Haitao; Ha, Don-Hyung; Wang, Deli; Yu, Yingchao; Abruña, Hector D.; Robinson, Richard D.; Ercius, Peter; Kourkoutis, Lena F.; Miao, Jianwei; Muller, David A.; Hovden, Robert

2016-01-01

Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co2P nanocrystal, platinum nanoparticles on a carbon nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data. PMID:27272459

On the biosorption, by brown seaweed, Lobophora variegata, of Ni(II) from aqueous solutions: equilibrium and thermodynamic studies.

PubMed

Basha, Shaik; Jaiswar, Santlal; Jha, Bhavanath

2010-09-01

The biosorption equilibrium isotherms of Ni(II) onto marine brown algae Lobophora variegata, which was chemically-modified by CaCl(2) were studied and modeled. To predict the biosorption isotherms and to determine the characteristic parameters for process design, twenty-three one-, two-, three-, four- and five-parameter isotherm models were applied to experimental data. The interaction among biosorbed molecules is attractive and biosorption is carried out on energetically different sites and is an endothermic process. The five-parameter Fritz-Schluender model gives the most accurate fit with high regression coefficient, R (2) (0.9911-0.9975) and F-ratio (118.03-179.96), and low standard error, SE (0.0902-0.0.1556) and the residual or sum of square error, SSE (0.0012-0.1789) values to all experimental data in comparison to other models. The biosorption isotherm models fitted the experimental data in the order: Fritz-Schluender (five-parameter) > Freundlich (two-parameter) > Langmuir (two-parameter) > Khan (three-parameter) > Fritz-Schluender (four-parameter). The thermodynamic parameters such as DeltaG (0), DeltaH (0) and DeltaS (0) have been determined, which indicates the sorption of Ni(II) onto L. variegata was spontaneous and endothermic in nature.

Exploring Experimental Design: An Excel-Based Simulation Using Steller Sea Lion Behavior

ERIC Educational Resources Information Center

Ryan, Wendy L.; St. Iago-McRae, Ezry

2016-01-01

Experimentation is the foundation of science and an important process for students to understand and experience. However, it can be difficult to teach some aspects of experimentation within the time and resource constraints of an academic semester. Interactive models can be a useful tool in bridging this gap. This freely accessible simulation…

Evaluating Expected Costs and Benefits of Granting Access to New Treatments on the Basis of Progression-Free Survival in Non-Small-Cell Lung Cancer.

PubMed

Lakdawalla, Darius N; Chou, Jacquelyn W; Linthicum, Mark T; MacEwan, Joanna P; Zhang, Jie; Goldman, Dana P

2015-05-01

Surrogate end points may be used as proxy for more robust clinical end points. One prominent example is the use of progression-free survival (PFS) as a surrogate for overall survival (OS) in trials for oncologic treatments. Decisions based on surrogate end points may expedite regulatory approval but may not accurately reflect drug efficacy. Payers and clinicians must balance the potential benefits of earlier treatment access based on surrogate end points against the risks of clinical uncertainty. To present a framework for evaluating the expected net benefit or cost of providing early access to new treatments on the basis of evidence of PFS benefits before OS results are available, using non-small-cell lung cancer (NSCLC) as an example. A probabilistic decision model was used to estimate expected incremental social value of the decision to grant access to a new treatment on the basis of PFS evidence. The model analyzed a hypothetical population of patients with NSCLC who could be treated during the period between PFS and OS evidence publication. Estimates for delay in publication of OS evidence following publication of PFS evidence, expected OS benefit given PFS benefit, incremental cost of new treatment, and other parameters were drawn from the literature on treatment of NSCLC. Incremental social value of early access for each additional patient per month (in 2014 US dollars). For "medium-value" model parameters, early reimbursement of drugs with any PFS benefit yields an incremental social cost of more than $170,000 per newly treated patient per month. In contrast, granting early access on the basis of PFS benefit between 1 and 3.5 months produces more than $73,000 in incremental social value. Across the full range of model parameter values, granting access for drugs with PFS benefit between 3 and 3.5 months is robustly beneficial, generating incremental social value ranging from $38,000 to more than $1 million per newly treated patient per month, whereas access for all drugs with any PFS benefit is usually not beneficial. The value of providing access to new treatments on the basis of surrogate end points, and PFS in particular, likely varies considerably. Payers and clinicians should carefully consider how to use PFS data in balancing potential benefits against costs in each particular disease.

Determination of JWL Parameters for Non-Ideal Explosive

NASA Astrophysics Data System (ADS)

Hamashima, H.; Kato, Y.; Itoh, S.

2004-07-01

JWL equation of state is widely used in numerical simulation of detonation phenomena. JWL parameters are determined by cylinder test. Detonation characteristics of non-ideal explosive depend strongly on confinement, and JWL parameters determined by cylinder test do not represent the state of detonation products in many applications. We developed a method to determine JWL parameters from the underwater explosion test. JWL parameters were determined through a method of characteristics applied to the configuration of the underwater shock waves of cylindrical explosives. The numerical results obtained using JWL parameters determined by the underwater explosion test and those obtained using JWL parameters determined by cylinder test were compared with experimental results for typical non-ideal explosive; emulsion explosive. Good agreement was confirmed between the results obtained using JWL parameters determined by the underwater explosion test and experimental results.

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach

PubMed Central

2014-01-01

Background Accurate estimation of parameters of biochemical models is required to characterize the dynamics of molecular processes. This problem is intimately linked to identifying the most informative experiments for accomplishing such tasks. While significant progress has been made, effective experimental strategies for parameter identification and for distinguishing among alternative network topologies remain unclear. We approached these questions in an unbiased manner using a unique community-based approach in the context of the DREAM initiative (Dialogue for Reverse Engineering Assessment of Methods). We created an in silico test framework under which participants could probe a network with hidden parameters by requesting a range of experimental assays; results of these experiments were simulated according to a model of network dynamics only partially revealed to participants. Results We proposed two challenges; in the first, participants were given the topology and underlying biochemical structure of a 9-gene regulatory network and were asked to determine its parameter values. In the second challenge, participants were given an incomplete topology with 11 genes and asked to find three missing links in the model. In both challenges, a budget was provided to buy experimental data generated in silico with the model and mimicking the features of different common experimental techniques, such as microarrays and fluorescence microscopy. Data could be bought at any stage, allowing participants to implement an iterative loop of experiments and computation. Conclusions A total of 19 teams participated in this competition. The results suggest that the combination of state-of-the-art parameter estimation and a varied set of experimental methods using a few datasets, mostly fluorescence imaging data, can accurately determine parameters of biochemical models of gene regulation. However, the task is considerably more difficult if the gene network topology is not completely defined, as in challenge 2. Importantly, we found that aggregating independent parameter predictions and network topology across submissions creates a solution that can be better than the one from the best-performing submission. PMID:24507381

Experimental Investigation and Optimization of Response Variables in WEDM of Inconel - 718

NASA Astrophysics Data System (ADS)

Karidkar, S. S.; Dabade, U. A.

2016-02-01

Effective utilisation of Wire Electrical Discharge Machining (WEDM) technology is challenge for modern manufacturing industries. Day by day new materials with high strengths and capabilities are being developed to fulfil the customers need. Inconel - 718 is similar kind of material which is extensively used in aerospace applications, such as gas turbine, rocket motors, and spacecraft as well as in nuclear reactors and pumps etc. This paper deals with the experimental investigation of optimal machining parameters in WEDM for Surface Roughness, Kerf Width and Dimensional Deviation using DoE such as Taguchi methodology, L9 orthogonal array. By keeping peak current constant at 70 A, the effect of other process parameters on above response variables were analysed. Obtained experimental results were statistically analysed using Minitab-16 software. Analysis of Variance (ANOVA) shows pulse on time as the most influential parameter followed by wire tension whereas spark gap set voltage is observed to be non-influencing parameter. Multi-objective optimization technique, Grey Relational Analysis (GRA), shows optimal machining parameters such as pulse on time 108 Machine unit, spark gap set voltage 50 V and wire tension 12 gm for optimal response variables considered for the experimental analysis.

Analysis of DNA replication associated chromatin decondensation: in vivo assay for understanding chromatin remodeling mechanisms of selected proteins.

PubMed

Borysov, Sergiy; Bryant, Victoria L; Alexandrow, Mark G

2015-01-01

Of critical importance to many of the events underlying transcriptional control of gene expression are modifications to core and linker histones that regulate the accessibility of trans-acting factors to the DNA substrate within the context of chromatin. Likewise, control over the initiation of DNA replication, as well as the ability of the replication machinery to proceed during elongation through the multiple levels of chromatin condensation that are likely to be encountered, is known to involve the creation of chromatin accessibility. In the latter case, chromatin access will likely need to be a transient event so as to prevent total genomic unraveling of the chromatin that would be deleterious to cells. While there are many molecular and biochemical approaches in use to study histone changes and their relationship to transcription and chromatin accessibility, few techniques exist that allow a molecular dissection of the events underlying DNA replication control as it pertains to chromatin changes and accessibility. Here, we outline a novel experimental strategy for addressing the ability of specific proteins to induce large-scale chromatin unfolding (decondensation) in vivo upon site-specific targeting to an engineered locus. Our laboratory has used this powerful system in novel ways to directly address the ability of DNA replication proteins to create chromatin accessibility, and have incorporated modifications to the basic approach that allow for a molecular genetic analysis of the mechanisms and associated factors involved in causing chromatin decondensation by a protein of interest. Alternative approaches involving co-expression of other proteins (competitors or stimulators), concurrent drug treatments, and analysis of co-localizing histone modifications are also addressed, all of which are illustrative of the utility of this experimental system for extending basic findings to physiologically relevant mechanisms. Although used by our group to analyze mechanisms underlying DNA replication associated chromatin accessibility, this unique and powerful experimental system has the propensity to be a valuable tool for understanding chromatin remodeling mechanisms orchestrated by other cellular processes such as DNA repair, recombination, mitotic chromosome condensation, or other chromosome dynamics involving chromatin alterations and accessibility.

Experimental tests of coherence and entanglement conservation under unitary evolutions

NASA Astrophysics Data System (ADS)

Černoch, Antonín; Bartkiewicz, Karol; Lemr, Karel; Soubusta, Jan

2018-04-01

We experimentally demonstrate the migration of coherence between composite quantum systems and their subsystems. The quantum systems are implemented using polarization states of photons in two experimental setups. The first setup is based on a linear optical controlled-phase quantum gate and the second scheme utilizes effects of nonlinear optics. Our experiment allows one to verify the relation between correlations of the subsystems and the coherence of the composite system, which was given in terms of a conservation law for maximal accessible coherence by Svozilík et al. [J. Svozilík et al., Phys. Rev. Lett. 115, 220501 (2015), 10.1103/PhysRevLett.115.220501]. We observe that the maximal accessible coherence is conserved for the implemented class of global evolutions of the composite system.

A Time of Flight Fast Neutron Imaging System Design Study

NASA Astrophysics Data System (ADS)

Canion, Bonnie; Glenn, Andrew; Sheets, Steven; Wurtz, Ron; Nakae, Les; Hausladen, Paul; McConchie, Seth; Blackston, Matthew; Fabris, Lorenzo; Newby, Jason

2017-09-01

LLNL and ORNL are designing an active/passive fast neutron imaging system that is flexible to non-ideal detector positioning. It is often not possible to move an inspection object in fieldable imager applications such as safeguards, arms control treaty verification, and emergency response. Particularly, we are interested in scenarios which inspectors do not have access to all sides of an inspection object, due to interfering objects or walls. This paper will present the results of a simulation-based design parameter study, that will determine the optimum system design parameters for a fieldable system to perform time-of-flight based imaging analysis. The imaging analysis is based on the use of an associated particle imaging deuterium-tritium (API DT) neutron generator to get the time-of-flight of radiation induced within an inspection object. This design study will investigate the optimum design parameters for such a system (e.g. detector size, ideal placement, etc.), as well as the upper and lower feasible design parameters that the system can expect to provide results within a reasonable amount of time (e.g. minimum/maximum detector efficiency, detector standoff, etc.). Ideally the final prototype from this project will be capable of using full-access techniques, such as transmission imaging, when the measurement circumstances allow, but with the additional capability of producing results at reduced accessibility.

Experimental Parameters Affecting Stripping of Rare Earth Elements from Loaded Sorptive Media in Simulated Geothermal Brines

DOE Data Explorer

Dean Stull

2016-05-24

Experimental results from several studies exploring the impact of pH and acid volume on the stripping of rare earth elements (REEs) loaded onto ligand-based media via an active column. The REEs in this experiment were loaded onto the media through exposure to a simulated geothermal brine with known mineral concentrations. The data include the experiment results, rare earth element concentrations, and the experimental parameters varied.

Collaborative Recommendation of E-Learning Resources: An Experimental Investigation

ERIC Educational Resources Information Center

Manouselis, N.; Vuorikari, R.; Van Assche, F.

2010-01-01

Repositories with educational resources can support the formation of online learning communities by providing a platform for collaboration. Users (e.g. teachers, tutors and learners) access repositories, search for interesting resources to access and use, and in many cases, also exchange experiences and opinions. A particular class of online…

Nonadiabatic dynamics of electron transfer in solution: Explicit and implicit solvent treatments that include multiple relaxation time scales

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

Schwerdtfeger, Christine A.; Soudackov, Alexander V.; Hammes-Schiffer, Sharon, E-mail: shs3@illinois.edu

2014-01-21

The development of efficient theoretical methods for describing electron transfer (ET) reactions in condensed phases is important for a variety of chemical and biological applications. Previously, dynamical dielectric continuum theory was used to derive Langevin equations for a single collective solvent coordinate describing ET in a polar solvent. In this theory, the parameters are directly related to the physical properties of the system and can be determined from experimental data or explicit molecular dynamics simulations. Herein, we combine these Langevin equations with surface hopping nonadiabatic dynamics methods to calculate the rate constants for thermal ET reactions in polar solvents formore » a wide range of electronic couplings and reaction free energies. Comparison of explicit and implicit solvent calculations illustrates that the mapping from explicit to implicit solvent models is valid even for solvents exhibiting complex relaxation behavior with multiple relaxation time scales and a short-time inertial response. The rate constants calculated for implicit solvent models with a single solvent relaxation time scale corresponding to water, acetonitrile, and methanol agree well with analytical theories in the Golden rule and solvent-controlled regimes, as well as in the intermediate regime. The implicit solvent models with two relaxation time scales are in qualitative agreement with the analytical theories but quantitatively overestimate the rate constants compared to these theories. Analysis of these simulations elucidates the importance of multiple relaxation time scales and the inertial component of the solvent response, as well as potential shortcomings of the analytical theories based on single time scale solvent relaxation models. This implicit solvent approach will enable the simulation of a wide range of ET reactions via the stochastic dynamics of a single collective solvent coordinate with parameters that are relevant to experimentally accessible systems.« less

Study of CO2 bubble dynamics in seawater from QICS field Experiment

NASA Astrophysics Data System (ADS)

Chen, B.; Dewar, M.; Sellami, N.; Stahl, H.; Blackford, J.

2011-12-01

One of the concerns of employing CCS at engineering scale is the risk of leakage of storage CO2 on the environment and especially on the marine life. QICS, a scientific research project was launched with an aim to study the effects of a potential leak from a CCS system on the UK marine environment [1]. The project involves the injection of CO2 from a shore-based lab into shallow marine sediments. One of the main objectives of the project is to generate experimental data to be compared with the developed physical models. The results of the models are vital for the biogeochemical and ecological models in order to predict the impact of a CO2 leak in a variety of situations. For the evaluation of the fate of the CO2 bubbles into the surrounding seawater, the physical model requires two key parameters to be used as input which are: (i) a correlation of the drag coefficient as function of the CO2 bubble Reynolds number and (ii) the CO2 bubble size distribution. By precisely measuring the CO2 bubble size and rising speed, these two parameters can be established. For this purpose, the dynamical characteristics of the rising CO2 bubbles in Scottish seawater were investigated experimentally within the QICS project. Observations of the CO2 bubbles plume rising freely in the in seawater column were captured by video survey using a ruler positioned at the leakage pockmark as dimension reference. This observation made it possible, for the first time, to discuss the dynamics of the CO2 bubbles released in seawater. [1] QICS, QICS: Quantifying and Monitoring Potential Ecosystem Impacts of Geological Carbon Storage. (Accessed 15.07.13), http://www.bgs.ac.uk/qics/home.html

Study of CO2 bubble dynamics in seawater from QICS field Experiment

NASA Astrophysics Data System (ADS)

Chen, B.; Dewar, M.; Sellami, N.; Stahl, H.; Blackford, J.

