WorldWideScience

Sample records for dense molecular systems

  1. Subtle Monte Carlo Updates in Dense Molecular Systems

    DEFF Research Database (Denmark)

    Bottaro, Sandro; Boomsma, Wouter; Johansson, Kristoffer E.

    2012-01-01

    Although Markov chain Monte Carlo (MC) simulation is a potentially powerful approach for exploring conformational space, it has been unable to compete with molecular dynamics (MD) in the analysis of high density structural states, such as the native state of globular proteins. Here, we introduce...... as correlations in a multivariate Gaussian distribution. We demonstrate that our method reproduces structural variation in proteins with greater efficiency than current state-of-the-art Monte Carlo methods and has real-time simulation performance on par with molecular dynamics simulations. The presented results...... suggest our method as a valuable tool in the study of molecules in atomic detail, offering a potential alternative to molecular dynamics for probing long time-scale conformational transitions....

  2. Molecular dynamics for dense matter

    International Nuclear Information System (INIS)

    Maruyama, Toshiki; Chiba, Satoshi; Watanabe, Gentaro

    2012-01-01

    We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear “pasta”, i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid–gas phase transition is not plausible at lower temperatures. (author)

  3. Molecular dynamics for dense matter

    Science.gov (United States)

    Maruyama, Toshiki; Watanabe, Gentaro; Chiba, Satoshi

    2012-08-01

    We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear "pasta", i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid-gas phase transition is not plausible at lower temperatures.

  4. Experimental and molecular dynamics characterization of dense micro emulsion systems morphology, conductivity and SAXS

    NARCIS (Netherlands)

    Negro, E.; Latsuzbaia, R.; de Vries, A. H.; Koper, G. J. M.

    2014-01-01

    Microemulsions are exciting systems that are promising as tuneable self-assembling templating reaction vessels at the nanoscale. Determination of the nano-structure of microemulsions is, however, not trivial, and there are fundamental questions regarding their design. We were able to reproduce

  5. PHOTOCHEMICAL HEATING OF DENSE MOLECULAR GAS

    Energy Technology Data Exchange (ETDEWEB)

    Glassgold, A. E. [Astronomy Department, University of California, Berkeley, CA 94720 (United States); Najita, J. R. [National Optical Astronomy Observatory, 950 North Cherry Avenue, Tucson, AZ 85719 (United States)

    2015-09-10

    Photochemical heating is analyzed with an emphasis on the heating generated by chemical reactions initiated by the products of photodissociation and photoionization. The immediate products are slowed down by collisions with the ambient gas and then heat the gas. In addition to this direct process, heating is also produced by the subsequent chemical reactions initiated by these products. Some of this chemical heating comes from the kinetic energy of the reaction products and the rest from collisional de-excitation of the product atoms and molecules. In considering dense gas dominated by molecular hydrogen, we find that the chemical heating is sometimes as large, if not much larger than, the direct heating. In very dense gas, the total photochemical heating approaches 10 eV per photodissociation (or photoionization), competitive with other ways of heating molecular gas.

  6. Quasi-molecular processes in dense plasmas

    International Nuclear Information System (INIS)

    Younger, S.M.

    1991-01-01

    Quasi-molecular phenomena occur in dense plasmas when the interatomic spacing is comparable to the characteristic wavelength of the electrons. If the electronic states are bound, covalent orbitals arise with different excitation energies, radiative rates, and collisional rates than for isolated ions. For continuum electrons, charge localization near transient clusters of nuclei can influence many scattering and transport processes. We identify several novel consequences of quasi-molecular phenomena in plasmas and give a possible explanation of high energy features associated with helium-like emissions lines observed in recent inertial fusion experiments. 7 refs

  7. Color molecular dynamics for dense matter

    International Nuclear Information System (INIS)

    Maruyama, Toshiki; Hatsuda, Tetsuo

    2000-01-01

    We propose a microscopic approach for quark many-body system based on molecular dynamics. Using color confinement and one-gluon exchange potentials together with meson exchange potentials between quarks, we construct nucleons and nuclear/quark matter. Dynamical transition between confinement and deconfinement phases are studied at high baryon density with this molecular dynamics simulation. (author)

  8. Carbon chemistry in dense molecular clouds: Theory and observational constraints

    International Nuclear Information System (INIS)

    Blake, G.A.

    1990-01-01

    For the most part, gas phase models of the chemistry of dense molecular clouds predict the abundances of simple species rather well. However, for larger molecules and even for small systems rich in carbon these models often fail spectacularly. Researchers present a brief review of the basic assumptions and results of large scale modeling of the carbon chemistry in dense molecular clouds. Particular attention is to the influence of the gas phase C/O ratio in molecular clouds, and the likely role grains play in maintaining this ratio as clouds evolve from initially diffuse objects to denser cores with associated stellar and planetary formation. Recent spectral line surveys at centimeter and millimeter wavelengths along with selected observations in the submillimeter have now produced an accurate inventory of the gas phase carbon budget in several different types of molecular clouds, though gaps in our knowledge clearly remain. The constraints these observations place on theoretical models of interstellar chemistry can be used to gain insights into why the models fail, and show also which neglected processes must be included in more complete analyses. Looking toward the future, larger molecules are especially difficult to study both experimentally and theoretically in such dense, cold regions, and some new methods are therefore outlined which may ultimately push the detectability of small carbon chains and rings to much heavier species

  9. DENSE MOLECULAR CORES BEING EXTERNALLY HEATED

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Gwanjeong; Lee, Chang Won; Kim, Mi-Ryang [Radio Astronomy division, Korea Astronomy and Space Science Institute, 776 Daedeokdae-ro, Yuseong-gu, Daejeon, 34055 (Korea, Republic of); Gopinathan, Maheswar [Aryabhatta Research Institute of Observational Sciences, Manora Peak, Nainital 263129 (India); Jeong, Woong-Seob, E-mail: archer81@kasi.re.kr [Department of Astronomy and Space Science, University of Science and Technology, 217 Gajungro, Yuseong-gu, Daejeon, 34113 (Korea, Republic of)

    2016-06-20

    We present results of our study of eight dense cores, previously classified as starless, using infrared (3–160 μ m) imaging observations with the AKARI telescope and molecular line (HCN and N{sub 2}H{sup +}) mapping observations with the KVN telescope. Combining our results with the archival IR to millimeter continuum data, we examined the starless nature of these eight cores. Two of the eight cores are found to harbor faint protostars having luminosities of ∼0.3–4.4 L {sub ⊙}. The other six cores are found to remain starless and probably are in a dynamically transitional state. The temperature maps produced using multi-wavelength images show an enhancement of about 3–6 K toward the outer boundary of these cores, suggesting that they are most likely being heated externally by nearby stars and/or interstellar radiation fields. Large virial parameters and an overdominance of red asymmetric line profiles over the cores may indicate that the cores are set into either an expansion or an oscillatory motion, probably due to the external heating. Most of the starless cores show a coreshine effect due to the scattering of light by the micron-sized dust grains. This may imply that the age of the cores is of the order of ∼10{sup 5} years, which is consistent with the timescale required for the cores to evolve into an oscillatory stage due to external perturbation. Our observational results support the idea that the external feedback from nearby stars and/or interstellar radiation fields may play an important role in the dynamical evolution of the cores.