2013-12-01

One of the concerns of employing CCS at engineering scale is the risk of leakage of storage CO2 on the environment and especially on the marine life. QICS, a scientific research project was launched with an aim to study the effects of a potential leak from a CCS system on the UK marine environment [1]. The project involves the injection of CO2 from a shore-based lab into shallow marine sediments. One of the main objectives of the project is to generate experimental data to be compared with the developed physical models. The results of the models are vital for the biogeochemical and ecological models in order to predict the impact of a CO2 leak in a variety of situations. For the evaluation of the fate of the CO2 bubbles into the surrounding seawater, the physical model requires two key parameters to be used as input which are: (i) a correlation of the drag coefficient as function of the CO2 bubble Reynolds number and (ii) the CO2 bubble size distribution. By precisely measuring the CO2 bubble size and rising speed, these two parameters can be established. For this purpose, the dynamical characteristics of the rising CO2 bubbles in Scottish seawater were investigated experimentally within the QICS project. Observations of the CO2 bubbles plume rising freely in the in seawater column were captured by video survey using a ruler positioned at the leakage pockmark as dimension reference. This observation made it possible, for the first time, to discuss the dynamics of the CO2 bubbles released in seawater. [1] QICS, QICS: Quantifying and Monitoring Potential Ecosystem Impacts of Geological Carbon Storage. (Accessed 15.07.13), http://www.bgs.ac.uk/qics/home.html

Measurement-induced-nonlocality for Dirac particles in Garfinkle-Horowitz-Strominger dilation space-time

NASA Astrophysics Data System (ADS)

He, Juan; Xu, Shuai; Ye, Liu

2016-05-01

We investigate the quantum correlation via measurement-induced-nonlocality (MIN) for Dirac particles in Garfinkle-Horowitz-Strominger (GHS) dilation space-time. It is shown that the physical accessible quantum correlation decreases as the dilation parameter increases monotonically. Unlike the case of scalar fields, the physical accessible correlation is not zero when the Hawking temperature is infinite owing to the Pauli exclusion principle and the differences between Fermi-Dirac and Bose-Einstein statistics. Meanwhile, the boundary of MIN related to Bell-violation is derived, which indicates that MIN is more general than quantum nonlocality captured by the violation of Bell-inequality. As a by-product, a tenable quantitative relation about MIN redistribution is obtained whatever the dilation parameter is. In addition, it is worth emphasizing that the underlying reason why the physical accessible correlation and mutual information decrease is that they are redistributed to the physical inaccessible regions.

A statistical analysis of RNA folding algorithms through thermodynamic parameter perturbation.

PubMed

Layton, D M; Bundschuh, R

2005-01-01

Computational RNA secondary structure prediction is rather well established. However, such prediction algorithms always depend on a large number of experimentally measured parameters. Here, we study how sensitive structure prediction algorithms are to changes in these parameters. We found already that for changes corresponding to the actual experimental error to which these parameters have been determined, 30% of the structure are falsely predicted whereas the ground state structure is preserved under parameter perturbation in only 5% of all the cases. We establish that base-pairing probabilities calculated in a thermal ensemble are viable although not a perfect measure for the reliability of the prediction of individual structure elements. Here, a new measure of stability using parameter perturbation is proposed, and its limitations are discussed.

Calculation of Optical Parameters of Liquid Crystals

NASA Astrophysics Data System (ADS)

Kumar, A.

2007-12-01

Validation of a modified four-parameter model describing temperature effect on liquid crystal refractive indices is being reported in the present article. This model is based upon the Vuks equation. Experimental data of ordinary and extraordinary refractive indices for two liquid crystal samples MLC-9200-000 and MLC-6608 are used to validate the above-mentioned theoretical model. Using these experimental data, birefringence, order parameter, normalized polarizabilities, and the temperature gradient of refractive indices are determined. Two methods: directly using birefringence measurements and using Haller's extrapolation procedure are adopted for the determination of order parameter. Both approches of order parameter calculation are compared. The temperature dependences of all these parameters are discussed. A close agreement between theory and experiment is obtained.

Experimental Design for Parameter Estimation of Gene Regulatory Networks

PubMed Central

Timmer, Jens

2012-01-01

Systems biology aims for building quantitative models to address unresolved issues in molecular biology. In order to describe the behavior of biological cells adequately, gene regulatory networks (GRNs) are intensively investigated. As the validity of models built for GRNs depends crucially on the kinetic rates, various methods have been developed to estimate these parameters from experimental data. For this purpose, it is favorable to choose the experimental conditions yielding maximal information. However, existing experimental design principles often rely on unfulfilled mathematical assumptions or become computationally demanding with growing model complexity. To solve this problem, we combined advanced methods for parameter and uncertainty estimation with experimental design considerations. As a showcase, we optimized three simulated GRNs in one of the challenges from the Dialogue for Reverse Engineering Assessment and Methods (DREAM). This article presents our approach, which was awarded the best performing procedure at the DREAM6 Estimation of Model Parameters challenge. For fast and reliable parameter estimation, local deterministic optimization of the likelihood was applied. We analyzed identifiability and precision of the estimates by calculating the profile likelihood. Furthermore, the profiles provided a way to uncover a selection of most informative experiments, from which the optimal one was chosen using additional criteria at every step of the design process. In conclusion, we provide a strategy for optimal experimental design and show its successful application on three highly nonlinear dynamic models. Although presented in the context of the GRNs to be inferred for the DREAM6 challenge, the approach is generic and applicable to most types of quantitative models in systems biology and other disciplines. PMID:22815723

Comparison of different morphological parameters with duration of obstruction created experimentally in unilateral upper ureters: an animal model.

PubMed

Panda, Shasanka Shekhar; Bajpai, Minu; Mallick, Saumyaranjan; Sharma, Mehar C

2014-01-01

The objective of the following study is to determine and to compare the different morphological parameters with duration of obstruction created experimentally in unilateral upper ureters of rats. Unilateral upper ureteric obstruction was created in 60 adult Wistar rats that were reversed after predetermined intervals. Rats were sacrificed and ipsilateral kidneys were subjected for analysis of morphological parameters such as renal height, cranio-caudal diameter, antero-posterior diameter, lateral diameter, volume of the pelvis and average cortical thickness: Renal height. Renal height and cranio-caudal diameter of renal pelvis after ipsilateral upper ureteric obstruction started rising as early as 7 days of creating obstruction and were affected earlier than antero-posterior and lateral diameter and also were reversed earlier than other parameters after reversal of obstruction. Renal cortical thickness and volume of the pelvis were affected after prolonged obstruction (> 3 weeks) and were the late parameters to be reversed after reversal of obstruction. Cranio-caudal diameter and renal height were the early morphological parameters to be affected and reversed after reversal of obstruction in experimentally created ipsilateral upper ureteric obstruction.

Influence of spray nozzle shape upon atomization process

NASA Astrophysics Data System (ADS)

Beniuga, Marius; Mihai, Ioan

2016-12-01

The atomization process is affected by a number of operating parameters (pressure, viscosity, temperature, etc.) [1-6] and the adopted constructive solution. In this article are compared parameters of atomized liquid jet with two nozzles that have different lifespan, one being new and the other one out. The last statement shows that the second nozzle was monitored as time of operation on the one hand and on the other hand, two dimensional nozzles have been analyzed using laser profilometry. To compare the experimental parameters was carried an experimental stand to change the period and pulse width in injecting liquid through two nozzles. Atomized liquid jets were photographed and filmed quickly. Images obtained were analyzed using a Matlab code that allowed to determine a number of parameters that characterize an atomized jet. Knowing the conditions and operating parameters of atomized jet, will establish a new wastewater nozzle block of parameter values that can be implemented in controller that provides dosing of the liquid injected. Experimental measurements to observe the myriad forms of atomized droplets to a wide range of operating conditions, realized using the electronic control module.

Experimental design approach to the process parameter optimization for laser welding of martensitic stainless steels in a constrained overlap configuration

NASA Astrophysics Data System (ADS)

Khan, M. M. A.; Romoli, L.; Fiaschi, M.; Dini, G.; Sarri, F.

2011-02-01

This paper presents an experimental design approach to process parameter optimization for the laser welding of martensitic AISI 416 and AISI 440FSe stainless steels in a constrained overlap configuration in which outer shell was 0.55 mm thick. To determine the optimal laser-welding parameters, a set of mathematical models were developed relating welding parameters to each of the weld characteristics. These were validated both statistically and experimentally. The quality criteria set for the weld to determine optimal parameters were the minimization of weld width and the maximization of weld penetration depth, resistance length and shearing force. Laser power and welding speed in the range 855-930 W and 4.50-4.65 m/min, respectively, with a fiber diameter of 300 μm were identified as the optimal set of process parameters. However, the laser power and welding speed can be reduced to 800-840 W and increased to 4.75-5.37 m/min, respectively, to obtain stronger and better welds.

Experimental determination of solvent-water partition coefficients and Abraham parameters for munition constituents.

PubMed

Liang, Yuzhen; Kuo, Dave T F; Allen, Herbert E; Di Toro, Dominic M

2016-10-01

There is concern about the environmental fate and effects of munition constituents (MCs). Polyparameter linear free energy relationships (pp-LFERs) that employ Abraham solute parameters can aid in evaluating the risk of MCs to the environment. However, poor predictions using pp-LFERs and ABSOLV estimated Abraham solute parameters are found for some key physico-chemical properties. In this work, the Abraham solute parameters are determined using experimental partition coefficients in various solvent-water systems. The compounds investigated include hexahydro-1,3,5-trinitro-1,3,5-triazacyclohexane (RDX), octahydro-1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane (HMX), hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine (MNX), hexahydro-1,3,5-trinitroso-1,3,5-triazine (TNX), hexahydro-1,3-dinitroso-5- nitro-1,3,5-triazine (DNX), 2,4,6-trinitrotoluene (TNT), 1,3,5-trinitrobenzene (TNB), and 4-nitroanisole. The solvents in the solvent-water systems are hexane, dichloromethane, trichloromethane, octanol, and toluene. The only available reported solvent-water partition coefficients are for octanol-water for some of the investigated compounds and they are in good agreement with the experimental measurements from this study. Solvent-water partition coefficients fitted using experimentally derived solute parameters from this study have significantly smaller root mean square errors (RMSE = 0.38) than predictions using ABSOLV estimated solute parameters (RMSE = 3.56) for the investigated compounds. Additionally, the predictions for various physico-chemical properties using the experimentally derived solute parameters agree with available literature reported values with prediction errors within 0.79 log units except for water solubility of RDX and HMX with errors of 1.48 and 2.16 log units respectively. However, predictions using ABSOLV estimated solute parameters have larger prediction errors of up to 7.68 log units. This large discrepancy is probably due to the missing R2NNO2 and R2NNO2 functional groups in the ABSOLV fragment database. Copyright © 2016. Published by Elsevier Ltd.

Two Studies of Complex Nonlinear Systems: Engineered Granular Crystals and Coarse-Graining Optimization Problems

NASA Astrophysics Data System (ADS)

Pozharskiy, Dmitry

In recent years a nonlinear, acoustic metamaterial, named granular crystals, has gained prominence due to its high accessibility, both experimentally and computationally. The observation of a wide range of dynamical phenomena in the system, due to its inherent nonlinearities, has suggested its importance in many engineering applications related to wave propagation. In the first part of this dissertation, we explore the nonlinear dynamics of damped-driven granular crystals. In one case, we consider a highly nonlinear setting, also known as a sonic vacuum, and derive a nonlinear analogue of a linear spectrum, corresponding to resonant periodic propagation and antiresonances. Experimental studies confirm the computational findings and the assimilation of experimental data into a numerical model is demonstrated. In the second case, global bifurcations in a precompressed granular crystal are examined, and their involvement in the appearance of chaotic dynamics is demonstrated. Both results highlight the importance of exploring the nonlinear dynamics, to gain insight into how a granular crystal responds to different external excitations. In the second part, we borrow established ideas from coarse-graining of dynamical systems, and extend them to optimization problems. We combine manifold learning algorithms, such as Diffusion Maps, with stochastic optimization methods, such as Simulated Annealing, and show that we can retrieve an ensemble, of few, important parameters that should be explored in detail. This framework can lead to acceleration of convergence when dealing with complex, high-dimensional optimization, and could potentially be applied to design engineered granular crystals.

Gravitational-wave stochastic background from cosmic strings.

PubMed

Siemens, Xavier; Mandic, Vuk; Creighton, Jolien

2007-03-16

We consider the stochastic background of gravitational waves produced by a network of cosmic strings and assess their accessibility to current and planned gravitational wave detectors, as well as to big bang nucleosynthesis (BBN), cosmic microwave background (CMB), and pulsar timing constraints. We find that current data from interferometric gravitational wave detectors, such as Laser Interferometer Gravitational Wave Observatory (LIGO), are sensitive to areas of parameter space of cosmic string models complementary to those accessible to pulsar, BBN, and CMB bounds. Future more sensitive LIGO runs and interferometers such as Advanced LIGO and Laser Interferometer Space Antenna (LISA) will be able to explore substantial parts of the parameter space.

J-Plus Web Portal

NASA Astrophysics Data System (ADS)

Civera Lorenzo, Tamara

2017-10-01

Brief presentation about the J-PLUS EDR data access web portal (http://archive.cefca.es/catalogues/jplus-edr) where the different services available to retrieve images and catalogues data have been presented.J-PLUS Early Data Release (EDR) archive includes two types of data: images and dual and single catalogue data which include parameters measured from images. J-PLUS web portal offers catalogue data and images through several different online data access tools or services each suited to a particular need. The different services offered are: Coverage map Sky navigator Object visualization Image search Cone search Object list search Virtual observatory services: Simple Cone Search Simple Image Access Protocol Simple Spectral Access Protocol Table Access Protocol

Experimental validation of a new heterogeneous mechanical test design

NASA Astrophysics Data System (ADS)

Aquino, J.; Campos, A. Andrade; Souto, N.; Thuillier, S.

2018-05-01

Standard material parameters identification strategies generally use an extensive number of classical tests for collecting the required experimental data. However, a great effort has been made recently by the scientific and industrial communities to support this experimental database on heterogeneous tests. These tests can provide richer information on the material behavior allowing the identification of a more complete set of material parameters. This is a result of the recent development of full-field measurements techniques, like digital image correlation (DIC), that can capture the heterogeneous deformation fields on the specimen surface during the test. Recently, new specimen geometries were designed to enhance the richness of the strain field and capture supplementary strain states. The butterfly specimen is an example of these new geometries, designed through a numerical optimization procedure where an indicator capable of evaluating the heterogeneity and the richness of strain information. However, no experimental validation was yet performed. The aim of this work is to experimentally validate the heterogeneous butterfly mechanical test in the parameter identification framework. For this aim, DIC technique and a Finite Element Model Up-date inverse strategy are used together for the parameter identification of a DC04 steel, as well as the calculation of the indicator. The experimental tests are carried out in a universal testing machine with the ARAMIS measuring system to provide the strain states on the specimen surface. The identification strategy is accomplished with the data obtained from the experimental tests and the results are compared to a reference numerical solution.

Technical Note: Using experimentally determined proton spot scanning timing parameters to accurately model beam delivery time.

PubMed

Shen, Jiajian; Tryggestad, Erik; Younkin, James E; Keole, Sameer R; Furutani, Keith M; Kang, Yixiu; Herman, Michael G; Bues, Martin

2017-10-01

To accurately model the beam delivery time (BDT) for a synchrotron-based proton spot scanning system using experimentally determined beam parameters. A model to simulate the proton spot delivery sequences was constructed, and BDT was calculated by summing times for layer switch, spot switch, and spot delivery. Test plans were designed to isolate and quantify the relevant beam parameters in the operation cycle of the proton beam therapy delivery system. These parameters included the layer switch time, magnet preparation and verification time, average beam scanning speeds in x- and y-directions, proton spill rate, and maximum charge and maximum extraction time for each spill. The experimentally determined parameters, as well as the nominal values initially provided by the vendor, served as inputs to the model to predict BDTs for 602 clinical proton beam deliveries. The calculated BDTs (T BDT ) were compared with the BDTs recorded in the treatment delivery log files (T Log ): ∆t = T Log -T BDT . The experimentally determined average layer switch time for all 97 energies was 1.91 s (ranging from 1.9 to 2.0 s for beam energies from 71.3 to 228.8 MeV), average magnet preparation and verification time was 1.93 ms, the average scanning speeds were 5.9 m/s in x-direction and 19.3 m/s in y-direction, the proton spill rate was 8.7 MU/s, and the maximum proton charge available for one acceleration is 2.0 ± 0.4 nC. Some of the measured parameters differed from the nominal values provided by the vendor. The calculated BDTs using experimentally determined parameters matched the recorded BDTs of 602 beam deliveries (∆t = -0.49 ± 1.44 s), which were significantly more accurate than BDTs calculated using nominal timing parameters (∆t = -7.48 ± 6.97 s). An accurate model for BDT prediction was achieved by using the experimentally determined proton beam therapy delivery parameters, which may be useful in modeling the interplay effect and patient throughput. The model may provide guidance on how to effectively reduce BDT and may be used to identifying deteriorating machine performance. © 2017 American Association of Physicists in Medicine.