  10. Orbital free molecular dynamics; Approche sans orbitale des plasmas denses

    Energy Technology Data Exchange (ETDEWEB)

    Lambert, F

    2007-08-15

    The microscopic properties of hot and dense plasmas stay a field essentially studied thanks to classical theories like the One Component Plasma, models which rely on free parameters, particularly ionization. In order to investigate these systems, we have used, in this PhD work, a semi-classical model, without free parameters, that is based on coupling consistently classical molecular dynamics for the nuclei and orbital free density functional theory for the electrons. The electronic fluid is represented by a free energy entirely determined by the local density. This approximation was validated by a comparison with an ab initio technique, quantum molecular dynamics. This one is identical to the previous except for the description of the free energy that depends on a quantum-independent-particle model. Orbital free molecular dynamics was then used to compute equation of state of boron and iron plasmas in the hot and dense regime. Furthermore, comparisons with classical theories were performed on structural and dynamical properties. Finally, equation of state and transport coefficients mixing laws were studied by direct simulation of a plasma composed of deuterium and copper. (author)

  11. Breaking Dense Structures: Proving Stability of Densely Structured Hybrid Systems

    Directory of Open Access Journals (Sweden)

    Eike Möhlmann

    2015-06-01

    Full Text Available Abstraction and refinement is widely used in software development. Such techniques are valuable since they allow to handle even more complex systems. One key point is the ability to decompose a large system into subsystems, analyze those subsystems and deduce properties of the larger system. As cyber-physical systems tend to become more and more complex, such techniques become more appealing. In 2009, Oehlerking and Theel presented a (de-composition technique for hybrid systems. This technique is graph-based and constructs a Lyapunov function for hybrid systems having a complex discrete state space. The technique consists of (1 decomposing the underlying graph of the hybrid system into subgraphs, (2 computing multiple local Lyapunov functions for the subgraphs, and finally (3 composing the local Lyapunov functions into a piecewise Lyapunov function. A Lyapunov function can serve multiple purposes, e.g., it certifies stability or termination of a system or allows to construct invariant sets, which in turn may be used to certify safety and security. In this paper, we propose an improvement to the decomposing technique, which relaxes the graph structure before applying the decomposition technique. Our relaxation significantly reduces the connectivity of the graph by exploiting super-dense switching. The relaxation makes the decomposition technique more efficient on one hand and on the other allows to decompose a wider range of graph structures.

  12. Composite systems of dilute and dense couplings

    International Nuclear Information System (INIS)

    Raymond, J R; Saad, D

    2008-01-01

    Composite systems, where couplings are of two types, a combination of strong dilute and weak dense couplings of Ising spins, are examined through the replica method. The dilute and dense parts are considered to have independent canonical disordered or uniform bond distributions; mixing the models by variation of a parameter γ alongside inverse temperature β we analyse the respective thermodynamic solutions. We describe the variation in high temperature transitions as mixing occurs; in the vicinity of these transitions we exactly analyse the competing effects of the dense and sparse models. By using the replica symmetric ansatz and population dynamics we described the low temperature behaviour of mixed systems

  13. DENSE CLUMPS AND CANDIDATES FOR MOLECULAR OUTFLOWS IN W40

    Energy Technology Data Exchange (ETDEWEB)

    Shimoikura, Tomomi; Dobashi, Kazuhito [Department of Astronomy and Earth Sciences, Tokyo Gakugei University, Koganei, Tokyo 184-8501 (Japan); Nakamura, Fumitaka; Hara, Chihomi; Kawabe, Ryohei [National Astronomical Observatory of Japan, Mitaka, Tokyo 181-8588 (Japan); Tanaka, Tomohiro [Department of Physical Science, Osaka Prefecture University, Sakai, Osaka 599-8531 (Japan); Shimajiri, Yoshito [Laboratoire AIM, CEA/DSM-CNRS-Université Paris Diderot, IRFU/Service d’Astrophysique, CEA Saclay, F-91191 Gif-sur-Yvette (France); Sugitani, Kouji, E-mail: ikura@u-gakugei.ac.jp [Graduate School of Natural Sciences, Nagoya City University, Mizuho-ku, Nagoya 467-8501 (Japan)

    2015-06-20

    We report the results of the {sup 12}CO (J = 3−2) and HCO{sup +} (J = 4−3) observations of the W40 H ii region with the Atacama Submillimeter Telescope Experiment (ASTE) 10 m telescope (HPBW ≃ 22″) to search for molecular outflows and dense clumps. We found that the velocity field in the region is highly complex, consisting of at least four distinct velocity components at V{sub LSR} ≃ 3, 5, 7, and 10 km s{sup −1}. The ∼7 km s{sup −1} component represents the systemic velocity of cold gas surrounding the entire region, and causes heavy absorption in the {sup 12}CO spectra over the velocity range 6 ≲ V{sub LSR} ≲ 9 km s{sup −1}. The ∼5 and ∼10 km s{sup −1} components exhibit high {sup 12}CO temperature (≳40 K) and are found mostly around the H ii region, suggesting that these components are likely to be tracing dense gas interacting with the expanding shell around the H ii region. Based on the {sup 12}CO data, we identified 13 regions of high velocity gas, which we interpret as candidate outflow lobes. Using the HCO{sup +} data, we also identified six clumps and estimated their physical parameters. On the basis of the ASTE data and near-infrared images from 2MASS, we present an updated three-dimensional model of this region. In order to investigate molecular outflows in W40, the SiO (J = 1−0, v = 0) emission line and some other emission lines at 40 GHz were also observed with the 45 m telescope at the Nobeyama Radio Observatory, but they were not detected at the present sensitivity.

  14. Fast Solvers for Dense Linear Systems

    Energy Technology Data Exchange (ETDEWEB)

    Kauers, Manuel [Research Institute for Symbolic Computation (RISC), Altenbergerstrasse 69, A4040 Linz (Austria)

    2008-10-15

    It appears that large scale calculations in particle physics often require to solve systems of linear equations with rational number coefficients exactly. If classical Gaussian elimination is applied to a dense system, the time needed to solve such a system grows exponentially in the size of the system. In this tutorial paper, we present a standard technique from computer algebra that avoids this exponential growth: homomorphic images. Using this technique, big dense linear systems can be solved in a much more reasonable time than using Gaussian elimination over the rationals.

  15. Bonding and structure in dense multi-component molecular mixtures.

    Science.gov (United States)

    Meyer, Edmund R; Ticknor, Christopher; Bethkenhagen, Mandy; Hamel, Sebastien; Redmer, Ronald; Kress, Joel D; Collins, Lee A

    2015-10-28

    We have performed finite-temperature density functional theory molecular dynamics simulations on dense methane, ammonia, and water mixtures (CH4:NH3:H2O) for various compositions and temperatures (2000 K ≤ T ≤ 10,000 K) that span a set of possible conditions in the interiors of ice-giant exoplanets. The equation-of-state, pair distribution functions, and bond autocorrelation functions (BACF) were used to probe the structure and dynamics of these complex fluids. In particular, an improvement to the choice of the cutoff in the BACF was developed that allowed analysis refinements for density and temperature effects. We note the relative changes in the nature of these systems engendered by variations in the concentration ratios. A basic tenet emerges from all these comparisons that varying the relative amounts of the three heavy components (C,N,O) can effect considerable changes in the nature of the fluid and may in turn have ramifications for the structure and composition of various planetary layers.

  16. ON THE FORMATION OF GLYCOLALDEHYDE IN DENSE MOLECULAR CORES

    Energy Technology Data Exchange (ETDEWEB)

    Woods, Paul M.; Kelly, George; Viti, Serena [Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT (United Kingdom); Slater, Ben; Brown, Wendy A.; Puletti, Fabrizio; Burke, Daren J.; Raza, Zamaan, E-mail: paul.woods@ucl.ac.uk [Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ (United Kingdom)

    2012-05-01

    Glycolaldehyde is a simple monosaccharide sugar linked to prebiotic chemistry. Recently, it was detected in a molecular core in the star-forming region G31.41+0.31 at a reasonably high abundance. We investigate the formation of glycolaldehyde at 10 K to determine whether it can form efficiently under typical dense core conditions. Using an astrochemical model, we test five different reaction mechanisms that have been proposed in the astrophysical literature, finding that a gas-phase formation route is unlikely. Of the grain-surface formation routes, only two are efficient enough at very low temperatures to produce sufficient glycolaldehyde to match the observational estimates, with the mechanism culminating in CH{sub 3}OH + HCO being favored. However, when we consider the feasibility of these mechanisms from a reaction chemistry perspective, the second grain-surface route looks more promising, H{sub 3}CO + HCO.

  17. ON THE FORMATION OF GLYCOLALDEHYDE IN DENSE MOLECULAR CORES

    International Nuclear Information System (INIS)

    Woods, Paul M.; Kelly, George; Viti, Serena; Slater, Ben; Brown, Wendy A.; Puletti, Fabrizio; Burke, Daren J.; Raza, Zamaan

    2012-01-01

    Glycolaldehyde is a simple monosaccharide sugar linked to prebiotic chemistry. Recently, it was detected in a molecular core in the star-forming region G31.41+0.31 at a reasonably high abundance. We investigate the formation of glycolaldehyde at 10 K to determine whether it can form efficiently under typical dense core conditions. Using an astrochemical model, we test five different reaction mechanisms that have been proposed in the astrophysical literature, finding that a gas-phase formation route is unlikely. Of the grain-surface formation routes, only two are efficient enough at very low temperatures to produce sufficient glycolaldehyde to match the observational estimates, with the mechanism culminating in CH 3 OH + HCO being favored. However, when we consider the feasibility of these mechanisms from a reaction chemistry perspective, the second grain-surface route looks more promising, H 3 CO + HCO.

  18. The CO Transition from Diffuse Molecular Gas to Dense Clouds

    Science.gov (United States)

    Rice, Johnathan S.; Federman, Steven

    2017-06-01

    The atomic to molecular transitions occurring in diffuse interstellar gas surrounding molecular clouds are affected by the local physical conditions (density and temperature) and the radiation field penetrating the material. Our optical observations of CH, CH^{+}, and CN absorption from McDonald Observatory and the European Southern Observatory are useful tracers of this gas and provide the velocity structure needed for analyzing lower resolution ultraviolet observations of CO and H_{2} absorption from Far Ultraviolet Spectroscopic Explorer. We explore the changing environment between diffuse and dense gas by using the column densities and excitation temperatures from CO and H_{2} to determine the gas density. The resulting gas densities from this method are compared to densities inferred from other methods such as C_{2} and CN chemistry. The densities allow us to interpret the trends from the combined set of tracers. Groupings of sight lines, such as those toward h and χ Persei or Chameleon provide a chance for further characterization of the environment. The Chameleon region in particular helps illuminate CO-dark gas, which is not associated with emission from H I at 21 cm or from CO at 2.6 mm. Expanding this analysis to include emission data from the GOT C+ survey allows the further characterization of neutral diffuse gas, including CO-dark gas.

  19. Dense time discretization technique for verification of real time systems

    International Nuclear Information System (INIS)

    Makackas, Dalius; Miseviciene, Regina

    2016-01-01

    Verifying the real-time system there are two different models to control the time: discrete and dense time based models. This paper argues a novel verification technique, which calculates discrete time intervals from dense time in order to create all the system states that can be reached from the initial system state. The technique is designed for real-time systems specified by a piece-linear aggregate approach. Key words: real-time system, dense time, verification, model checking, piece-linear aggregate

  20. Particle identification system based on dense aerogel

    Energy Technology Data Exchange (ETDEWEB)

    Barnyakov, A.Yu. [Budker Institute of Nuclear Physics, 11, akademika Lavrentieva prospect, Novosibirsk 630090 (Russian Federation); Barnyakov, M.Yu. [Budker Institute of Nuclear Physics, 11, akademika Lavrentieva prospect, Novosibirsk 630090 (Russian Federation); Novosibirsk State Technical University, 20, Karl Marx prospect, Novosibirsk, 630092 (Russian Federation); Beloborodov, K.I., E-mail: K.I.Beloborodov@inp.nsk.su [Budker Institute of Nuclear Physics, 11, akademika Lavrentieva prospect, Novosibirsk 630090 (Russian Federation); Novosibirsk State University, 2, Pirogova Street, Novosibirsk 630090 (Russian Federation); Bobrovnikov, V.S.; Buzykaev, A.R. [Budker Institute of Nuclear Physics, 11, akademika Lavrentieva prospect, Novosibirsk 630090 (Russian Federation); Danilyuk, A.F. [Boreskov Institute of Catalysis, 5, akademika Lavrentieva prospect, Novosibirsk 630090 (Russian Federation); Golubev, V.B. [Budker Institute of Nuclear Physics, 11, akademika Lavrentieva prospect, Novosibirsk 630090 (Russian Federation); Novosibirsk State University, 2, Pirogova Street, Novosibirsk 630090 (Russian Federation); Gulevich, V.V. [Budker Institute of Nuclear Physics, 11, akademika Lavrentieva prospect, Novosibirsk 630090 (Russian Federation); Kononov, S.A.; Kravchenko, E.A. [Budker Institute of Nuclear Physics, 11, akademika Lavrentieva prospect, Novosibirsk 630090 (Russian Federation); Novosibirsk State University, 2, Pirogova Street, Novosibirsk 630090 (Russian Federation); Onuchin, A.P.; Martin, K.A. [Budker Institute of Nuclear Physics, 11, akademika Lavrentieva prospect, Novosibirsk 630090 (Russian Federation); Novosibirsk State Technical University, 20, Karl Marx prospect, Novosibirsk, 630092 (Russian Federation); Serednyakov, S.I. [Budker Institute of Nuclear Physics, 11, akademika Lavrentieva prospect, Novosibirsk 630090 (Russian Federation); Novosibirsk State University, 2, Pirogova Street, Novosibirsk 630090 (Russian Federation); and others

    2013-12-21

    A threshold Cherenkov counter based on dense aerogel with refraction index n=1.13 is described. This counter is used for kaon identification at momenta below 1 GeV/c in the SND detector, which takes data at the VEPP-2000 e{sup +}e{sup −} collider. The results of measurements of the counter efficiency using electrons, muons, pions, and kaons produced in e{sup +}e{sup −} annihilation are presented.