The momentum transfer of incompressible turbulent separated flow due to cavities with steps

NASA Technical Reports Server (NTRS)

White, R. E.; Norton, D. J.

1977-01-01

An experimental study was conducted using a plate test bed having a turbulent boundary layer to determine the momentum transfer to the faces of step/cavity combinations on the plate. Experimental data were obtained from configurations including an isolated configuration and an array of blocks in tile patterns. A momentum transfer correlation model of pressure forces on an isolated step/cavity was developed with experimental results to relate flow and geometry parameters. Results of the experiments reveal that isolated step/cavity excrecences do not have a unique and unifying parameter group due in part to cavity depth effects and in part to width parameter scale effects. Drag predictions for tile patterns by a kinetic pressure empirical method predict experimental results well. Trends were not, however, predicted by a method of variable roughness density phenomenology.

Resistance to the Whitefly, Aleurotrachelus socialis, in Wild Populations of Cassava, Manihot Tristis

PubMed Central

Carabalí, A.; Bellotti, A. C.; Montoya-Lerma, J.; Fregene, Martin

2010-01-01

The levels of resistance in the wild species of cassava, Manihot tristis Muell-Arg. (Malpighiales: Euphorbiaceae), to the whitefly, Aleurotrachelus socialis Bondar (Hemiptera: Alelyrodidae), the most important economic pest in cassava, Manihot esculenta Crantz (Malpighiales: Euphorbiaceae) crops in South America, were estimated under glasshouse conditions. The parameters of the life history of A. socialis were studied on TST-26 and TST-18 accessions of the wild parent and compared with the susceptible (CMC-40) and resistant (MEcu-72) cultivars. The average longevity on the wild accessions (TST-26, 4.1; TST-18, 4.6 days) and oviposition rates (TST-26, 2.0; TST-18, 1.6 eggs/female/2 days) of the A. socialis females were not significantly different from those of MEcu-72 (5.1 days and 3.4 eggs/female/2days). The longevity and oviposition rates on CMC-40 were highest (11 days and 8.6 eggs/female/2days). Analyses of the demographic parameters (Ro, rm; DT) showed a significant impact of the M. tristis accessions on the potential growth of A. socialis. The average survival time of adults that fed on TST-26, TST-18, and MEcu-72 were significantly different from those recorded on the susceptible genotype. Results from this study revealed important levels of resistance to the whitefly A. socialis on the TST-26 and TST-18 accessions due to the marked differences found for longevity and reproduction, which influenced and were consistent with the differences found in the net reproduction rate (Ro), intrinsic growth rate (rm) and population doubling time (DT). The combined effect of these parameters indicated that M. tristis accessions were inappropriate hosts for A. socialis. PMID:21062208

Experimental aspect of solid-state nuclear magnetic resonance studies of biomaterials such as bones.

PubMed

Singh, Chandan; Rai, Ratan Kumar; Sinha, Neeraj

2013-01-01

Solid-state nuclear magnetic resonance (SSNMR) spectroscopy is increasingly becoming a popular technique to probe micro-structural details of biomaterial such as bone with pico-meter resolution. Due to high-resolution structural details probed by SSNMR methods, handling of bone samples and experimental protocol are very crucial aspects of study. We present here first report of the effect of various experimental protocols and handling methods of bone samples on measured SSNMR parameters. Various popular SSNMR experiments were performed on intact cortical bone sample collected from fresh animal, immediately after removal from animal systems, and results were compared with bone samples preserved in different conditions. We find that the best experimental conditions for SSNMR parameters of bones correspond to preservation at -20 °C and in 70% ethanol solution. Various other SSNMR parameters were compared corresponding to different experimental conditions. Our study has helped in finding best experimental protocol for SSNMR studies of bone. This study will be of further help in the application of SSNMR studies on large bone disease related animal model systems for statistically significant results. © 2013 Elsevier Inc. All rights reserved.

Investigation on gas medium parameters for an ArF excimer laser through orthogonal experimental design

NASA Astrophysics Data System (ADS)

Song, Xingliang; Sha, Pengfei; Fan, Yuanyuan; Jiang, R.; Zhao, Jiangshan; Zhou, Yi; Yang, Junhong; Xiong, Guangliang; Wang, Yu

2018-02-01

Due to complex kinetics of formation and loss mechanisms, such as ion-ion recombination reaction, neutral species harpoon reaction, excited state quenching and photon absorption, as well as their interactions, the performance behavior of different laser gas medium parameters for excimer laser varies greatly. Therefore, the effects of gas composition and total gas pressure on excimer laser performance attract continual research studies. In this work, orthogonal experimental design (OED) is used to investigate quantitative and qualitative correlations between output laser energy characteristics and gas medium parameters for an ArF excimer laser with plano-plano optical resonator operation. Optimized output laser energy with good pulse to pulse stability can be obtained effectively by proper selection of the gas medium parameters, which makes the most of the ArF excimer laser device. Simple and efficient method for gas medium optimization is proposed and demonstrated experimentally, which provides a global and systematic solution. By detailed statistical analysis, the significance sequence of relevant parameter factors and the optimized composition for gas medium parameters are obtained. Compared with conventional route of varying single gas parameter factor sequentially, this paper presents a more comprehensive way of considering multivariables simultaneously, which seems promising in striking an appropriate balance among various complicated parameters for power scaling study of an excimer laser.

An Experimental Analysis of Another Privacy

ERIC Educational Resources Information Center

Okouchi, Hiroto

2006-01-01

The present article discusses how events outside a subject's skin and not accessible to another subject but to an experimenter may contribute to experimental analyses of private events. Of 16 undergraduates, 8, referred to as instructors, first learned conditional discriminations (i.e., B1C1, B2C2, B3C3, and B4C4) in a standard matching-to-sample…

Experimental Research on Selective Laser Melting AlSi10Mg Alloys: Process, Densification and Performance

NASA Astrophysics Data System (ADS)

Chen, Zhen; Wei, Zhengying; Wei, Pei; Chen, Shenggui; Lu, Bingheng; Du, Jun; Li, Junfeng; Zhang, Shuzhe

2017-12-01

In this work, a set of experiments was designed to investigate the effect of process parameters on the relative density of the AlSi10Mg parts manufactured by SLM. The influence of laser scan speed v, laser power P and hatch space H, which were considered as the dominant parameters, on the powder melting and densification behavior was also studied experimentally. In addition, the laser energy density was introduced to evaluate the combined effect of the above dominant parameters, so as to control the SLM process integrally. As a result, a high relative density (> 97%) was obtained by SLM at an optimized laser energy density of 3.5-5.5 J/mm2. Moreover, a parameter-densification map was established to visually select the optimum process parameters for the SLM-processed AlSi10Mg parts with elevated density and required mechanical properties. The results provide an important experimental guidance for obtaining AlSi10Mg components with full density and gradient functional porosity by SLM.

Rate-equation modelling and ensemble approach to extraction of parameters for viral infection-induced cell apoptosis and necrosis

NASA Astrophysics Data System (ADS)

Domanskyi, Sergii; Schilling, Joshua E.; Gorshkov, Vyacheslav; Libert, Sergiy; Privman, Vladimir

2016-09-01

We develop a theoretical approach that uses physiochemical kinetics modelling to describe cell population dynamics upon progression of viral infection in cell culture, which results in cell apoptosis (programmed cell death) and necrosis (direct cell death). Several model parameters necessary for computer simulation were determined by reviewing and analyzing available published experimental data. By comparing experimental data to computer modelling results, we identify the parameters that are the most sensitive to the measured system properties and allow for the best data fitting. Our model allows extraction of parameters from experimental data and also has predictive power. Using the model we describe interesting time-dependent quantities that were not directly measured in the experiment and identify correlations among the fitted parameter values. Numerical simulation of viral infection progression is done by a rate-equation approach resulting in a system of "stiff" equations, which are solved by using a novel variant of the stochastic ensemble modelling approach. The latter was originally developed for coupled chemical reactions.

Rate-equation modelling and ensemble approach to extraction of parameters for viral infection-induced cell apoptosis and necrosis

NASA Astrophysics Data System (ADS)

Domanskyi, Sergii; Schilling, Joshua; Gorshkov, Vyacheslav; Libert, Sergiy; Privman, Vladimir

We develop a theoretical approach that uses physiochemical kinetics modelling to describe cell population dynamics upon progression of viral infection in cell culture, which results in cell apoptosis (programmed cell death) and necrosis (direct cell death). Several model parameters necessary for computer simulation were determined by reviewing and analyzing available published experimental data. By comparing experimental data to computer modelling results, we identify the parameters that are the most sensitive to the measured system properties and allow for the best data fitting. Our model allows extraction of parameters from experimental data and also has predictive power. Using the model we describe interesting time-dependent quantities that were not directly measured in the experiment and identify correlations among the fitted parameter values. Numerical simulation of viral infection progression is done by a rate-equation approach resulting in a system of ``stiff'' equations, which are solved by using a novel variant of the stochastic ensemble modelling approach. The latter was originally developed for coupled chemical reactions.

Parameter space of experimental chaotic circuits with high-precision control parameters.

PubMed

de Sousa, Francisco F G; Rubinger, Rero M; Sartorelli, José C; Albuquerque, Holokx A; Baptista, Murilo S

2016-08-01

We report high-resolution measurements that experimentally confirm a spiral cascade structure and a scaling relationship of shrimps in the Chua's circuit. Circuits constructed using this component allow for a comprehensive characterization of the circuit behaviors through high resolution parameter spaces. To illustrate the power of our technological development for the creation and the study of chaotic circuits, we constructed a Chua circuit and study its high resolution parameter space. The reliability and stability of the designed component allowed us to obtain data for long periods of time (∼21 weeks), a data set from which an accurate estimation of Lyapunov exponents for the circuit characterization was possible. Moreover, this data, rigorously characterized by the Lyapunov exponents, allows us to reassure experimentally that the shrimps, stable islands embedded in a domain of chaos in the parameter spaces, can be observed in the laboratory. Finally, we confirm that their sizes decay exponentially with the period of the attractor, a result expected to be found in maps of the quadratic family.

An experimental and modeling study of isothermal charge/discharge behavior of commercial Ni-MH cells

NASA Astrophysics Data System (ADS)

Pan, Y. H.; Srinivasan, V.; Wang, C. Y.

In this study, a previously developed nickel-metal hydride (Ni-MH) battery model is applied in conjunction with experimental characterization. Important geometric parameters, including the active surface area and micro-diffusion length for both electrodes, are measured and incorporated in the model. The kinetic parameters of the oxygen evolution reaction are also characterized using constant potential experiments. Two separate equilibrium equations for the Ni electrode, one for charge and the other for discharge, are determined to provide a better description of the electrode hysteresis effect, and their use results in better agreement of simulation results with experimental data on both charge and discharge. The Ni electrode kinetic parameters are re-calibrated for the battery studied. The Ni-MH cell model coupled with the updated electrochemical properties is then used to simulate a wide range of experimental discharge and charge curves with satisfactory agreement. The experimentally validated model is used to predict and compare various charge algorithms so as to provide guidelines for application-specific optimization.

Three-dimensional (3D) evaluation of liquid distribution in shake flask using an optical fluorescence technique.

PubMed

Azizan, Amizon; Büchs, Jochen

2017-01-01

Biotechnological development in shake flask necessitates vital engineering parameters e.g. volumetric power input, mixing time, gas liquid mass transfer coefficient, hydromechanical stress and effective shear rate. Determination and optimization of these parameters through experiments are labor-intensive and time-consuming. Computational Fluid Dynamics (CFD) provides the ability to predict and validate these parameters in bioprocess engineering. This work provides ample experimental data which are easily accessible for future validations to represent the hydrodynamics of the fluid flow in the shake flask. A non-invasive measuring technique using an optical fluorescence method was developed for shake flasks containing a fluorescent solution with a waterlike viscosity at varying filling volume (V L  = 15 to 40 mL) and shaking frequency ( n  = 150 to 450 rpm) at a constant shaking diameter (d o  = 25 mm). The method detected the leading edge (LB) and tail of the rotating bulk liquid (TB) relative to the direction of the centrifugal acceleration at varying circumferential heights from the base of the shake flask. The determined LB and TB points were translated into three-dimensional (3D) circumferential liquid distribution plots. The maximum liquid height (H max ) of the bulk liquid increased with increasing filling volume and shaking frequency of the shaking flask, as expected. The toroidal shapes of LB and TB are clearly asymmetrical and the measured TB differed by the elongation of the liquid particularly towards the torus part of the shake flask. The 3D liquid distribution data collected at varying filling volume and shaking frequency, comprising of LB and TB values relative to the direction of the centrifugal acceleration are essential for validating future numerical solutions using CFD to predict vital engineering parameters in shake flask.

Combining 27Al Solid-State NMR and First-Principles Simulations To Explore Crystal Structure in Disordered Aluminum Oxynitride.

PubMed

Tu, Bingtian; Liu, Xin; Wang, Hao; Wang, Weimin; Zhai, Pengcheng; Fu, Zhengyi

2016-12-19

The nuclear magnetic resonance (NMR) technique gives insight into the local information in a crystal structure, while Rietveld refinement of powder X-ray diffraction (PXRD) sketches out the framework of a crystal lattice. In this work, first-principles calculations were combined with the solid-state NMR technique and Rietveld refinement to explore the crystal structure of a disordered aluminum oxynitride (γ-alon). The theoretical NMR parameters (chemical shift, δ iso , quadrupolar coupling constants, C Q , and asymmetry parameter, η) of Al 22.5 O 28.5 N 3.5 , predicted by the gauge-including projector augmented wave (GIPAW) algorithm, were used to facilitate the analytical investigation of the 27 Al magic-angle spinning (MAS) NMR spectra of the as-prepared sample, whose formula was confirmed to be Al 2.811 O 3.565 N 0.435 by quantitative analysis. The experimental δ iso , C Q , and η of 27 Al showed a small discrepancy compared with theoretical models. The ratio of aluminum located at the 8a to 16d sites was calculated to be 0.531 from the relative integration of peaks in the 27 Al NMR spectra. The occupancies of aluminum at the 8a and 16d positions were determined through NMR investigations to be 0.9755 and 0.9178, respectively, and were used in the Rietveld refinement to obtain the lattice parameter and anion parameter of Al 2.811 O 3.565 N 0.435 . The results from 27 Al NMR investigations and PXRD structural refinement complemented each other. This work provides a powerful and accessible strategy to precisely understand the crystal structure of novel oxynitride materials with multiple disorder.

Ultrasonic monitoring of yoghurt formation by using AT-cut quartz: lighting of casein micelles interactions process during the acidification.

PubMed

Ould-Ehssein, C; Serfaty, S; Griesmar, P; Le Huérou, J-Y; Caplain, E; Martinez, L; Wilkie-Chancellier, N; Gindre, M

2006-12-22

The behavior of weak gels during their formation singularly attracts attention of dairy products factories. In our study we investigate acidified pre-heated milk gels formation that are fairly often used to product yoghurts. The gel formation requires a tight control of the first step of micelles modification process and the kinetics reaction parameters. The most current rheological parameters used to achieve the monitoring are the storage G' and the loss G'' shear moduli and the gelation time. The study of these parameters is commonly performed at very low frequencies (1 Hz). Our technique uses a 6 MHz AT-cut quartz crystal immersed in an acidified milk solution kept at a constant temperature. This method is singularly effective to ensure a complete and a reliable follow-up of the viscoelastic parameters of casein gels. A suitable new model enables a complete follow-up of the micelles evolution from the viscoelastic properties. The experimental results of the G' and G'' moduli versus temperature and versus glucono-delta-lactone (GDL) added to milk are analyzed. In order to understand the micelles modifications, an analysis of the viscoelastic evolution try to explain the validity of the various models of micelles modification. In addition a new accurate kinetics characteristic time is proposed. This time corresponds to the moment for which the elastic effect of material becomes significant. From the kinetics study of casein gels at various temperatures, the Arrhenius relationship and a modified Flory-Stockmayer relationship give us access to the activation energy. By using the proposed technique and the suitable models developed, the structure thus quality of dairy products may be better controlled.