  1. Consequences of the Solar System passage through dense interstellar clouds

    Directory of Open Access Journals (Sweden)

    A. G. Yeghikyan

    2003-06-01

    Full Text Available Several consequences of the passage of the solar system through dense interstellar molecular clouds are discussed. These clouds, dense (more than 100 cm-3, cold (10–50 K and extended (larger than 1 pc, are characterized by a gas-to-dust mass ratio of about 100, by a specific power grain size spectrum (grain radii usually cover the range 0.001–3 micron and by an average dust-to-gas number density ratio of about 10-12. Frequently these clouds contain small-scale (10–100 AU condensations with gas concentrations ranging up to 10 5 cm-3. At their casual passage over the solar system they exert pressures very much enhanced with respect to today’s standards. Under these conditions it will occur that the Earth is exposed directly to the interstellar flow. It is shown first that even close to the Sun, at 1 AU, the cloud’s matter is only partly ionized and should mainly interact with the solar wind by charge exchange processes. Dust particles of the cloud serve as a source of neutrals, generated by the solar UV irradiation of dust grains, causing the evaporation of icy materials. The release of neutral atoms from dust grains is then followed by strong influences on the solar wind plasma flow. The behavior of the neutral gas inflow parameters is investigated by a 2-D hydrodynamic approach to model the interaction processes. Because of a reduction of the heliospheric dimension down to 1 AU, direct influence of the cloud’s matter to the terrestrial environment and atmosphere could be envisaged.Key words. Interplanetary physics (heliopause and solar wind termination; interplanetary dust; interstellar gas

  2. Consequences of the Solar System passage through dense interstellar clouds

    Directory of Open Access Journals (Sweden)

    A. G. Yeghikyan

    Full Text Available Several consequences of the passage of the solar system through dense interstellar molecular clouds are discussed. These clouds, dense (more than 100 cm-3, cold (10–50 K and extended (larger than 1 pc, are characterized by a gas-to-dust mass ratio of about 100, by a specific power grain size spectrum (grain radii usually cover the range 0.001–3 micron and by an average dust-to-gas number density ratio of about 10-12. Frequently these clouds contain small-scale (10–100 AU condensations with gas concentrations ranging up to 10 5 cm-3. At their casual passage over the solar system they exert pressures very much enhanced with respect to today’s standards. Under these conditions it will occur that the Earth is exposed directly to the interstellar flow. It is shown first that even close to the Sun, at 1 AU, the cloud’s matter is only partly ionized and should mainly interact with the solar wind by charge exchange processes. Dust particles of the cloud serve as a source of neutrals, generated by the solar UV irradiation of dust grains, causing the evaporation of icy materials. The release of neutral atoms from dust grains is then followed by strong influences on the solar wind plasma flow. The behavior of the neutral gas inflow parameters is investigated by a 2-D hydrodynamic approach to model the interaction processes. Because of a reduction of the heliospheric dimension down to 1 AU, direct influence of the cloud’s matter to the terrestrial environment and atmosphere could be envisaged.

    Key words. Interplanetary physics (heliopause and solar wind termination; interplanetary dust; interstellar gas

  3. The Dense Molecular Gas and Nuclear Activity in the ULIRG IRAS 13120–5453

    Energy Technology Data Exchange (ETDEWEB)

    Privon, G. C.; Treister, E. [Instituto de Astrofśica, Facultad de Física, Pontificia Universidad Católica de Chile, Casilla 306, Santiago 22 (Chile); Aalto, S.; Falstad, N.; Muller, S.; Costagliola, F. [Department of Earth and Space Sciences, Chalmers University of Technology, Onsala Space Observatory, SE-439 94 Onsala (Sweden); González-Alfonso, E. [Universidad de Alcalá, Departamento de Física y Matemáticas, Campus Universitario, E-28871 Alcalá de Henares, Madrid (Spain); Sliwa, K. [Max Planck Institute for Astronomy, Königstuhl 17, D-69117 Heidelberg (Germany); Armus, L. [Spitzer Science Center, California Institute of Technology, MS 220-6, Pasadena, CA, 91125 (United States); Evans, A. S. [Department of Astronomy, University of Virginia, Charlottesville, VA 22903 (United States); Garcia-Burillo, S. [Observatorio de Madrid, OAN-IGN, Alfonso XII, 3, E-28014-Madrid (Spain); Izumi, T. [Institute of Astronomy, School of Science, The University of Tokyo, 2-21-1 Osawa, Mitaka, Tokyo 181-0015 (Japan); Sakamoto, K. [Institute of Astronomy and Astrophysics, Academia Sinica, P.O. Box 23-141, 10617, Taipei, Taiwan (China); Werf, P. van der [Leiden Observatory, Leiden University, P.O. Box 9513, 2300 RA Leiden (Netherlands); Chu, J. K. [Institute for Astronomy, University of Hawaii, 2680 Woodlawn Drive, Honolulu, HI 96822 (United States)

    2017-02-01

    We present new Atacama Large Millimeter/submillimeter Array Band 7 (∼340 GHz) observations of the dense gas tracers HCN, HCO{sup +}, and CS in the local, single-nucleus, ultraluminous infrared galaxy IRAS 13120–5453. We find centrally enhanced HCN (4–3) emission, relative to HCO{sup +} (4–3), but do not find evidence for radiative pumping of HCN. Considering the size of the starburst (0.5 kpc) and the estimated supernovae rate of ∼1.2 yr{sup −1}, the high HCN/HCO{sup +} ratio can be explained by an enhanced HCN abundance as a result of mechanical heating by the supernovae, though the active galactic nucleus and winds may also contribute additional mechanical heating. The starburst size implies a high Σ{sub IR} of 4.7 × 10{sup 12} L {sub ⊙} kpc{sup −2}, slightly below predictions of radiation-pressure limited starbursts. The HCN line profile has low-level wings, which we tentatively interpret as evidence for outflowing dense molecular gas. However, the dense molecular outflow seen in the HCN line wings is unlikely to escape the Galaxy and is destined to return to the nucleus and fuel future star formation. We also present modeling of Herschel observations of the H{sub 2}O lines and find a nuclear dust temperature of ∼40 K. IRAS 13120–5453 has a lower dust temperature and Σ{sub IR} than is inferred for the systems termed “compact obscured nuclei (CONs)” (such as Arp 220 and Mrk 231). If IRAS 13120–5453 has undergone a CON phase, we are likely witnessing it at a time when the feedback has already inflated the nuclear ISM and diluted star formation in the starburst/active galactic nucleus core.