The multimodal magnetoelectric effect in the ring-shaped magnetostrictive-piezoelectric bulk composites

NASA Astrophysics Data System (ADS)

Radchenko, G. S.; Filippov, D. A.; Laletin, V. M.

2015-11-01

The theoretical and experimental investigation of the direct magnetoelectric effect in the ring-type structures made of the bulk magnetostrictive-piezoelectric composites has been presented. The analytical expression for the magnetoelectric voltage coefficient has been obtained using the effective parameters method. The frequency dependence of this parameter is also analyzed. The dependence of the resonant frequency and the amplitude of this effect of the geometrical parameters of the ring for the first and second oscillation modes are presented. The experimental investigation of the direct magnetoelectric effect for the ring-type composite specimens consisting of the nickel ferrite spinel-PZT bulk composite is done. The obtained experimental data are in good agreement with the theoretical predictions.

Chickpea seeds germination rational parameters optimization

NASA Astrophysics Data System (ADS)

Safonova, Yu A.; Ivliev, M. N.; Lemeshkin, A. V.

2018-05-01

The paper presents the influence of chickpea seeds bioactivation parameters on their enzymatic activity experimental results. Optimal bioactivation process modes were obtained by regression-factor analysis: process temperature - 13.6 °C, process duration - 71.5 h. It was found that in the germination process, the proteolytic, amylolytic and lipolytic enzymes activity increased, and the urease enzyme activity is reduced. The dependences of enzyme activity on chickpea seeds germination conditions were obtained by mathematical processing of experimental data. The calculated data are in good agreement with the experimental ones. This confirms the optimization efficiency based on experiments mathematical planning in order to determine the enzymatic activity of chickpea seeds germination optimal parameters of bioactivated seeds.

Automated Optimization of Potential Parameters

PubMed Central

Michele, Di Pierro; Ron, Elber

2013-01-01

An algorithm and software to refine parameters of empirical energy functions according to condensed phase experimental measurements are discussed. The algorithm is based on sensitivity analysis and local minimization of the differences between experiment and simulation as a function of potential parameters. It is illustrated for a toy problem of alanine dipeptide and is applied to folding of the peptide WAAAH. The helix fraction is highly sensitive to the potential parameters while the slope of the melting curve is not. The sensitivity variations make it difficult to satisfy both observations simultaneously. We conjecture that there is no set of parameters that reproduces experimental melting curves of short peptides that are modeled with the usual functional form of a force field. PMID:24015115

NCAR's Research Data Archive: OPeNDAP Access for Complex Datasets

NASA Astrophysics Data System (ADS)

Dattore, R.; Worley, S. J.

2014-12-01

Many datasets have complex structures including hundreds of parameters and numerous vertical levels, grid resolutions, and temporal products. Making these data accessible is a challenge for a data provider. OPeNDAP is powerful protocol for delivering in real-time multi-file datasets that can be ingested by many analysis and visualization tools, but for these datasets there are too many choices about how to aggregate. Simple aggregation schemes can fail to support, or at least make it very challenging, for many potential studies based on complex datasets. We address this issue by using a rich file content metadata collection to create a real-time customized OPeNDAP service to match the full suite of access possibilities for complex datasets. The Climate Forecast System Reanalysis (CFSR) and it's extension, the Climate Forecast System Version 2 (CFSv2) datasets produced by the National Centers for Environmental Prediction (NCEP) and hosted by the Research Data Archive (RDA) at the Computational and Information Systems Laboratory (CISL) at NCAR are examples of complex datasets that are difficult to aggregate with existing data server software. CFSR and CFSv2 contain 141 distinct parameters on 152 vertical levels, six grid resolutions and 36 products (analyses, n-hour forecasts, multi-hour averages, etc.) where not all parameter/level combinations are available at all grid resolution/product combinations. These data are archived in the RDA with the data structure provided by the producer; no additional re-organization or aggregation have been applied. Since 2011, users have been able to request customized subsets (e.g. - temporal, parameter, spatial) from the CFSR/CFSv2, which are processed in delayed-mode and then downloaded to a user's system. Until now, the complexity has made it difficult to provide real-time OPeNDAP access to the data. We have developed a service that leverages the already-existing subsetting interface and allows users to create a virtual dataset with its own structure (das, dds). The user receives a URL to the customized dataset that can be used by existing tools to ingest, analyze, and visualize the data. This presentation will detail the metadata system and OPeNDAP server that enable user-customized real-time access and show an example of how a visualization tool can access the data.

Anisotropy enhanced X-ray scattering from solvated transition metal complexes

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

Biasin, Elisa; van Driel, Tim B.; Levi, Gianluca

Time-resolved X-ray scattering patterns from photoexcited molecules in solution are in many cases anisotropic at the ultrafast time scales accessible at X-ray free-electron lasers (XFELs). This anisotropy arises from the interaction of a linearly polarized UV–Vis pump laser pulse with the sample, which induces anisotropic structural changes that can be captured by femtosecond X-ray pulses. In this work, a method for quantitative analysis of the anisotropic scattering signal arising from an ensemble of molecules is described, and it is demonstrated how its use can enhance the structural sensitivity of the time-resolved X-ray scattering experiment. This method is applied on time-resolvedmore » X-ray scattering patterns measured upon photoexcitation of a solvated di-platinum complex at an XFEL, and the key parameters involved are explored. Here it is shown that a combined analysis of the anisotropic and isotropic difference scattering signals in this experiment allows a more precise determination of the main photoinduced structural change in the solute,i.e.the change in Pt—Pt bond length, and yields more information on the excitation channels than the analysis of the isotropic scattering only. Finally, it is discussed how the anisotropic transient response of the solvent can enable the determination of key experimental parameters such as the instrument response function.« less

Renal and metabolic effects of three months of decarbonated cola beverages in rats.

PubMed

Celec, Peter; Pálffy, Roland; Gardlík, Roman; Behuliak, Michal; Hodosy, Július; Jáni, Peter; Bozek, Peter; Sebeková, Katarína

2010-11-01

Epidemiological studies have shown an association between the intake of cola beverages and chronic kidney diseases. Experimental evidence for the negative effects of cola intake on kidneys is lacking. Male Wistar rats had ad libitum access to water (control group) or three different sugar-sweetened cola beverages for three months. Despite very high cola intake (daily cca 140 mL), no differences were found in body weight, kidney weight, glomerular morphology, oxidative and carbonyl stress or expression of selected marker genes in the renal cortex. Interestingly, all groups consuming cola beverages had lower blood glucose levels during an oral glucose tolerance test, suggesting improved insulin sensitivity. Despite hyperfiltration (5-6-fold increase in diuresis), cola beverages had no effect on assessed parameters of renal function, histology, gene expression or oxidative stress. Moreover, cola intake seems to increase creatinine clearance and to decrease plasma levels of urea. In our study increased insulin sensitivity and altered renal functional parameters were observed in rats receiving cola beverages for three months. Whether the findings are due to the short duration of the study or interspecies metabolic differences should be uncovered in further studies. Even more interesting might be the analysis of effects of cola intake in animal models of diabetes.

Soil and water characteristics of a young surface mine wetland

NASA Astrophysics Data System (ADS)

Andrew Cole, C.; Lefebvre, Eugene A.

1991-05-01

Coal companies are reluctant to include wetland development in reclamation plans partly due to a lack of information on the resulting characteristics of such sites. It is easier for coal companies to recreate terrestrial habitats than to attempt experimental methods and possibly face significant regulatory disapproval. Therefore, we studied a young (10 years) wetland on a reclaimed surface coal mine in southern Illinois so as to ascertain soil and water characteristics such that the site might serve as a model for wetland development on surface mines. Water pH was not measured because of equipment problems, but evidence (plant life, fish, herpetofauna) suggests suitable pH levels. Other water parameters (conductivity, salinity, alkalinity, chloride, copper, total hardness, iron, manganese, nitrate, nitrite, phosphate, and sulfate) were measured, and only copper was seen in potentially high concentrations (but with no obvious toxic effects). Soil variables measured included pH, nitrate, nitrite, ammonia, potassium, calcium, magnesium, manganese, aluminum, iron, sulfate, chloride, and percent organic matter. Soils were slightly alkaline and most parameters fell within levels reported for other studies on both natural and manmade wetlands. Aluminum was high, but this might be indicative more of large amounts complexed with soils and therefore unavailable, than amounts actually accessible to plants. Organic matter was moderate, somewhat surprising given the age of the system.

Anisotropy enhanced X-ray scattering from solvated transition metal complexes

DOE PAGES

Biasin, Elisa; van Driel, Tim B.; Levi, Gianluca; ...

2018-02-13

Time-resolved X-ray scattering patterns from photoexcited molecules in solution are in many cases anisotropic at the ultrafast time scales accessible at X-ray free-electron lasers (XFELs). This anisotropy arises from the interaction of a linearly polarized UV–Vis pump laser pulse with the sample, which induces anisotropic structural changes that can be captured by femtosecond X-ray pulses. In this work, a method for quantitative analysis of the anisotropic scattering signal arising from an ensemble of molecules is described, and it is demonstrated how its use can enhance the structural sensitivity of the time-resolved X-ray scattering experiment. This method is applied on time-resolvedmore » X-ray scattering patterns measured upon photoexcitation of a solvated di-platinum complex at an XFEL, and the key parameters involved are explored. Here it is shown that a combined analysis of the anisotropic and isotropic difference scattering signals in this experiment allows a more precise determination of the main photoinduced structural change in the solute,i.e.the change in Pt—Pt bond length, and yields more information on the excitation channels than the analysis of the isotropic scattering only. Finally, it is discussed how the anisotropic transient response of the solvent can enable the determination of key experimental parameters such as the instrument response function.« less

Analysis Tools for the Ion Cyclotron Emission Diagnostic on DIII-D

NASA Astrophysics Data System (ADS)

Del Castillo, C. A.; Thome, K. E.; Pinsker, R. I.; Meneghini, O.; Pace, D. C.

2017-10-01

Ion cyclotron emission (ICE) waves are excited by suprathermal particles such as neutral beam particles and fusion products. An ICE diagnostic is in consideration for use at ITER, where it could provide important passive measurement of fast ions location and losses, which are otherwise difficult to determine. Simple ICE data analysis codes had previously been developed, but more sophisticated codes are required to facilitate data analysis. Several terabytes of ICE data were collected on DIII-D during the 2015-2017 campaign. The ICE diagnostic consists of antenna straps and dedicated magnetic probes that are both digitized at 200 MHz. A suite of Python spectral analysis tools within the OMFIT framework is under development to perform the memory-intensive analysis of this data. A fast and optimized analysis allows ready access to data visualizations as spectrograms and as plots of both frequency and time cuts of the data. A database of processed ICE data is being constructed to understand the relationship between the frequency and intensity of ICE and a variety of experimental parameters including neutral beam power and geometry, local and global plasma parameters, magnetic fields, and many others. Work supported in part by US DoE under the Science Undergraduate Laboratory Internship (SULI) program and under DE-FC02-04ER54698.

A Model Parameter Extraction Method for Dielectric Barrier Discharge Ozone Chamber using Differential Evolution

NASA Astrophysics Data System (ADS)

Amjad, M.; Salam, Z.; Ishaque, K.

2014-04-01

In order to design an efficient resonant power supply for ozone gas generator, it is necessary to accurately determine the parameters of the ozone chamber. In the conventional method, the information from Lissajous plot is used to estimate the values of these parameters. However, the experimental setup for this purpose can only predict the parameters at one operating frequency and there is no guarantee that it results in the highest ozone gas yield. This paper proposes a new approach to determine the parameters using a search and optimization technique known as Differential Evolution (DE). The desired objective function of DE is set at the resonance condition and the chamber parameter values can be searched regardless of experimental constraints. The chamber parameters obtained from the DE technique are validated by experiment.

Advanced Method to Estimate Fuel Slosh Simulation Parameters

NASA Technical Reports Server (NTRS)

Schlee, Keith; Gangadharan, Sathya; Ristow, James; Sudermann, James; Walker, Charles; Hubert, Carl

2005-01-01

The nutation (wobble) of a spinning spacecraft in the presence of energy dissipation is a well-known problem in dynamics and is of particular concern for space missions. The nutation of a spacecraft spinning about its minor axis typically grows exponentially and the rate of growth is characterized by the Nutation Time Constant (NTC). For launch vehicles using spin-stabilized upper stages, fuel slosh in the spacecraft propellant tanks is usually the primary source of energy dissipation. For analytical prediction of the NTC this fuel slosh is commonly modeled using simple mechanical analogies such as pendulums or rigid rotors coupled to the spacecraft. Identifying model parameter values which adequately represent the sloshing dynamics is the most important step in obtaining an accurate NTC estimate. Analytic determination of the slosh model parameters has met with mixed success and is made even more difficult by the introduction of propellant management devices and elastomeric diaphragms. By subjecting full-sized fuel tanks with actual flight fuel loads to motion similar to that experienced in flight and measuring the forces experienced by the tanks these parameters can be determined experimentally. Currently, the identification of the model parameters is a laborious trial-and-error process in which the equations of motion for the mechanical analog are hand-derived, evaluated, and their results are compared with the experimental results. The proposed research is an effort to automate the process of identifying the parameters of the slosh model using a MATLAB/SimMechanics-based computer simulation of the experimental setup. Different parameter estimation and optimization approaches are evaluated and compared in order to arrive at a reliable and effective parameter identification process. To evaluate each parameter identification approach, a simple one-degree-of-freedom pendulum experiment is constructed and motion is induced using an electric motor. By applying the estimation approach to a simple, accurately modeled system, its effectiveness and accuracy can be evaluated. The same experimental setup can then be used with fluid-filled tanks to further evaluate the effectiveness of the process. Ultimately, the proven process can be applied to the full-sized spinning experimental setup to quickly and accurately determine the slosh model parameters for a particular spacecraft mission. Automating the parameter identification process will save time, allow more changes to be made to proposed designs, and lower the cost in the initial design stages.

45 CFR 153.100 - State notice of benefit and payment parameters.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 45 Public Welfare 1 2013-10-01 2013-10-01 false State notice of benefit and payment parameters. 153.100 Section 153.100 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES REQUIREMENTS RELATING TO HEALTH CARE ACCESS STANDARDS RELATED TO REINSURANCE, RISK CORRIDORS, AND RISK ADJUSTMENT UNDER THE...

45 CFR 153.100 - State notice of benefit and payment parameters.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 45 Public Welfare 1 2014-10-01 2014-10-01 false State notice of benefit and payment parameters. 153.100 Section 153.100 Public Welfare Department of Health and Human Services REQUIREMENTS RELATING TO HEALTH CARE ACCESS STANDARDS RELATED TO REINSURANCE, RISK CORRIDORS, AND RISK ADJUSTMENT UNDER THE...

45 CFR 153.100 - State notice of benefit and payment parameters.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 45 Public Welfare 1 2012-10-01 2012-10-01 false State notice of benefit and payment parameters. 153.100 Section 153.100 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES REQUIREMENTS RELATING TO HEALTH CARE ACCESS STANDARDS RELATED TO REINSURANCE, RISK CORRIDORS, AND RISK ADJUSTMENT UNDER THE...

Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding.