  4. MALT90 Kinematic Distances to Dense Molecular Clumps

    Energy Technology Data Exchange (ETDEWEB)

    Whitaker, J. Scott [Physics Department, Boston University, 590 Commonwealth Avenue, Boston, MA 02215 (United States); Jackson, James M.; Sanhueza, Patricio; Stephens, Ian W. [Institute for Astrophysical Research, Boston University, Boston, MA 02215 (United States); Rathborne, J. M. [CSIRO Astronomy and Space Science, P.O. Box 76, Epping NSW 1710 (Australia); Foster, J. B. [Department of Astronomy, Yale University, P.O. Box 28101, New Haven, CT 06520-8101 (United States); Contreras, Y. [Leiden Observatory, Leiden University, P.O. Box 9513, 2300 RA Leiden (Netherlands); Longmore, S. N., E-mail: scott@bu.edu [Astrophysics Research Institute, Liverpool John Moores University, Egerton Wharf, Birkenhead CH41 1LD (United Kingdom)

    2017-10-01

    Using molecular-line data from the Millimetre Astronomy Legacy Team 90 GHz Survey (MALT90), we have estimated kinematic distances to 1905 molecular clumps identified in the ATLASGAL 870 μ m continuum survey over the longitude range 295° <  l  < 350°. The clump velocities were determined using a flux-weighted average of the velocities obtained from Gaussian fits to the HCO{sup +}, HNC, and N{sub 2}H{sup +} (1–0) transitions. The near/far kinematic distance ambiguity was addressed by searching for the presence or absence of absorption or self-absorption features in 21 cm atomic hydrogen spectra from the Southern Galactic Plane Survey. Our algorithm provides an estimation of the reliability of the ambiguity resolution. The Galactic distribution of the clumps indicates positions where the clumps are bunched together, and these locations probably trace the locations of spiral arms. Several clumps fall at the predicted location of the far side of the Scutum–Centaurus arm. Moreover, a number of clumps with positive radial velocities are unambiguously located on the far side of the Milky Way at galactocentric radii beyond the solar circle. The measurement of these kinematic distances, in combination with continuum or molecular-line data, now enables the determination of fundamental parameters such as mass, size, and luminosity for each clump.

  5. Simulations of vibrational relaxation in dense molecular fluids

    International Nuclear Information System (INIS)

    Holian, B.L.

    1985-07-01

    In the understanding of high-temperatre and -pressure chemistry in explosives, first step is the study of the transfer of energy from translational degrees of freedom into internal vibrations of the molecules. We present new methods using nonequilibrium molecular dynamics (NEMD) for measuring vibrational relaxation in a diatomic fluid, where we expect a classical treatment of many-body collisions to be relevant because of the high densities (2 to 3 times compressed compared to the normal fluid) and high temperatures (2000 to 4000 K) involved behind detonation waves. NEMD techniques are discussed, including their limitations, and qualitative results presented

  6. On the nature of intramolecular vibrational energy transfer in dense molecular environments

    Energy Technology Data Exchange (ETDEWEB)

    Benten, Rebekka S. von [Institut fuer Physikalische Chemie der Universitaet Goettingen, Tammannstrasse 6, D-37077 Goettingen (Germany); Abel, Bernd, E-mail: Bernd.Abel@uni-lepzig.de [Wilhelm-Ostwald-Institut fuer Physikalische und Theoretische Chemie, Universitaet Leipzig, Linne-Strasse 2, D-04103 Leipzig (Germany)

    2010-12-09

    Graphical abstract: Mechanisms of IVR in multi-tiers of intramolecular energy levels in different molecular environments are investigated. - Abstract: Transient femtosecond-IR-pump-UV-absorption probe-spectroscopy has been employed to shed light on the nature of intramolecular vibrational energy transfer (IVR) in dense molecular environments ranging from the diluted gas phase to the liquid. A general feature in our experiments and those of others is that IVR proceeds via multiple timescales if overtones or combination vibrations of high frequency modes are excited. It has been found that collisions enhance IVR if its (slower) timescales can compete with collisions. This enhancement is, however, much more weaker and rather inefficient as opposed to the effect of collisions on intermolecular energy transfer which is well known. In a series of experiments we found that IVR depends not significantly on the average energy transferred in a collision but rather on the number of collisions. The collisions are much less efficient in affecting IVR than VET. We conclude that collision induced broadening of vibrational energy levels reduces the energy gaps and enhances existing couplings between tiers. The present results are an important step forward to rationalize and understand apparently different and not consistent results from different groups on different molecular systems between gas and liquid phases.

  7. Influence of galactic arm scale dynamics on the molecular composition of the cold and dense ISM. I. Observed abundance gradients in dense clouds

    Science.gov (United States)

    Ruaud, M.; Wakelam, V.; Gratier, P.; Bonnell, I. A.

    2018-04-01

    Aim. We study the effect of large scale dynamics on the molecular composition of the dense interstellar medium during the transition between diffuse to dense clouds. Methods: We followed the formation of dense clouds (on sub-parsec scales) through the dynamics of the interstellar medium at galactic scales. We used results from smoothed particle hydrodynamics (SPH) simulations from which we extracted physical parameters that are used as inputs for our full gas-grain chemical model. In these simulations, the evolution of the interstellar matter is followed for 50 Myr. The warm low-density interstellar medium gas flows into spiral arms where orbit crowding produces the shock formation of dense clouds, which are held together temporarily by the external pressure. Results: We show that depending on the physical history of each SPH particle, the molecular composition of the modeled dense clouds presents a high dispersion in the computed abundances even if the local physical properties are similar. We find that carbon chains are the most affected species and show that these differences are directly connected to differences in (1) the electronic fraction, (2) the C/O ratio, and (3) the local physical conditions. We argue that differences in the dynamical evolution of the gas that formed dense clouds could account for the molecular diversity observed between and within these clouds. Conclusions: This study shows the importance of past physical conditions in establishing the chemical composition of the dense medium.

  8. Carbon molecular sieve dense film membranes derived from Matrimid® for ethylene/ethane separation

    KAUST Repository

    Rungta, Meha; Xu, Liren; Koros, William J.

    2012-01-01

    Development of dense film carbon molecular sieve (CMS) membranes for ethylene/ethane (C 2H 4/C 2H 6) separation is reported. A commercial polyimide, Matrimid®, was pyrolyzed under vacuum and inert argon atmosphere, and the resultant CMS films were

  9. Green-function description of dense polymeric systems

    NARCIS (Netherlands)

    Schoot, van der P.P.A.M.