PubMed

Min, Xu; Zeng, Wanwen; Chen, Ning; Chen, Ting; Jiang, Rui

2017-07-15

Experimental techniques for measuring chromatin accessibility are expensive and time consuming, appealing for the development of computational approaches to predict open chromatin regions from DNA sequences. Along this direction, existing methods fall into two classes: one based on handcrafted k -mer features and the other based on convolutional neural networks. Although both categories have shown good performance in specific applications thus far, there still lacks a comprehensive framework to integrate useful k -mer co-occurrence information with recent advances in deep learning. We fill this gap by addressing the problem of chromatin accessibility prediction with a convolutional Long Short-Term Memory (LSTM) network with k -mer embedding. We first split DNA sequences into k -mers and pre-train k -mer embedding vectors based on the co-occurrence matrix of k -mers by using an unsupervised representation learning approach. We then construct a supervised deep learning architecture comprised of an embedding layer, three convolutional layers and a Bidirectional LSTM (BLSTM) layer for feature learning and classification. We demonstrate that our method gains high-quality fixed-length features from variable-length sequences and consistently outperforms baseline methods. We show that k -mer embedding can effectively enhance model performance by exploring different embedding strategies. We also prove the efficacy of both the convolution and the BLSTM layers by comparing two variations of the network architecture. We confirm the robustness of our model to hyper-parameters by performing sensitivity analysis. We hope our method can eventually reinforce our understanding of employing deep learning in genomic studies and shed light on research regarding mechanisms of chromatin accessibility. The source code can be downloaded from https://github.com/minxueric/ismb2017_lstm . tingchen@tsinghua.edu.cn or ruijiang@tsinghua.edu.cn. Supplementary materials are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding

PubMed Central

Min, Xu; Zeng, Wanwen; Chen, Ning; Chen, Ting; Jiang, Rui

2017-01-01

Abstract Motivation: Experimental techniques for measuring chromatin accessibility are expensive and time consuming, appealing for the development of computational approaches to predict open chromatin regions from DNA sequences. Along this direction, existing methods fall into two classes: one based on handcrafted k-mer features and the other based on convolutional neural networks. Although both categories have shown good performance in specific applications thus far, there still lacks a comprehensive framework to integrate useful k-mer co-occurrence information with recent advances in deep learning. Results: We fill this gap by addressing the problem of chromatin accessibility prediction with a convolutional Long Short-Term Memory (LSTM) network with k-mer embedding. We first split DNA sequences into k-mers and pre-train k-mer embedding vectors based on the co-occurrence matrix of k-mers by using an unsupervised representation learning approach. We then construct a supervised deep learning architecture comprised of an embedding layer, three convolutional layers and a Bidirectional LSTM (BLSTM) layer for feature learning and classification. We demonstrate that our method gains high-quality fixed-length features from variable-length sequences and consistently outperforms baseline methods. We show that k-mer embedding can effectively enhance model performance by exploring different embedding strategies. We also prove the efficacy of both the convolution and the BLSTM layers by comparing two variations of the network architecture. We confirm the robustness of our model to hyper-parameters by performing sensitivity analysis. We hope our method can eventually reinforce our understanding of employing deep learning in genomic studies and shed light on research regarding mechanisms of chromatin accessibility. Availability and implementation: The source code can be downloaded from https://github.com/minxueric/ismb2017_lstm. Contact: tingchen@tsinghua.edu.cn or ruijiang@tsinghua.edu.cn Supplementary information: Supplementary materials are available at Bioinformatics online. PMID:28881969

Charge Transport in Nonaqueous Liquid Electrolytes: A Paradigm Shift

DTIC Science & Technology

2015-05-18

that provide inadequate descriptions of experimental data, often using empirical equations whose fitting parameters have no physical significance...provide inadequate descriptions of experimental data, often using empirical equations whose fitting parameters have no physical significance...Ea The hydrodynamic model, utilizing the Stokes equation describes isothermal conductivity, self-diffusion coefficient, and the dielectric

Optimization of an angle-beam ultrasonic approach for characterization of impact damage in composites

NASA Astrophysics Data System (ADS)

Henry, Christine; Kramb, Victoria; Welter, John T.; Wertz, John N.; Lindgren, Eric A.; Aldrin, John C.; Zainey, David

2018-04-01

Advances in NDE method development are greatly improved through model-guided experimentation. In the case of ultrasonic inspections, models which provide insight into complex mode conversion processes and sound propagation paths are essential for understanding the experimental data and inverting the experimental data into relevant information. However, models must also be verified using experimental data obtained under well-documented and understood conditions. Ideally, researchers would utilize the model simulations and experimental approach to efficiently converge on the optimal solution. However, variability in experimental parameters introduce extraneous signals that are difficult to differentiate from the anticipated response. This paper discusses the results of an ultrasonic experiment designed to evaluate the effect of controllable variables on the anticipated signal, and the effect of unaccounted for experimental variables on the uncertainty in those results. Controlled experimental parameters include the transducer frequency, incidence beam angle and focal depth.

Data management routines for reproducible research using the G-Node Python Client library

PubMed Central

Sobolev, Andrey; Stoewer, Adrian; Pereira, Michael; Kellner, Christian J.; Garbers, Christian; Rautenberg, Philipp L.; Wachtler, Thomas

2014-01-01

Structured, efficient, and secure storage of experimental data and associated meta-information constitutes one of the most pressing technical challenges in modern neuroscience, and does so particularly in electrophysiology. The German INCF Node aims to provide open-source solutions for this domain that support the scientific data management and analysis workflow, and thus facilitate future data access and reproducible research. G-Node provides a data management system, accessible through an application interface, that is based on a combination of standardized data representation and flexible data annotation to account for the variety of experimental paradigms in electrophysiology. The G-Node Python Library exposes these services to the Python environment, enabling researchers to organize and access their experimental data using their familiar tools while gaining the advantages that a centralized storage entails. The library provides powerful query features, including data slicing and selection by metadata, as well as fine-grained permission control for collaboration and data sharing. Here we demonstrate key actions in working with experimental neuroscience data, such as building a metadata structure, organizing recorded data in datasets, annotating data, or selecting data regions of interest, that can be automated to large degree using the library. Compliant with existing de-facto standards, the G-Node Python Library is compatible with many Python tools in the field of neurophysiology and thus enables seamless integration of data organization into the scientific data workflow. PMID:24634654

Data management routines for reproducible research using the G-Node Python Client library.

PubMed

Sobolev, Andrey; Stoewer, Adrian; Pereira, Michael; Kellner, Christian J; Garbers, Christian; Rautenberg, Philipp L; Wachtler, Thomas

2014-01-01

Structured, efficient, and secure storage of experimental data and associated meta-information constitutes one of the most pressing technical challenges in modern neuroscience, and does so particularly in electrophysiology. The German INCF Node aims to provide open-source solutions for this domain that support the scientific data management and analysis workflow, and thus facilitate future data access and reproducible research. G-Node provides a data management system, accessible through an application interface, that is based on a combination of standardized data representation and flexible data annotation to account for the variety of experimental paradigms in electrophysiology. The G-Node Python Library exposes these services to the Python environment, enabling researchers to organize and access their experimental data using their familiar tools while gaining the advantages that a centralized storage entails. The library provides powerful query features, including data slicing and selection by metadata, as well as fine-grained permission control for collaboration and data sharing. Here we demonstrate key actions in working with experimental neuroscience data, such as building a metadata structure, organizing recorded data in datasets, annotating data, or selecting data regions of interest, that can be automated to large degree using the library. Compliant with existing de-facto standards, the G-Node Python Library is compatible with many Python tools in the field of neurophysiology and thus enables seamless integration of data organization into the scientific data workflow.

An antenna-pointing mechanism for the ETS-6 K-band Single Access (KSA) antenna

NASA Technical Reports Server (NTRS)

Takada, Noboru; Amano, Takahiro; Ohhashi, Toshiro; Wachi, Shigeo

1991-01-01

Both the design philosophy for the Antenna Pointing Mechanism (APM) to be used for the K-band Single Access (KSA) antenna system and experimental results of the APM Engineering Model (EM) tests are described. The KSA antenna system will be flown on the Engineering Test Satellite 6 (ETS-6).

Ionic Liquids Database- (ILThermo)

National Institute of Standards and Technology Data Gateway

SRD 147 NIST Ionic Liquids Database- (ILThermo) (Web, free access)   IUPAC Ionic Liquids Database, ILThermo, is a free web research tool that allows users worldwide to access an up-to-date data collection from the publications on experimental investigations of thermodynamic, and transport properties of ionic liquids as well as binary and ternary mixtures containing ionic liquids.

Access. Challenge for Change/Societe Nouvelle Number Eleven.

ERIC Educational Resources Information Center

Prinn, Elizabeth, Ed.

Access is a journal published three or four times a year by Challenge for Change/Societe Nouvelle (CCSN). CCSN is an experimental program established by the Government of Canada as a cooperative effort between the National Film Board of Canada and certain of the Government's departments. Its purposes are to improve communications, create greater…

A scintillator-based online detector for the angularly resolved measurement of laser-accelerated proton spectra.

PubMed

Metzkes, J; Karsch, L; Kraft, S D; Pawelke, J; Richter, C; Schürer, M; Sobiella, M; Stiller, N; Zeil, K; Schramm, U

2012-12-01

In recent years, a new generation of high repetition rate (~10 Hz), high power (~100 TW) laser systems has stimulated intense research on laser-driven sources for fast protons. Considering experimental instrumentation, this development requires online diagnostics for protons to be added to the established offline detection tools such as solid state track detectors or radiochromic films. In this article, we present the design and characterization of a scintillator-based online detector that gives access to the angularly resolved proton distribution along one spatial dimension and resolves 10 different proton energy ranges. Conceived as an online detector for key parameters in laser-proton acceleration, such as the maximum proton energy and the angular distribution, the detector features a spatial resolution of ~1.3 mm and a spectral resolution better than 1.5 MeV for a maximum proton energy above 12 MeV in the current design. Regarding its areas of application, we consider the detector a useful complement to radiochromic films and Thomson parabola spectrometers, capable to give immediate feedback on the experimental performance. The detector was characterized at an electrostatic Van de Graaff tandetron accelerator and tested in a laser-proton acceleration experiment, proving its suitability as a diagnostic device for laser-accelerated protons.

Plasma-Jet-Driven Magneto-Inertial Fusion (PJMIF): Physics and Design for a Plasma Liner Formation Experiment

NASA Astrophysics Data System (ADS)

Hsu, Scott; Cassibry, Jason; Witherspoon, F. Douglas

2014-10-01

Spherically imploding plasma liners are a potential standoff compression driver for magneto-inertial fusion, which is a hybrid of and operates in an intermediate density between those of magnetic and inertial fusion. We propose to use an array of merging supersonic plasma jets to form a spherically imploding plasma liner. The jets are to be formed by pulsed coaxial guns with contoured electrodes that are placed sufficiently far from the location of target compression such that no hardware is repetitively destroyed. As such, the repetition rate can be higher (e.g., 1 Hz) and ultimately the power-plant economics can be more attractive than most other MIF approaches. During the R&D phase, a high experimental shot rate at reasonably low cost (e.g., < 1 k/shot) may be achieved with excellent diagnostic access, thus enabling a rapid learning rate. After some background on PJMIF and its prospects for reactor-relevant energy gain, this poster describes the physics objectives and design of a proposed 60-gun plasma-liner-formation experiment, which will provide experimental data on: (i) scaling of peak liner ram pressure versus initial jet parameters, (ii) liner non-uniformity characterization and control, and (iii) control of liner profiles for eventual gain optimization.

Analytical Model for Estimating the Zenith Angle Dependence of Terrestrial Cosmic Ray Fluxes

PubMed Central

Sato, Tatsuhiko

2016-01-01

A new model called “PHITS-based Analytical Radiation Model in the Atmosphere (PARMA) version 4.0” was developed to facilitate instantaneous estimation of not only omnidirectional but also angular differential energy spectra of cosmic ray fluxes anywhere in Earth’s atmosphere at nearly any given time. It consists of its previous version, PARMA3.0, for calculating the omnidirectional fluxes and several mathematical functions proposed in this study for expressing their zenith-angle dependences. The numerical values of the parameters used in these functions were fitted to reproduce the results of the extensive air shower simulation performed by Particle and Heavy Ion Transport code System (PHITS). The angular distributions of ground-level muons at large zenith angles were specially determined by introducing an optional function developed on the basis of experimental data. The accuracy of PARMA4.0 was closely verified using multiple sets of experimental data obtained under various global conditions. This extension enlarges the model’s applicability to more areas of research, including design of cosmic-ray detectors, muon radiography, soil moisture monitoring, and cosmic-ray shielding calculation. PARMA4.0 is available freely and is easy to use, as implemented in the open-access EXcel-based Program for Calculating Atmospheric Cosmic-ray Spectrum (EXPACS). PMID:27490175

Analytical Model for Estimating the Zenith Angle Dependence of Terrestrial Cosmic Ray Fluxes.

PubMed

Sato, Tatsuhiko

2016-01-01

A new model called "PHITS-based Analytical Radiation Model in the Atmosphere (PARMA) version 4.0" was developed to facilitate instantaneous estimation of not only omnidirectional but also angular differential energy spectra of cosmic ray fluxes anywhere in Earth's atmosphere at nearly any given time. It consists of its previous version, PARMA3.0, for calculating the omnidirectional fluxes and several mathematical functions proposed in this study for expressing their zenith-angle dependences. The numerical values of the parameters used in these functions were fitted to reproduce the results of the extensive air shower simulation performed by Particle and Heavy Ion Transport code System (PHITS). The angular distributions of ground-level muons at large zenith angles were specially determined by introducing an optional function developed on the basis of experimental data. The accuracy of PARMA4.0 was closely verified using multiple sets of experimental data obtained under various global conditions. This extension enlarges the model's applicability to more areas of research, including design of cosmic-ray detectors, muon radiography, soil moisture monitoring, and cosmic-ray shielding calculation. PARMA4.0 is available freely and is easy to use, as implemented in the open-access EXcel-based Program for Calculating Atmospheric Cosmic-ray Spectrum (EXPACS).

Integrated Scenario Modeling of NSTX Advanced Plasma Configurations

NASA Astrophysics Data System (ADS)

Kessel, Charles; Synakowski, Edward

2003-10-01

The Spherical Torus will provide an attractive fusion energy source if it can demonstrate the following major features: high elongation and triangularity, 100% non-inductive current with a credible path to high bootstrap fractions, non-solenoidal startup and current rampup, high beta with stabilization of RWM instabilities, and sufficiently high energy confinement. NSTX has specific experimental milestones to examine these features, and integrated scenario modeling is helping to understand how these configurations might be produced and what tools are needed to access this operating space. Simulations with the Tokamak Simulation Code (TSC), CURRAY, and JSOLVER/BALMSC/PEST2 have identified fully non-inductively sustained, high beta plasmas that rely on strong plasma shaping accomplished with a PF coil modification, off-axis current drive from Electron Bernstein Waves (EBW), flexible on-axis heating and CD from High Harmonic Fast Wave (HHFW) and Neutral Beam Injection (NBI), and density control. Ideal MHD stability shows that with wall stabilization through plasma rotation and/or RWM feedback coils, a beta of 40% is achievable, with 100% non-inductive current sustained for 4 current diffusion times. Experimental data and theory are combined to produce a best extrapolation to these regimes, which is continuously improved as the discharges approach these parameters, and theoretical/computational methods expand. Further investigations and development for integrated scenario modeling on NSTX is discussed.

Optimization of Culture Conditions for Production of the Anti-Leukemic Glutaminase Free L-Asparaginase by Newly Isolated Streptomyces olivaceus NEAE-119 Using Response Surface Methodology.

PubMed

El-Naggar, Noura El-Ahmady; Moawad, Hassan; El-Shweihy, Nancy M; El-Ewasy, Sara M

2015-01-01

Among the antitumor drugs, bacterial enzyme L-asparaginase has been employed as the most effective chemotherapeutic agent in pediatric oncotherapy especially for acute lymphoblastic leukemia. Glutaminase free L-asparaginase producing actinomycetes were isolated from soil samples collected from Egypt. Among them, a potential culture, strain NEAE-119, was selected and identified on the basis of morphological, cultural, physiological, and biochemical properties together with 16S rRNA sequence as Streptomyces olivaceus NEAE-119 and sequencing product (1509 bp) was deposited in the GenBank database under accession number KJ200342. The optimization of different process parameters for L-asparaginase production by Streptomyces olivaceus NEAE-119 using Plackett-Burman experimental design and response surface methodology was carried out. Fifteen variables (temperature, pH, incubation time, inoculum size, inoculum age, agitation speed, dextrose, starch, L-asparagine, KNO3, yeast extract, K2HPO4, MgSO4·7H2O, NaCl, and FeSO4·7H2O) were screened using Plackett-Burman experimental design. The most positive significant independent variables affecting enzyme production (temperature, inoculum age, and agitation speed) were further optimized by the face-centered central composite design-response surface methodology.

Optimization of Culture Conditions for Production of the Anti-Leukemic Glutaminase Free L-Asparaginase by Newly Isolated Streptomyces olivaceus NEAE-119 Using Response Surface Methodology

PubMed Central

El-Naggar, Noura El-Ahmady; Moawad, Hassan; El-Shweihy, Nancy M.; El-Ewasy, Sara M.