    2000-01-01

    A self-consistent Green-function description of concentrated polymer solutions and dense polymeric melts is presented. The method, which applies to both uniform and nonuniform systems, is used in this work to calculate the static structure factor of a homogeneous fluid of Gaussian model chains.

  10. Sparse symmetric preconditioners for dense linear systems in electromagnetism

    NARCIS (Netherlands)

    Carpentieri, Bruno; Duff, Iain S.; Giraud, Luc; Monga Made, M. Magolu

    2004-01-01

    We consider symmetric preconditioning strategies for the iterative solution of dense complex symmetric non-Hermitian systems arising in computational electromagnetics. In particular, we report on the numerical behaviour of the classical incomplete Cholesky factorization as well as some of its recent

  11. Dense gas and star formation in individual Giant Molecular Clouds in M31

    Science.gov (United States)

    Viaene, S.; Forbrich, J.; Fritz, J.

    2018-04-01

    Studies both of entire galaxies and of local Galactic star formation indicate a dependency of a molecular cloud's star formation rate (SFR) on its dense gas mass. In external galaxies, such measurements are derived from HCN(1-0) observations, usually encompassing many Giant Molecular Clouds (GMCs) at once. The Andromeda galaxy (M31) is a unique laboratory to study the relation of the SFR and HCN emission down to GMC scales at solar-like metallicities. In this work, we correlate our composite SFR determinations with archival HCN, HCO+, and CO observations, resulting in a sample of nine reasonably representative GMCs. We find that, at the scale of individual clouds, it is important to take into account both obscured and unobscured star formation to determine the SFR. When correlated against the dense-gas mass from HCN, we find that the SFR is low, in spite of these refinements. We nevertheless retrieve an SFR-dense-gas mass correlation, confirming that these SFR tracers are still meaningful on GMC scales. The correlation improves markedly when we consider the HCN/CO ratio instead of HCN by itself. This nominally indicates a dependency of the SFR on the dense-gas fraction, in contradiction to local studies. However, we hypothesize that this partly reflects the limited dynamic range in dense-gas mass, and partly that the ratio of single-pointing HCN and CO measurements may be less prone to systematics like sidelobes. In this case, the HCN/CO ratio would importantly be a better empirical measure of the dense-gas content itself.

  12. An extended GS method for dense linear systems

    Science.gov (United States)

    Niki, Hiroshi; Kohno, Toshiyuki; Abe, Kuniyoshi

    2009-09-01

    Davey and Rosindale [K. Davey, I. Rosindale, An iterative solution scheme for systems of boundary element equations, Internat. J. Numer. Methods Engrg. 37 (1994) 1399-1411] derived the GSOR method, which uses an upper triangular matrix [Omega] in order to solve dense linear systems. By applying functional analysis, the authors presented an expression for the optimum [Omega]. Moreover, Davey and Bounds [K. Davey, S. Bounds, A generalized SOR method for dense linear systems of boundary element equations, SIAM J. Comput. 19 (1998) 953-967] also introduced further interesting results. In this note, we employ a matrix analysis approach to investigate these schemes, and derive theorems that compare these schemes with existing preconditioners for dense linear systems. We show that the convergence rate of the Gauss-Seidel method with preconditioner PG is superior to that of the GSOR method. Moreover, we define some splittings associated with the iterative schemes. Some numerical examples are reported to confirm the theoretical analysis. We show that the EGS method with preconditioner produces an extremely small spectral radius in comparison with the other schemes considered.

  13. Dense molecular clumps associated with the Large Magellanic Cloud supergiant shells LMC 4 and LMC 5

    Energy Technology Data Exchange (ETDEWEB)

    Fujii, Kosuke; Mizuno, Norikazu [Department of Astronomy, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 133-0033 (Japan); Minamidani, Tetsuhiro [Nobeyama Radio Observatory, 462-2 Nobeyama Minamimaki-mura, Minamisaku-gun, Nagano 384-1305 (Japan); Onishi, Toshikazu; Muraoka, Kazuyuki [Department of Physical Science, Osaka Prefecture University, Gakuen 1-1, Sakai, Osaka 599-8531 (Japan); Kawamura, Akiko; Muller, Erik; Tatematsu, Ken' ichi; Hasegawa, Tetsuo; Miura, Rie E.; Ezawa, Hajime [National Astronomical Observatory of Japan, 2-21-1 Osawa, Mitaka, Tokyo 181-8588 (Japan); Dawson, Joanne [Australia Telescope National Facility, CSIRO Astronomy and Space Science, P.O. Box 76, Epping, NSW 1710 (Australia); Tosaki, Tomoka [Joetsu University of Education, Yamayashiki-machi, Joetsu, Niigata 943-8512 (Japan); Sakai, Takeshi [Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu, Tokyo 182-8585 (Japan); Tsukagoshi, Takashi [College of Science, Ibaraki University, Bunkyo 2-1-1, Mito 310-8512 (Japan); Tanaka, Kunihiko [Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Yokohama, Kanagawa 223-8522 (Japan); Fukui, Yasuo, E-mail: kosuke.fujii@nao.ac.jp [Department of Astrophysics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan)

    2014-12-01

    We investigate the effects of supergiant shells (SGSs) and their interaction on dense molecular clumps by observing the Large Magellanic Cloud (LMC) star-forming regions N48 and N49, which are located between two SGSs, LMC 4 and LMC 5. {sup 12}CO (J = 3-2, 1-0) and {sup 13}CO(J = 1-0) observations with the ASTE and Mopra telescopes have been carried out toward these regions. A clumpy distribution of dense molecular clumps is revealed with 7 pc spatial resolution. Large velocity gradient analysis shows that the molecular hydrogen densities (n(H{sub 2})) of the clumps are distributed from low to high density (10{sup 3}-10{sup 5} cm{sup –3}) and their kinetic temperatures (T {sub kin}) are typically high (greater than 50 K). These clumps seem to be in the early stages of star formation, as also indicated from the distribution of Hα, young stellar object candidates, and IR emission. We found that the N48 region is located in the high column density H I envelope at the interface of the two SGSs and the star formation is relatively evolved, whereas the N49 region is associated with LMC 5 alone and the star formation is quiet. The clumps in the N48 region typically show high n(H{sub 2}) and T {sub kin}, which are as dense and warm as the clumps in LMC massive cluster-forming areas (30 Dor, N159). These results suggest that the large-scale structure of the SGSs, especially the interaction of two SGSs, works efficiently on the formation of dense molecular clumps and stars.