2015-01-01

Among the antitumor drugs, bacterial enzyme L-asparaginase has been employed as the most effective chemotherapeutic agent in pediatric oncotherapy especially for acute lymphoblastic leukemia. Glutaminase free L-asparaginase producing actinomycetes were isolated from soil samples collected from Egypt. Among them, a potential culture, strain NEAE-119, was selected and identified on the basis of morphological, cultural, physiological, and biochemical properties together with 16S rRNA sequence as Streptomyces olivaceus NEAE-119 and sequencing product (1509 bp) was deposited in the GenBank database under accession number KJ200342. The optimization of different process parameters for L-asparaginase production by Streptomyces olivaceus NEAE-119 using Plackett-Burman experimental design and response surface methodology was carried out. Fifteen variables (temperature, pH, incubation time, inoculum size, inoculum age, agitation speed, dextrose, starch, L-asparagine, KNO3, yeast extract, K2HPO4, MgSO4·7H2O, NaCl, and FeSO4·7H2O) were screened using Plackett-Burman experimental design. The most positive significant independent variables affecting enzyme production (temperature, inoculum age, and agitation speed) were further optimized by the face-centered central composite design-response surface methodology. PMID:26180806

disLocate: tools to rapidly quantify local intermolecular structure to assess two-dimensional order in self-assembled systems.

PubMed

Bumstead, Matt; Liang, Kunyu; Hanta, Gregory; Hui, Lok Shu; Turak, Ayse

2018-01-24

Order classification is particularly important in photonics, optoelectronics, nanotechnology, biology, and biomedicine, as self-assembled and living systems tend to be ordered well but not perfectly. Engineering sets of experimental protocols that can accurately reproduce specific desired patterns can be a challenge when (dis)ordered outcomes look visually similar. Robust comparisons between similar samples, especially with limited data sets, need a finely tuned ensemble of accurate analysis tools. Here we introduce our numerical Mathematica package disLocate, a suite of tools to rapidly quantify the spatial structure of a two-dimensional dispersion of objects. The full range of tools available in disLocate give different insights into the quality and type of order present in a given dispersion, accessing the translational, orientational and entropic order. The utility of this package allows for researchers to extract the variation and confidence range within finite sets of data (single images) using different structure metrics to quantify local variation in disorder. Containing all metrics within one package allows for researchers to easily and rapidly extract many different parameters simultaneously, allowing robust conclusions to be drawn on the order of a given system. Quantifying the experimental trends which produce desired morphologies enables engineering of novel methods to direct self-assembly.

Evaluation of clinical and paraclinical effects of intraosseous vs intravenous administration of propofol on general anesthesia in rabbits

PubMed Central

Mazaheri-Khameneh, Ramin; Sarrafzadeh-Rezaei, Farshid; Asri-Rezaei, Siamak; Dalir-Naghadeh, Bahram

2012-01-01

This prospective study aimed to compare the intraosseous (IO) and intravenous (IV) effects of propofol on selected blood parameters and physiological variables during general anesthesia in rabbits. Thirty New Zealand White rabbits were studied. Six rabbits received IV propofol (group 1) and another 6 rabbits, were injected propofol intraosseously (Group 2) for 30 minutes (experimental groups). Rabbits of the third and fourth groups received IV and IO normal saline at the same volume given to the experimental groups, respectively. In the fifth group IO cannulation was performed but neither propofol nor normal saline were administered. Blood profiles were assayed before induction and after recovery of anesthesia. Heart and respiratory rates, rectal temperature, saturation of peripheral oxygen and mean arterial blood pressure were recorded. Heart rate increased significantly 1 to 5 minutes after induction of anesthesia in experimental groups (P < 0.05). Although mean arterial blood pressure decreased significantly from baseline, values remained above 60 mm Hg (P < 0.05). Respiratory rate decreased significantly in experimental groups, but remained higher in group 2 (P < 0.05). The lymphocyte count decreased significantly in group 1 (P < 0.05). The concentration of alkaline phosphatase in all rabbits, aspartate aminotransferase and gamma-glutamyl transferase in the first group and gamma-glutamyl transferase in the third group increased significantly (P < 0.05). Total bilirubin decreased significantly in group 2 (P < 0.05). All measured values remained within normal limits. Based on the least significant physiological, hematological and biochemical effects, the IO injection of propofol appears to be safe and suitable method of anesthesia in rabbits with limited vascular access. PMID:25653755

Evaluation of clinical and paraclinical effects of intraosseous vs intravenous administration of propofol on general anesthesia in rabbits.

PubMed

Mazaheri-Khameneh, Ramin; Sarrafzadeh-Rezaei, Farshid; Asri-Rezaei, Siamak; Dalir-Naghadeh, Bahram

2012-01-01

This prospective study aimed to compare the intraosseous (IO) and intravenous (IV) effects of propofol on selected blood parameters and physiological variables during general anesthesia in rabbits. Thirty New Zealand White rabbits were studied. Six rabbits received IV propofol (group 1) and another 6 rabbits, were injected propofol intraosseously (Group 2) for 30 minutes (experimental groups). Rabbits of the third and fourth groups received IV and IO normal saline at the same volume given to the experimental groups, respectively. In the fifth group IO cannulation was performed but neither propofol nor normal saline were administered. Blood profiles were assayed before induction and after recovery of anesthesia. Heart and respiratory rates, rectal temperature, saturation of peripheral oxygen and mean arterial blood pressure were recorded. Heart rate increased significantly 1 to 5 minutes after induction of anesthesia in experimental groups (P < 0.05). Although mean arterial blood pressure decreased significantly from baseline, values remained above 60 mm Hg (P < 0.05). Respiratory rate decreased significantly in experimental groups, but remained higher in group 2 (P < 0.05). The lymphocyte count decreased significantly in group 1 (P < 0.05). The concentration of alkaline phosphatase in all rabbits, aspartate aminotransferase and gamma-glutamyl transferase in the first group and gamma-glutamyl transferase in the third group increased significantly (P < 0.05). Total bilirubin decreased significantly in group 2 (P < 0.05). All measured values remained within normal limits. Based on the least significant physiological, hematological and biochemical effects, the IO injection of propofol appears to be safe and suitable method of anesthesia in rabbits with limited vascular access.

Dual-mode ultraflow access networks: a hybrid solution for the access bottleneck

NASA Astrophysics Data System (ADS)

Kazovsky, Leonid G.; Shen, Thomas Shunrong; Dhaini, Ahmad R.; Yin, Shuang; De Leenheer, Marc; Detwiler, Benjamin A.

2013-12-01

Optical Flow Switching (OFS) is a promising solution for large Internet data transfers. In this paper, we introduce UltraFlow Access, a novel optical access network architecture that offers dual-mode service to its end-users: IP and OFS. With UltraFlow Access, we design and implement a new dual-mode control plane and a new dual-mode network stack to ensure efficient connection setup and reliable and optimal data transmission. We study the impact of the UltraFlow system's design on the network throughput. Our experimental results show that with an optimized system design, near optimal (around 10 Gb/s) OFS data throughput can be attained when the line rate is 10Gb/s.

The Oxford Probe: an open access five-hole probe for aerodynamic measurements

NASA Astrophysics Data System (ADS)

Hall, B. F.; Povey, T.

2017-03-01

The Oxford Probe is an open access five-hole probe designed for experimental aerodynamic measurements. The open access probe can be manufactured by the end user via additive manufacturing (metal or plastic). The probe geometry, drawings, calibration maps, and software are available under a creative commons license. The purpose is to widen access to aerodynamic measurement techniques in education and research environments. There are many situations in which the open access probe will allow results of comparable accuracy to a well-calibrated commercial probe. We discuss the applications and limitations of the probe, and compare the calibration maps for 16 probes manufactured in different materials and at different scales, but with the same geometrical design.

Replication Strategy for Spatiotemporal Data Based on Distributed Caching System

PubMed Central

Xiong, Lian; Tao, Yang; Xu, Juan; Zhao, Lun

2018-01-01

The replica strategy in distributed cache can effectively reduce user access delay and improve system performance. However, developing a replica strategy suitable for varied application scenarios is still quite challenging, owing to differences in user access behavior and preferences. In this paper, a replication strategy for spatiotemporal data (RSSD) based on a distributed caching system is proposed. By taking advantage of the spatiotemporal locality and correlation of user access, RSSD mines high popularity and associated files from historical user access information, and then generates replicas and selects appropriate cache node for placement. Experimental results show that the RSSD algorithm is simple and efficient, and succeeds in significantly reducing user access delay. PMID:29342897

Modeling spatial accessibility of immigrants to culturally diverse family physicians.

PubMed

Wanga, Lu; Roisman, Deborah

2011-01-01

This article uses accessibility as an analytical tool to examine health care access among immigrants in a multicultural urban setting. It applies and improves on two widely used accessibility models—the gravity model and the two-step floating catchment area model—in measuring spatial accessibility by Mainland Chinese immigrants in the Toronto Census Metropolitan Area. Empirical data on physician-seeking behaviors are collected through two rounds of questionnaire surveys. Attention is focused on journey to physician location and utilization of linguistically matched family physicians. Based on the survey data, a two-zone accessibility model is developed by relaxing the travel threshold and distance impedance parameters that are traditionally treated as a constant in the accessibility models. General linear models are used to identify relationships among spatial accessibility, geography, and socioeconomic characteristics of Mainland Chinese immigrants. The results suggest a spatial mismatch in the supply of and demand for culturally sensitive care, and residential location is the primary factor that determines spatial accessibility to family physicians. The article yields important policy implications.

The role of structural parameters in DNA cyclization

DOE PAGES

Alexandrov, Ludmil B.; Bishop, Alan R.; Rasmussen, Kim O.; ...

2016-02-04

The intrinsic bendability of DNA plays an important role with relevance for myriad of essential cellular mechanisms. The flexibility of a DNA fragment can be experimentally and computationally examined by its propensity for cyclization, quantified by the Jacobson-Stockmayer J factor. In this paper, we use a well-established coarse-grained three-dimensional model of DNA and seven distinct sets of experimentally and computationally derived conformational parameters of the double helix to evaluate the role of structural parameters in calculating DNA cyclization.

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

Jorgensen, S.

Testing the behavior of metals in extreme environments is not always feasible, so material scientists use models to try and predict the behavior. To achieve accurate results it is necessary to use the appropriate model and material-specific parameters. This research evaluated the performance of six material models available in the MIDAS database [1] to determine at which temperatures and strain-rates they perform best, and to determine to which experimental data their parameters were optimized. Additionally, parameters were optimized for the Johnson-Cook model using experimental data from Lassila et al [2].

Band head spin assignment of superdeformed bands in 133Pr using two-parameter formulae

NASA Astrophysics Data System (ADS)

Sharma, Honey; Mittal, H. M.

2018-03-01

The two-parameter formulae viz. the power index formula, the nuclear softness formula and the VMI model are adopted to accredit the band head spin (I0) of four superdeformed rotational bands in 133Pr. The technique of least square fitting is used to accredit the band head spin for four superdeformed rotational bands in 133Pr. The root mean deviation among the computed transition energies and well-known experimental transition energies are attained by extracting the model parameters from the two-parameter formulae. The determined transition energies are in excellent agreement with the experimental transition energies, whenever exact spins are accredited. The power index formula coincides well with the experimental data and provides minimum root mean deviation. So, the power index formula is more efficient tool than the nuclear softness formula and the VMI model. The deviation of dynamic moment of inertia J(2) against the rotational frequency is also examined.

Four-body decays of B meson with lepton number violation

NASA Astrophysics Data System (ADS)

Yuan, Han; Wang, Tianhong; Jiang, Yue; Li, Qiang; Wang, Guo-Li

2018-06-01

The existence of heavy meson lepton number violating (LNV) processes shows the Majorana nature of the neutrino. Much of this theoretical and experimental researche focuses on this type of decay. Four-body epton-number violation (LNV) processes of the B meson may have sizable branching ratios as they share the same vertex and mixing parameters with the three-body case. Mixing parameters between the heavy Majorana neutrino and charged leptons extracted from the three-body case can be used to constrain the branching ratios of four-body decays of the B meson. So we can update the upper limits of these mixing parameters with new experimental data of the three-body LNV decays. We also analyze {B}0\\to {D}* -{{\\ell }}1+{{\\ell }}2+{M}2- using the updated parameters and estimate some channels’ reconstruction events using current experimental data from Belle.

Parameter optimization for transitions between memory states in small arrays of Josephson junctions

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

Rezac, Jacob D.; Imam, Neena; Braiman, Yehuda

Coupled arrays of Josephson junctions possess multiple stable zero voltage states. Such states can store information and consequently can be utilized for cryogenic memory applications. Basic memory operations can be implemented by sending a pulse to one of the junctions and studying transitions between the states. In order to be suitable for memory operations, such transitions between the states have to be fast and energy efficient. Here in this article we employed simulated annealing, a stochastic optimization algorithm, to study parameter optimization of array parameters which minimizes times and energies of transitions between specifically chosen states that can be utilizedmore » for memory operations (Read, Write, and Reset). Simulation results show that such transitions occur with access times on the order of 10–100 ps and access energies on the order of 10 -19–5×10 -18 J. Numerical simulations are validated with approximate analytical results.« less

Evaluation of various molecular parameters as predictors of bioconcentration in fish

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

Connell, D.W.; Schueuermann G3

1988-06-01

A reliable set of data on the bioconcentration factors (KB) of a diverse range of compounds in fish was selected from the literature. Using the structures of these compounds, the following molecular parameters were calculated: molecular weight (MW), solvent accessible molecular surface area (SASA), solvent accessible molecular volume (SAV), molar refraction (MR), largest principal moment of inertia (LPMI) and several molecular connectivity indices of the Randic type (1 chi, 2 chi, 3 chi, 1 chi vr, 3 chi c). The relationships between these parameters and log KB were evaluated for all compounds and the following subgroups: chlorinated hydrocarbons (CHC), polyaromaticmore » hydrocarbons (PAH), and CHC and PAH combined. These relationships indicated that SASA, SAV, and MR were good predictors of log KB for the CHC and PAH combined or alone and the other parameters were less satisfactory with these groups. In addition with the CHC, the log of these parameters displayed an improved correlation with log KB due to apparent nonlinearity in the log to linear relationship. Thus, with these groups of compounds, calculated values of SASA, SAV, and MR provide a satisfactory means of estimating log KB without measured data.« less

Novel methods to estimate the enantiomeric ratio and the kinetic parameters of enantiospecific enzymatic reactions.

PubMed

Machado, G D.C.; Paiva, L M.C.; Pinto, G F.; Oestreicher, E G.

2001-03-08

1The Enantiomeric Ratio (E) of the enzyme, acting as specific catalysts in resolution of enantiomers, is an important parameter in the quantitative description of these chiral resolution processes. In the present work, two novel methods hereby called Method I and II, for estimating E and the kinetic parameters Km and Vm of enantiomers were developed. These methods are based upon initial rate (v) measurements using different concentrations of enantiomeric mixtures (C) with several molar fractions of the substrate (x). Both methods were tested using simulated "experimental data" and actual experimental data. Method I is easier to use than Method II but requires that one of the enantiomers is available in pure form. Method II, besides not requiring the enantiomers in pure form shown better results, as indicated by the magnitude of the standard errors of estimates. The theoretical predictions were experimentally confirmed by using the oxidation of 2-butanol and 2-pentanol catalyzed by Thermoanaerobium brockii alcohol dehydrogenase as reaction models. The parameters E, Km and Vm were estimated by Methods I and II with precision and were not significantly different from those obtained experimentally by direct estimation of E from the kinetic parameters of each enantiomer available in pure form.

High fidelity studies of exploding foil initiator bridges, Part 3: ALEGRA MHD simulations

NASA Astrophysics Data System (ADS)

Neal, William; Garasi, Christopher

2017-01-01

Simulations of high voltage detonators, such as Exploding Bridgewire (EBW) and Exploding Foil Initiators (EFI), have historically been simple, often empirical, one-dimensional models capable of predicting parameters such as current, voltage, and in the case of EFIs, flyer velocity. Experimental methods have correspondingly generally been limited to the same parameters. With the advent of complex, first principles magnetohydrodynamic codes such as ALEGRA and ALE-MHD, it is now possible to simulate these components in three dimensions, and predict a much greater range of parameters than before. A significant improvement in experimental capability was therefore required to ensure these simulations could be adequately verified. In this third paper of a three part study, the experimental results presented in part 2 are compared against 3-dimensional MHD simulations. This improved experimental capability, along with advanced simulations, offer an opportunity to gain a greater understanding of the processes behind the functioning of EBW and EFI detonators.

Experimental results on current-driven turbulence in plasmas - a survey

NASA Astrophysics Data System (ADS)

de Kluiver, H.; Perepelkin, N. F.; Hirose, A.

1991-01-01

The experimental consequences of plasma turbulence driven by a current parallel to a magnetic field and concurrent anomalous plasma heating are reviewed, with an attempt to deduce universalities in key parameters such as the anomalous electrical conductivities observed in diverse devices. It has been found that the nature of plasma turbulence and turbulent heating depends on several parameters including the electric field, current and magnetic fields. A classification of turbulence regimes based on these parameters has been made. Experimental observations of the anomalous electrical conductivity, plasma heating, skin effect, runaway electron braking and turbulent fluctuations are surveyed, and current theoretical understanding is briefly reviewed. Experimental results recently obtained in stellarators (SIRIUS, URAGAN at Kharkov), and in tokamaks (TORTUR at Nieuwegein, STOR-1M at Saskatoon) are presented in some detail in the light of investigating the feasibility of using turbulent heating as a means of injecting a large power into toroidal devices.

Influence of experimental parameters on the microencapsulation of a photopolymerizable phase.

PubMed

Pernot, J M; Brun, H; Pouyet, B; Sergent, M; Phan-Tan-Luu, R

1993-01-01

Conditions of microencapsulation by in situ polycondensation, using melamine-formaldehyde as wall material, are influenced by the chemical nature of the core to encapsulate. In our study concerning the encapsulation of a photopolymerizable phase containing an electrically charged compound, it was necessary to modify the experimental process to obtain capsules of good quality. We used the factorial design method of screening by utilization of an asymmetric matrix, according to the collapsing principle of Addleman. The advantage of this method is that it allows determination of the simultaneous influences of the 11 experimental parameters involved in this preparation. The calculation method can be applied to more than two levels for some of the factors. The continuously varying parameters were altered between two extreme levels, chosen to allow encapsulation. For discontinuous factors, such as the molecular weight of the modifying system or nature of the aminoplast, we used the commercially available compounds, respectively three and four kinds. The results of the obtained capsules were determined by comparing microphotographic pictures. With 16 experiments we found four more factors influencing quality of capsules. We also determined the most favourable levels for the other seven parameters. The results allowed us to find optimal conditions in the experimental field. We obtained capsules of a satisfactory quality for this purpose, using only minimum experimentation.

Software aspects of the Geant4 validation repository

NASA Astrophysics Data System (ADS)

Dotti, Andrea; Wenzel, Hans; Elvira, Daniel; Genser, Krzysztof; Yarba, Julia; Carminati, Federico; Folger, Gunter; Konstantinov, Dmitri; Pokorski, Witold; Ribon, Alberto

2017-10-01

The Geant4, GeantV and GENIE collaborations regularly perform validation and regression tests for simulation results. DoSSiER (Database of Scientific Simulation and Experimental Results) is being developed as a central repository to store the simulation results as well as the experimental data used for validation. DoSSiER is easily accessible via a web application. In addition, a web service allows for programmatic access to the repository to extract records in JSON or XML exchange formats. In this article, we describe the functionality and the current status of various components of DoSSiER as well as the technology choices we made.

Software Aspects of the Geant4 Validation Repository

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

Dotti, Andrea; Wenzel, Hans; Elvira, Daniel

2016-01-01

The Geant4, GeantV and GENIE collaborations regularly perform validation and regression tests for simulation results. DoSSiER (Database of Scientic Simulation and Experimental Results) is being developed as a central repository to store the simulation results as well as the experimental data used for validation. DoSSiER is easily accessible via a web application. In addition, a web service allows for programmatic access to the repository to extract records in JSON or XML exchange formats. In this article, we describe the functionality and the current status of various components of DoSSiER as well as the technology choices we made.

Deployment of a Testbed in a Brazilian Research Network using IPv6 and Optical Access Technologies

NASA Astrophysics Data System (ADS)

Martins, Luciano; Ferramola Pozzuto, João; Olimpio Tognolli, João; Chaves, Niudomar Siqueira De A.; Reggiani, Atilio Eduardo; Hortêncio, Claudio Antonio

2012-04-01

This article presents the implementation of a testbed and the experimental results obtained with it on the Brazilian Experimental Network of the government-sponsored "GIGA Project." The use of IPv6 integrated to current and emerging optical architectures and technologies, such as dense wavelength division multiplexing and 10-gigabit Ethernet on the core and gigabit capable passive optical network and optical distribution network on access, were tested. These protocols, architectures, and optical technologies are promising and part of a brand new worldwide technological scenario that has being fairly adopted in the networks of enterprises and providers of the world.

Semi-experimental equilibrium structure of pyrazinamide from gas-phase electron diffraction. How much experimental is it?

NASA Astrophysics Data System (ADS)

Tikhonov, Denis S.; Vishnevskiy, Yury V.; Rykov, Anatolii N.; Grikina, Olga E.; Khaikin, Leonid S.

2017-03-01

A semi-experimental equilibrium structure of free molecules of pyrazinamide has been determined for the first time using gas electron diffraction method. The refinement was carried using regularization of geometry by calculated quantum chemical parameters. It is discussed to which extent is the final structure experimental. A numerical approach for estimation of the amount of experimental information in the refined parameters is suggested. The following values of selected internuclear distances were determined (values are in Å with 1σ in the parentheses): re(Cpyrazine-Cpyrazine)av = 1.397(2), re(Npyrazine-Cpyrazine)av = 1.332(3), re(Cpyrazine-Camide) = 1.493(1), re(Namide-Camide) = 1.335(2), re(Oamide-Camide) = 1.219(1). The given standard deviations represent pure experimental uncertainties without the influence of regularization.

Hydrologic and geologic characterization of Tenderfoot Creek Experimental Forest, Montana

Treesearch

Phillip E. Farnes; Ward W. McCaughey; Katherine J. Hansen

1994-01-01

Tenderfoot Creek Experimental Forest (TCEF) is located in Central Montana 24 miles north of White Sulphur Springs and 9 miles northwest of Highway 89 from Kings Hill via Forest Road #839. The experimental forest can also be accessed by Forest Road #586 via Sheep Creek. A general view of TCEF showing roads and drainages is shown in figure 2. The road down Tenderfoot...

Macroscopic characterisations of Web accessibility

NASA Astrophysics Data System (ADS)

Lopes, Rui; Carriço, Luis

2010-12-01

The Web Science framework poses fundamental questions on the analysis of the Web, by focusing on how microscopic properties (e.g. at the level of a Web page or Web site) emerge into macroscopic properties and phenomena. One research topic on the analysis of the Web is Web accessibility evaluation, which centres on understanding how accessible a Web page is for people with disabilities. However, when framing Web accessibility evaluation on Web Science, we have found that existing research stays at the microscopic level. This article presents an experimental study on framing Web accessibility evaluation into Web Science's goals. This study resulted in novel accessibility properties of the Web not found at microscopic levels, as well as of Web accessibility evaluation processes themselves. We observed at large scale some of the empirical knowledge on how accessibility is perceived by designers and developers, such as the disparity of interpretations of accessibility evaluation tools warnings. We also found a direct relation between accessibility quality and Web page complexity. We provide a set of guidelines for designing Web pages, education on Web accessibility, as well as on the computational limits of large-scale Web accessibility evaluations.

Effects of juniper essential oil on growth performance, some rumen protozoa, rumen fermentation and antioxidant blood enzyme parameters of growing Saanen kids.

PubMed

Yesilbag, D; Biricik, H; Cetin, I; Kara, C; Meral, Y; Cengiz, S S; Orman, A; Udum, D

2017-10-01

This study aimed to evaluate the effects of juniper essential oil on the growth performance, rumen fermentation parameters, rumen protozoa population, blood antioxidant enzyme parameters and faecal content in growing Saanen kids. Thirty-six male Saanen kids (36 ± 14 days of age) were used in the study. Each group consisted of 9 kids. The control group (G1) was fed with a diet that consisted of the above concentrated feed and oat hay, whereas the experimental groups consumed the same diet but with the concentrated feed uniformly sprayed with juniper essential oil 0.4 ml/kg (G2), 0.8 ml/kg (G3) or 2 ml/kg (G4). There were no differences (p > 0.05) in live weight, live weight gain or feed consumption between the control and experimental groups. There was a significant improvement (p < 0.05) in feed efficiency in the G3 group. There were no differences in the rumen pH, rumen volatile fatty acid (VFA) profile or faecal pH of the control and experimental groups. The rumen NH 3 N values were similar at the middle and end of the experiment, but at the start of the experiment, the rumen NH 3 N values differed between the control and experimental groups (p < 0.05). The faecal score value was significantly (p < 0.05) decreased in the experimental groups. The addition of juniper essential oil supplementation to the rations caused significant effects on the kids' antioxidant blood parameters. Although the superoxide dismutase (SOD) activity, total antioxidant capacity (TAC) and catalase values were significantly (p < 0.05) increased in the experimental groups (G2, G3 and G4), especially group G4, the blood glutathione peroxidase (GPX) value significantly decreased in the experimental groups. The results of this study suggest that supplementation of juniper oil is more effective on antioxidant parameters than on performance parameters and may be used as a natural antioxidant product. Journal of Animal Physiology and Animal Nutrition © 2016 Blackwell Verlag GmbH.

An automated analysis workflow for optimization of force-field parameters using neutron scattering data

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

Lynch, Vickie E.; Borreguero, Jose M.; Bhowmik, Debsindhu

Graphical abstract: - Highlights: • An automated workflow to optimize force-field parameters. • Used the workflow to optimize force-field parameter for a system containing nanodiamond and tRNA. • The mechanism relies on molecular dynamics simulation and neutron scattering experimental data. • The workflow can be generalized to any other experimental and simulation techniques. - Abstract: Large-scale simulations and data analysis are often required to explain neutron scattering experiments to establish a connection between the fundamental physics at the nanoscale and data probed by neutrons. However, to perform simulations at experimental conditions it is critical to use correct force-field (FF) parametersmore » which are unfortunately not available for most complex experimental systems. In this work, we have developed a workflow optimization technique to provide optimized FF parameters by comparing molecular dynamics (MD) to neutron scattering data. We describe the workflow in detail by using an example system consisting of tRNA and hydrophilic nanodiamonds in a deuterated water (D{sub 2}O) environment. Quasi-elastic neutron scattering (QENS) data show a faster motion of the tRNA in the presence of nanodiamond than without the ND. To compare the QENS and MD results quantitatively, a proper choice of FF parameters is necessary. We use an efficient workflow to optimize the FF parameters between the hydrophilic nanodiamond and water by comparing to the QENS data. Our results show that we can obtain accurate FF parameters by using this technique. The workflow can be generalized to other types of neutron data for FF optimization, such as vibrational spectroscopy and spin echo.« less

Calculation of Derivative Thermodynamic Hydration and Aqueous Partial Molar Properties of Ions Based on Atomistic Simulations.

PubMed

Dahlgren, Björn; Reif, Maria M; Hünenberger, Philippe H; Hansen, Niels

2012-10-09

The raw ionic solvation free energies calculated on the basis of atomistic (explicit-solvent) simulations are extremely sensitive to the boundary conditions and treatment of electrostatic interactions used during these simulations. However, as shown recently [Kastenholz, M. A.; Hünenberger, P. H. J. Chem. Phys.2006, 124, 224501 and Reif, M. M.; Hünenberger, P. H. J. Chem. Phys.2011, 134, 144104], the application of an appropriate correction scheme allows for a conversion of the methodology-dependent raw data into methodology-independent results. In this work, methodology-independent derivative thermodynamic hydration and aqueous partial molar properties are calculated for the Na(+) and Cl(-) ions at P° = 1 bar and T(-) = 298.15 K, based on the SPC water model and on ion-solvent Lennard-Jones interaction coefficients previously reoptimized against experimental hydration free energies. The hydration parameters considered are the hydration free energy and enthalpy. The aqueous partial molar parameters considered are the partial molar entropy, volume, heat capacity, volume-compressibility, and volume-expansivity. Two alternative calculation methods are employed to access these properties. Method I relies on the difference in average volume and energy between two aqueous systems involving the same number of water molecules, either in the absence or in the presence of the ion, along with variations of these differences corresponding to finite pressure or/and temperature changes. Method II relies on the calculation of the hydration free energy of the ion, along with variations of this free energy corresponding to finite pressure or/and temperature changes. Both methods are used considering two distinct variants in the application of the correction scheme. In variant A, the raw values from the simulations are corrected after the application of finite difference in pressure or/and temperature, based on correction terms specifically designed for derivative parameters at P° and T(-). In variant B, these raw values are corrected prior to differentiation, based on corresponding correction terms appropriate for the different simulation pressures P and temperatures T. The results corresponding to the different calculation schemes show that, except for the hydration free energy itself, accurate methodological independence and quantitative agreement with even the most reliable experimental parameters (ion-pair properties) are not yet reached. Nevertheless, approximate internal consistency and qualitative agreement with experimental results can be achieved, but only when an appropriate correction scheme is applied, along with a careful consideration of standard-state issues. In this sense, the main merit of the present study is to set a clear framework for these types of calculations and to point toward directions for future improvements, with the ultimate goal of reaching a consistent and quantitative description of single-ion hydration thermodynamics in molecular dynamics simulations.

Women and Development: Three Experimental Projects

ERIC Educational Resources Information Center

Clason, Carla

1975-01-01

A review of three experimental projects implemented by Unesco in the late 1960's to improve the status and equal educational opportunities of women includes: (1) Upper Volta, education for rural women; (2) Nepal, training primary school teachers; and (3) Chile, access of women to technical education. (LH)

Rendering the "Not-So-Simple" Pendulum Experimentally Accessible.

ERIC Educational Resources Information Center

Jackson, David P.

1996-01-01

Presents three methods for obtaining experimental data related to acceleration of a simple pendulum. Two of the methods involve angular position measurements and the subsequent calculation of the acceleration while the third method involves a direct measurement of the acceleration. Compares these results with theoretical calculations and…

78 FR 37228 - Cooperative Agreement To Support the Western Center for Food Safety

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-20

... Davis main campus and experimental stations provide invaluable access to one of the leading food... sites for experimental trials is instrumental to FDA receiving the most current scientifically validated... facilitate industry compliance with preventive control standards. Information gleaned from this research has...

Lessons from Helen Keller: How to Make the Comics Accessible?

PubMed

Dupire, Jérôme; Boude, Yvan

2017-01-01

This paper addresses the lack of accessibility of the comics for deaf or hard-of-hearing readers. Comics are a major cultural object, used in many different contexts with, as much as different purposes (leisure, education, advertising, etc.). We report here the results of an experimentation during a communication operation, including a regular exhibition made of panels and a digital mirroring of the contents, with extra materials and information. This digital part, accessible through our institution website, is the basement of this paper.

An overview of the EASE/ACCESS space construction demonstration

NASA Technical Reports Server (NTRS)

Levin, George M.; Ross, Jerry L.; Spring, Sherwood C.

1988-01-01

Consideration is given to the development of the Experimental Assembly of Structures in EVA/Assembly Concept for Construction of Erectable Space Structures (EASE/ACCESS) space construction demonstration, which was performed during Space Shuttle mission 61-B. The mission equipment is described and illustrated and the EASE/ACCESS mission management structure is outlined. Simulations of the assembly and disassembly in the NASA neutral buoyancy simulators were used to test the mission plans. In addition, EVA training and crew performance for the mission are discussed.

BMC Blood Disorders becomes BMC Hematology: evolving along with the hematology field.

PubMed

Chap, Christna

2013-04-10

This Editorial marks the launch of BMC Hematology, formerly known as BMC Blood Disorders, within the BMC series of journals published by BioMed Central. The scope of BMC Hematology encompasses basic, experimental and clinical research related to hematology. In this Editorial we will discuss the rationale behind this relaunch and how, as an open access journal providing unrestricted and free access to scientific and scholarly work, BMC Hematology will help disseminate research in the hematology field in a freely-accessible manner.

Description, accessibility and usage of SOIR/Venus Express atmospheric profiles of Venus distributed in VESPA (Virtual European Solar and Planetary Access)

NASA Astrophysics Data System (ADS)

Trompet, L.; Geunes, Y.; Ooms, T.; Mahieux, A.; Wilquet, V.; Chamberlain, S.; Robert, S.; Thomas, I. R.; Erard, S.; Cecconi, B.; Le Sidaner, P.; Vandaele, A. C.