  14. Toward Measuring Galactic Dense Molecular Gas Properties and 3D Distribution with Hi-GAL

    Science.gov (United States)

    Zetterlund, Erika; Glenn, Jason; Maloney, Phil

    2016-01-01

    The Herschel Space Observatory's submillimeter dust continuum survey Hi-GAL provides a powerful new dataset for characterizing the structure of the dense interstellar medium of the Milky Way. Hi-GAL observed a 2° wide strip covering the entire 360° of the Galactic plane in broad bands centered at 70, 160, 250, 350, and 500 μm, with angular resolution ranging from 10 to 40 arcseconds. We are adapting a molecular cloud clump-finding algorithm and a distance probability density function distance-determination method developed for the Bolocam Galactic Plane Survey (BGPS) to the Hi-GAL data. Using these methods we expect to generate a database of 105 cloud clumps, derive distance information for roughly half the clumps, and derive precise distances for approximately 20% of them. With five-color photometry and distances, we will measure the cloud clump properties, such as luminosities, physical sizes, and masses, and construct a three-dimensional map of the Milky Way's dense molecular gas distribution.The cloud clump properties and the dense gas distribution will provide critical ground truths for comparison to theoretical models of molecular cloud structure formation and galaxy evolution models that seek to emulate spiral galaxies. For example, such models cannot resolve star formation and use prescriptive recipes, such as converting a fixed fraction of interstellar gas to stars at a specified interstellar medium density threshold. The models should be compared to observed dense molecular gas properties and galactic distributions.As a pilot survey to refine the clump-finding and distance measurement algorithms developed for BGPS, we have identified molecular cloud clumps in six 2° × 2° patches of the Galactic plane, including one in the inner Galaxy along the line of sight through the Molecular Ring and the termination of the Galactic bar and one toward the outer Galaxy. Distances have been derived for the inner Galaxy clumps and compared to Bolocam Galactic Plane

  15. Quantum Control of Open Systems and Dense Atomic Ensembles

    Science.gov (United States)

    DiLoreto, Christopher

    Controlling the dynamics of open quantum systems; i.e. quantum systems that decohere because of interactions with the environment, is an active area of research with many applications in quantum optics and quantum computation. My thesis expands the scope of this inquiry by seeking to control open systems in proximity to an additional system. The latter could be a classical system such as metal nanoparticles, or a quantum system such as a cluster of similar atoms. By modelling the interactions between the systems, we are able to expand the accessible state space of the quantum system in question. For a single, three-level quantum system, I examine isolated systems that have only normal spontaneous emission. I then show that intensity-intensity correlation spectra, which depend directly on the density matrix of the system, can be used detect whether transitions share a common energy level. This detection is possible due to the presence of quantum interference effects between two transitions if they are connected. This effect allows one to asses energy level structure diagrams in complex atoms/molecules. By placing an open quantum system near a nanoparticle dimer, I show that the spontaneous emission rate of the system can be changed "on demand" by changing the polarization of an incident, driving field. In a three-level, Lambda system, this allows a qubit to both retain high qubit fidelity when it is operating, and to be rapidly initialized to a pure state once it is rendered unusable by decoherence. This type of behaviour is not possible in a single open quantum system; therefore adding a classical system nearby extends the overall control space of the quantum system. An open quantum system near identical neighbours in a dense ensemble is another example of how the accessible state space can be expanded. I show that a dense ensemble of atoms rapidly becomes disordered with states that are not directly excited by an incident field becoming significantly populated

  16. Dense Molecular Gas Around Protostars and in Galactic Nuclei European Workshop on Astronomical Molecules 2004

    CERN Document Server

    Baan, W A; Langevelde, H J

    2004-01-01

    The phenomena observed in young stellar objects (YSO), circumstellar regions and extra-galactic nuclei show some similarity in their morphology, dynamical and physical processes, though they may differ in scale and energy. The European Workshop on Astronomical Molecules 2004 gave astronomers a unique opportunity to discuss the links among the observational results and to generate common interpretations of the phenomena in stars and galaxies, using the available diagnostic tools such as masers and dense molecular gas. Their theoretical understanding involves physics, numerical simulations and chemistry. Including a dozen introductory reviews, topics of papers in this book also cover: maser and dense gas diagnostics and related phenomena, evolution of circumstellar regions around protostars, evolution of circumnuclear regions of active galaxies, diagnostics of the circumnuclear gas in stars and galactic nuclei. This book summarizes our present knowledge in these topics, highlights major problems to be addressed...

  17. Diffusion constant in hot and dense hadronic matter. A hadro-molecular-dynamic calculation

    International Nuclear Information System (INIS)

    Sasaki, N.; Miyamura, O.; Muroya, S.; Nonaka, C.

    2002-01-01

    We evaluate baryon/charge diffusion constant of dense and hot hadronic matter based on the molecular dynamical method by using a hadronic collision generator which describes nuclear collisions at energies 10 1-2 GeV/A and satisfies detailed balance at low temperatures (T ≤ 200 MeV). For the hot and dense hadronic matter of the temperature range, T = 100 - 200 MeV and baryon number density, n B =0.16 fm -3 - 0.32 fm -3 , charge diffusion constant D gradually increases from 0.5 fmc to 2 fmc with temperature and is almost independent of baryon number density. Based on the obtained diffusion constant we make simple discussions on the diffusion of charge fluctuation in ultrarelativistic nuclear collisions. (author)

  18. A parallel solver for huge dense linear systems

    Science.gov (United States)

    Badia, J. M.; Movilla, J. L.; Climente, J. I.; Castillo, M.; Marqués, M.; Mayo, R.; Quintana-Ortí, E. S.; Planelles, J.

    2011-11-01

    HDSS (Huge Dense Linear System Solver) is a Fortran Application Programming Interface (API) to facilitate the parallel solution of very large dense systems to scientists and engineers. The API makes use of parallelism to yield an efficient solution of the systems on a wide range of parallel platforms, from clusters of processors to massively parallel multiprocessors. It exploits out-of-core strategies to leverage the secondary memory in order to solve huge linear systems O(100.000). The API is based on the parallel linear algebra library PLAPACK, and on its Out-Of-Core (OOC) extension POOCLAPACK. Both PLAPACK and POOCLAPACK use the Message Passing Interface (MPI) as the communication layer and BLAS to perform the local matrix operations. The API provides a friendly interface to the users, hiding almost all the technical aspects related to the parallel execution of the code and the use of the secondary memory to solve the systems. In particular, the API can automatically select the best way to store and solve the systems, depending of the dimension of the system, the number of processes and the main memory of the platform. Experimental results on several parallel platforms report high performance, reaching more than 1 TFLOP with 64 cores to solve a system with more than 200 000 equations and more than 10 000 right-hand side vectors. New version program summaryProgram title: Huge Dense System Solver (HDSS) Catalogue identifier: AEHU_v1_1 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHU_v1_1.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.: 87 062 No. of bytes in distributed program, including test data, etc.: 1 069 110 Distribution format: tar.gz Programming language: Fortran90, C Computer: Parallel architectures: multiprocessors, computer clusters Operating system

  19. Oblique Multi-Camera Systems - Orientation and Dense Matching Issues

    Science.gov (United States)

    Rupnik, E.; Nex, F.; Remondino, F.