2018-01-01

Venus Express SOIR profiles of pressure, temperature and number densities of different constituents of the mesosphere and lower thermosphere of Venus are the only experimental data covering the 60 km to 220 km range of altitudes at the terminator of Venus. This unique dataset is now available in the open access VESPA infrastructure. This paper describes the content of these data products and provides some use cases.

Are cytological parameters of maize landraces (Zea mays ssp. mays) adapted along an altitudinal cline?

PubMed

Fourastié, María Florencia; Gottlieb, Alexandra Marina; Poggio, Lidia; González, Graciela Esther

2018-03-01

The Northwestern Argentina (NWA) highland region is one of the southernmost areas of native maize cultivation. We studied variations of different cytological parameters, such as DNA contents, presence/absence of B chromosomes (Bs), and number and sequence composition of heterochromatic knobs in ten accessions of four maize landraces growing along a broad altitudinal cline in NWA. The aim of this work was to assess variations in cytological parameters and their relationship with the crop altitude of cultivation, in an adaptive context. The A-DNA content of the A chromosome complements showed 40% of difference between the lowest (4.5 pg) and the highest (6.3 pg) 2C value. This variation could be attributed to differences in number and size of heterochromatic knobs. Fluorescent in situ hybridization studies revealed the sequence composition of each knob, with a higher proportion of knobs composed of 180-bp repeats rather than TR-1 repeats, in all accessions. We also found numerical polymorphisms and the highest frequency of Bs reported in maize to this date. These results lead us to propose that the frequencies and doses of Bs are influenced by the landrace genotypical make-up. The Bs might be maintained in higher frequencies in those accessions having lower heterochromatin content, so as to preserve an optimal nucleotype. Furthermore, selective forces acting along the altitudinal gradient might be modulating the cytological parameters studied, as suggested by the significant correlations found among them.

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

Boussaa, S. Anas, E-mail: sabiha.anas@gmail.com; Kheloufi, A.; Kefaifi, A.

Raw materials are essential for the functioning of modern societies, and access to these raw materials is vital to the world economy. Sustainable development, both globally level, raises important new challenges associated with access and efficient use of raw materials. High purity quartz, is consider as a critical raw material and it is a rare commodity that only forms under geological conditions where a narrow set of chemical and physical parameters is fulfilled. When identified and following special beneficiation techniques, high purity quartz obtains very attractive prices and is applied in high technology sectors that currently are under rapid expansionmore » such as photovoltaic solar cells, silicon metal - oxide wafers in the semiconductor industry and long distance optical fibers that are used in communication networks. Crystalline silicon remains the principal material for photovoltaic technology. Metallurgical silicon is produced industrially by the reduction of silica with carbon in an electric arc furnace at temperatures higher than 2000 °C in the hottest parts, by a reaction that can be written ideally as: SiO{sub 2} + 2C = Si + 2CO. The aim of this study has been to test experimental methods for investigating the various physical and chemical proprieties of Hoggar quartz with different techniques: X Ray Fluorescence, infra-red spectroscopy, Scanning Electron Microscopy, Optic Microscopy, Carbon Analyzer and Vickers Hardness. The results show finally that the quartz has got good result in purity but need enrichment for the photovoltaic application.« less

Overview of Alcator C-Mod Research

NASA Astrophysics Data System (ADS)

White, A. E.

2017-10-01

Alcator C-Mod, a compact (R =0.68m, a =0.21m), high magnetic field, Bt <= 8T, tokamak accesses a variety of naturally ELM-suppressed high confinement regimes that feature extreme power density into the divertor, q|| <= 3 GW/m2, with SOL heat flux widths λq <0.5mm, exceeding conditions expected in ITER and approaching those foreseen in power plants. The unique parameter range provides much of the physics basis of a high-field, compact tokamak reactor. Research spans the topics of core transport and turbulence, RF heating and current drive, pedestal physics, scrape-off layer, divertor and plasma wall interactions. In the last experimental campaign, Super H-mode was explored and featured the highest pedestal pressures ever recorded, pped 90 kPa (90% of ITER target), consistent with EPED predictions. Optimization of naturally ELM-suppressed EDA H-modes accessed the highest volume averaged pressures ever achieved (〈p〉>2 atm), with pped 60 kPa. The SOL heat flux width has been measured at Bpol = 1.25T, confirming the Eich scaling over a broader poloidal field range than before. Multi-channel transport studies focus on the relationship between momentum transport and heat transport with perturbative experiments and new multi-scale gyrokinetic simulation validation techniques were developed. U.S. Department of Energy Grant No. DE-FC02-99ER54512.

MelanomaDB: A Web Tool for Integrative Analysis of Melanoma Genomic Information to Identify Disease-Associated Molecular Pathways

PubMed Central

Trevarton, Alexander J.; Mann, Michael B.; Knapp, Christoph; Araki, Hiromitsu; Wren, Jonathan D.; Stones-Havas, Steven; Black, Michael A.; Print, Cristin G.

2013-01-01

Despite on-going research, metastatic melanoma survival rates remain low and treatment options are limited. Researchers can now access a rapidly growing amount of molecular and clinical information about melanoma. This information is becoming difficult to assemble and interpret due to its dispersed nature, yet as it grows it becomes increasingly valuable for understanding melanoma. Integration of this information into a comprehensive resource to aid rational experimental design and patient stratification is needed. As an initial step in this direction, we have assembled a web-accessible melanoma database, MelanomaDB, which incorporates clinical and molecular data from publically available sources, which will be regularly updated as new information becomes available. This database allows complex links to be drawn between many different aspects of melanoma biology: genetic changes (e.g., mutations) in individual melanomas revealed by DNA sequencing, associations between gene expression and patient survival, data concerning drug targets, biomarkers, druggability, and clinical trials, as well as our own statistical analysis of relationships between molecular pathways and clinical parameters that have been produced using these data sets. The database is freely available at http://genesetdb.auckland.ac.nz/melanomadb/about.html. A subset of the information in the database can also be accessed through a freely available web application in the Illumina genomic cloud computing platform BaseSpace at http://www.biomatters.com/apps/melanoma-profiler-for-research. The MelanomaDB database illustrates dysregulation of specific signaling pathways across 310 exome-sequenced melanomas and in individual tumors and identifies the distribution of somatic variants in melanoma. We suggest that MelanomaDB can provide a context in which to interpret the tumor molecular profiles of individual melanoma patients relative to biological information and available drug therapies. PMID:23875173

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.

Simultaneous versus sequential optimal experiment design for the identification of multi-parameter microbial growth kinetics as a function of temperature.

PubMed

Van Derlinden, E; Bernaerts, K; Van Impe, J F

2010-05-21

Optimal experiment design for parameter estimation (OED/PE) has become a popular tool for efficient and accurate estimation of kinetic model parameters. When the kinetic model under study encloses multiple parameters, different optimization strategies can be constructed. The most straightforward approach is to estimate all parameters simultaneously from one optimal experiment (single OED/PE strategy). However, due to the complexity of the optimization problem or the stringent limitations on the system's dynamics, the experimental information can be limited and parameter estimation convergence problems can arise. As an alternative, we propose to reduce the optimization problem to a series of two-parameter estimation problems, i.e., an optimal experiment is designed for a combination of two parameters while presuming the other parameters known. Two different approaches can be followed: (i) all two-parameter optimal experiments are designed based on identical initial parameter estimates and parameters are estimated simultaneously from all resulting experimental data (global OED/PE strategy), and (ii) optimal experiments are calculated and implemented sequentially whereby the parameter values are updated intermediately (sequential OED/PE strategy). This work exploits OED/PE for the identification of the Cardinal Temperature Model with Inflection (CTMI) (Rosso et al., 1993). This kinetic model describes the effect of temperature on the microbial growth rate and encloses four parameters. The three OED/PE strategies are considered and the impact of the OED/PE design strategy on the accuracy of the CTMI parameter estimation is evaluated. Based on a simulation study, it is observed that the parameter values derived from the sequential approach deviate more from the true parameters than the single and global strategy estimates. The single and global OED/PE strategies are further compared based on experimental data obtained from design implementation in a bioreactor. Comparable estimates are obtained, but global OED/PE estimates are, in general, more accurate and reliable. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Analysis of Network Topologies Underlying Ethylene Growth Response Kinetics

PubMed Central

Prescott, Aaron M.; McCollough, Forest W.; Eldreth, Bryan L.; Binder, Brad M.; Abel, Steven M.

2016-01-01

Most models for ethylene signaling involve a linear pathway. However, measurements of seedling growth kinetics when ethylene is applied and removed have resulted in more complex network models that include coherent feedforward, negative feedback, and positive feedback motifs. The dynamical responses of the proposed networks have not been explored in a quantitative manner. Here, we explore (i) whether any of the proposed models are capable of producing growth-response behaviors consistent with experimental observations and (ii) what mechanistic roles various parts of the network topologies play in ethylene signaling. To address this, we used computational methods to explore two general network topologies: The first contains a coherent feedforward loop that inhibits growth and a negative feedback from growth onto itself (CFF/NFB). In the second, ethylene promotes the cleavage of EIN2, with the product of the cleavage inhibiting growth and promoting the production of EIN2 through a positive feedback loop (PFB). Since few network parameters for ethylene signaling are known in detail, we used an evolutionary algorithm to explore sets of parameters that produce behaviors similar to experimental growth response kinetics of both wildtype and mutant seedlings. We generated a library of parameter sets by independently running the evolutionary algorithm many times. Both network topologies produce behavior consistent with experimental observations, and analysis of the parameter sets allows us to identify important network interactions and parameter constraints. We additionally screened these parameter sets for growth recovery in the presence of sub-saturating ethylene doses, which is an experimentally-observed property that emerges in some of the evolved parameter sets. Finally, we probed simplified networks maintaining key features of the CFF/NFB and PFB topologies. From this, we verified observations drawn from the larger networks about mechanisms underlying ethylene signaling. Analysis of each network topology results in predictions about changes that occur in network components that can be experimentally tested to give insights into which, if either, network underlies ethylene responses. PMID:27625669

Influence of novel gallium complexes on the homeostasis of some biochemical and hematological parameters in rats.

PubMed

Gârban, Gabriela; Silaghi-Dumitrescu, Radu; Ioniţă, Hortensia; Gârban, Zeno; Hădărugă, Nicoleta-Gabriela; Ghibu, George-Daniel; Baltă, Cornel; Simiz, Florin-Dan; Mitar, Carmen

2013-12-01

The aim of this study was to detect possible homeostasis changes in some biochemical and hematological parameters after the administration of gallium (Ga) complexes C (24) and C (85) on an experimental animal model (Wistar strain rats). In order to observe chronobiological aspects, a morning (m) and an evening (e) animal series were constituted. Further on, each series were divided into three groups: control (C), experimental I (EI), and experimental II (EII). Both Ga complexes were solubilized in a carrier solution containing polyethylene glycol (PEG) 400, water, and ethanol. Animals of the C groups received the carrier solution by intraperitoneal injection, those from the EI groups received the solubilized C(24) gallium complex, and those of the EII groups received the solubilized C(85) gallium complex. At the end of the experiment, blood and tissue samples were taken and the following parameters were determined: serum concentration of the nonprotein nitrogenous compounds (uric acid, creatinine, and blood urea nitrogen), hematological parameters (erythrocytes, hemoglobin, leukocytes, and platelets), and the kidney tissue concentration of three essential trace elements (Fe, Cu, and Zn). With the exception of uric acid, the results revealed increased concentrations of the nonprotein nitrogenous compounds both in the morning and in the evening experimental groups. Hematological data showed increased levels of erythrocytes, hemoglobin, and leukocytes and decreased platelet levels in the experimental group given the C(24) gallium complex in the morning (EI-m) group; increased levels of leukocytes and decreased levels of the other parameters in the experimental group given the C(24) gallium complex in the evening (EI-e) group; and increased levels of all hematological parameters in the experimental groups receiving the C(85) gallium complex in the morning (EII-m) group and in the evening (EII-e) group. Decreased kidney tissue concentrations of metals were found in all the experimental groups. Fe levels were significantly decreased in the EI-m receiving the C(24) gallium complex and EII-m which received the C(85) gallium complex and in the EII-e group which received the C(85) gallium complex. In the EI-e group which received the C(24) gallium complex, a significant decrease of Cu concentration was reported.

THERMUS—A thermal model package for ROOT

NASA Astrophysics Data System (ADS)

Wheaton, S.; Cleymans, J.; Hauer, M.

2009-01-01

THERMUS is a package of C++ classes and functions allowing statistical-thermal model analyses of particle production in relativistic heavy-ion collisions to be performed within the ROOT framework of analysis. Calculations are possible within three statistical ensembles; a grand-canonical treatment of the conserved charges B, S and Q, a fully canonical treatment of the conserved charges, and a mixed-canonical ensemble combining a canonical treatment of strangeness with a grand-canonical treatment of baryon number and electric charge. THERMUS allows for the assignment of decay chains and detector efficiencies specific to each particle yield, which enables sensible fitting of model parameters to experimental data. Program summaryProgram title: THERMUS, version 2.1 Catalogue identifier: AEBW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 17 152 No. of bytes in distributed program, including test data, etc.: 93 581 Distribution format: tar.gz Programming language: C++ Computer: PC, Pentium 4, 1 GB RAM (not hardware dependent) Operating system: Linux: FEDORA, RedHat, etc. Classification: 17.7 External routines: Numerical Recipes in C [1], ROOT [2] Nature of problem: Statistical-thermal model analyses of heavy-ion collision data require the calculation of both primordial particle densities and contributions from resonance decay. A set of thermal parameters (the number depending on the particular model imposed) and a set of thermalized particles, with their decays specified, is required as input to these models. The output is then a complete set of primordial thermal quantities for each particle, together with the contributions to the final particle yields from resonance decay. In many applications of statistical-thermal models it is required to fit experimental particle multiplicities or particle ratios. In such analyses, the input is a set of experimental yields and ratios, a set of particles comprising the assumed hadron resonance gas formed in the collision and the constraints to be placed on the system. The thermal model parameters consistent with the specified constraints leading to the best-fit to the experimental data are then output. Solution method: THERMUS is a package designed for incorporation into the ROOT [2] framework, used extensively by the heavy-ion community. As such, it utilizes a great deal of ROOT's functionality in its operation. ROOT features used in THERMUS include its containers, the wrapper TMinuit implementing the MINUIT fitting package, and the TMath class of mathematical functions and routines. Arguably the most useful feature is the utilization of CINT as the control language, which allows interactive access to the THERMUS objects. Three distinct statistical ensembles are included in THERMUS, while additional options to include quantum statistics, resonance width and excluded volume corrections are also available. THERMUS provides a default particle list including all mesons (up to the K4∗ (2045)) and baryons (up to the Ω) listed in the July 2002 Particle Physics Booklet [3]. For each typically unstable particle in this list, THERMUS includes a text-file listing its decays. With thermal parameters specified, THERMUS calculates primordial thermal densities either by performing numerical integrations or else, in the case of the Boltzmann approximation without resonance width in the grand-canonical ensemble, by evaluating Bessel functions. Particle decay chains are then used to evaluate experimental observables (i.e. particle yields following resonance decay). Additional detector efficiency factors allow fine-tuning of the model predictions to a specific detector arrangement. When parameters are required to be constrained, use is made of the 'Numerical Recipes in C' [1] function which applies the Broyden globally convergent secant method of solving nonlinear systems of equations. Since the NRC software is not freely-available, it has to be purchased by the user. THERMUS provides the means of imposing a large number of constraints on the chosen model (amongst others, THERMUS can fix the baryon-to-charge ratio of the system, the strangeness density of the system and the primordial energy per hadron). Fits to experimental data are accomplished in THERMUS by using the ROOT TMinuit class. In its default operation, the standard χ function is minimized, yielding the set of best-fit thermal parameters. THERMUS allows the assignment of separate decay chains to each experimental input. In this way, the model is able to match the specific feed-down corrections of a particular data set. Running time: Depending on the analysis required, run-times vary from seconds (for the evaluation of particle multiplicities given a set of parameters) to several minutes (for fits to experimental data subject to constraints). References:W.H. Press, S.A. Teukolsky, W.T. Vetterling, B.P. Flannery, Numerical Recipes in C: The Art of Scientific Computing, Cambridge University Press, Cambridge, 2002. R. Brun, F. Rademakers, Nucl. Inst. Meth. Phys. Res. A 389 (1997) 81. See also http://root.cern.ch/. K. Hagiwara et al., Phys. Rev. D 66 (2002) 010001.