    2014-03-01

    The use of oblique imagery has become a standard for many civil and mapping applications, thanks to the development of airborne digital multi-camera systems, as proposed by many companies (Blomoblique, IGI, Leica, Midas, Pictometry, Vexcel/Microsoft, VisionMap, etc.). The indisputable virtue of oblique photography lies in its simplicity of interpretation and understanding for inexperienced users allowing their use of oblique images in very different applications, such as building detection and reconstruction, building structural damage classification, road land updating and administration services, etc. The paper reports an overview of the actual oblique commercial systems and presents a workflow for the automated orientation and dense matching of large image blocks. Perspectives, potentialities, pitfalls and suggestions for achieving satisfactory results are given. Tests performed on two datasets acquired with two multi-camera systems over urban areas are also reported.

  20. Equation of state and transport properties of warm dense helium via quantum molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Li, Zhi-Guo [College of Physical Science and Technology, Sichuan University, Chengdu 610064 (China); National Key Laboratory for Shock Wave and Detonation Physics Research, Institute of Fluid Physics, Chinese Academy of Engineering Physics, Mianyang 621900 (China); Key Laboratory of High Energy Density Physics and Technology of Ministry of Education, Sichuan University, Chengdu 610064 (China); Cheng, Yan [College of Physical Science and Technology, Sichuan University, Chengdu 610064 (China); Key Laboratory of High Energy Density Physics and Technology of Ministry of Education, Sichuan University, Chengdu 610064 (China); Chen, Qi-Feng, E-mail: chenqf01@gmail.com, E-mail: xrchen@scu.edu.cn [National Key Laboratory for Shock Wave and Detonation Physics Research, Institute of Fluid Physics, Chinese Academy of Engineering Physics, Mianyang 621900 (China); Chen, Xiang-Rong, E-mail: chenqf01@gmail.com, E-mail: xrchen@scu.edu.cn [College of Physical Science and Technology, Sichuan University, Chengdu 610064 (China)

    2016-05-15

    The equation of state, self-diffusion, and viscosity coefficients of helium have been investigated by quantum molecular dynamics (QMD) simulations in the warm dense matter regime. Our simulations are validated through the comparison with the reliable experimental data. The calculated principal and reshock Hugoniots of liquid helium are in good agreement with the gas-gun data. On this basis, we revisit the issue for helium, i.e., the possibility of the instabilities predicted by chemical models at around 2000 GPa and 10 g/cm{sup 3} along the pressure isotherms of 6309, 15 849, and 31 623 K. Our calculations show no indications of instability in this pressure-temperature region, which reconfirm the predictions of previous QMD simulations. The self-diffusion and viscosity coefficients of warm dense helium have been systematically investigated by the QMD simulations. We carefully test the finite-size effects and convergences of statistics, and obtain numerically converged self-diffusion and viscosity coefficients by using the Kubo-Green formulas. The present results have been used to evaluate the existing one component plasma models. Finally, the validation of the Stokes-Einstein relationship for helium in the warm dense regime is discussed.

  1. Testing the universality of the star-formation efficiency in dense molecular gas

    Science.gov (United States)

    Shimajiri, Y.; André, Ph.; Braine, J.; Könyves, V.; Schneider, N.; Bontemps, S.; Ladjelate, B.; Roy, A.; Gao, Y.; Chen, H.

    2017-08-01

    Context. Recent studies with, for example, Spitzer and Herschel have suggested that star formation in dense molecular gas may be governed by essentially the same "law" in Galactic clouds and external galaxies. This conclusion remains controversial, however, in large part because different tracers have been used to probe the mass of dense molecular gas in Galactic and extragalactic studies. Aims: We aimed to calibrate the HCN and HCO+ lines commonly used as dense gas tracers in extragalactic studies and to test the possible universality of the star-formation efficiency in dense gas (≳104 cm-3), SFEdense. Methods: We conducted wide-field mapping of the Aquila, Ophiuchus, and Orion B clouds at 0.04 pc resolution in the J = 1 - 0 transition of HCN, HCO+, and their isotopomers. For each cloud, we derived a reference estimate of the dense gas mass MHerschelAV > 8, as well as the strength of the local far-ultraviolet (FUV) radiation field, using Herschel Gould Belt survey data products, and estimated the star-formation rate from direct counting of the number of Spitzer young stellar objects. Results: The H13CO+(1-0) and H13CN(1-0) lines were observed to be good tracers of the dense star-forming filaments detected with Herschel. Comparing the luminosities LHCN and LHCO+ measured in the HCN and HCO+ lines with the reference masses MHerschelAV > 8, the empirical conversion factors αHerschel - HCN (=MHerschelAV > 8/LHCN) and αHerschel - HCO+ (=MHerschelAV > 8/LHCO+) were found to be significantly anti-correlated with the local FUV strength. In agreement with a recent independent study of Orion B by Pety et al., the HCN and HCO+ lines were found to trace gas down to AV ≳ 2. As a result, published extragalactic HCN studies must be tracing all of the moderate density gas down to nH2 ≲ 103 cm-3. Estimating the contribution of this moderate density gas from the typical column density probability distribution functions in nearby clouds, we obtained the following G0

  2. The Effect of an Inert Solid Reservoir on Molecular Abundances in Dense Interstellar Clouds

    Directory of Open Access Journals (Sweden)

    Kalvāns Juris

    2012-12-01

    Full Text Available The question, what is the role of freeze-out of chemical species in determining the molecular abundances in the interstellar gas is a matter of debate. We investigate a theoretical case of a dense interstellar molecular cloud core by time-dependent modeling of chemical kinetics, where grain surface reactions deliberately are not included. That means, the gas-phase and solid-phase abundances are influenced only by gas reactions, accretion on grains and desorption. We compare the results to a reference model where no accretion occurs, and only gas-phase reactions are included. We can trace that the purely physical processes of molecule accretion and desorption have major chemical consequences on the gas-phase chemistry. The main effect of introduction of the gas-grain interaction is long-term molecule abundance changes that come nowhere near an equilibrium during the typical lifetime of a prestellar core.

  3. Dense fluid self-diffusion coefficient calculations using perturbation theory and molecular dynamics

    Directory of Open Access Journals (Sweden)

    COELHO L. A. F.

    1999-01-01

    Full Text Available A procedure to correlate self-diffusion coefficients in dense fluids by using the perturbation theory (WCA coupled with the smooth-hard-sphere theory is presented and tested against molecular simulations and experimental data. This simple algebraic expression correlates well the self-diffusion coefficients of carbon dioxide, ethane, propane, ethylene, and sulfur hexafluoride. We have also performed canonical ensemble molecular dynamics simulations by using the Hoover-Nosé thermostat and the mean-square displacement formula to compute self-diffusion coefficients for the reference WCA intermolecular potential. The good agreement obtained from both methods, when compared with experimental data, suggests that the smooth-effective-sphere theory is a useful procedure to correlate diffusivity of pure substances.

  4. Penetration of Cosmic Rays into Dense Molecular Clouds: Role of Diffuse Envelopes

    Science.gov (United States)

    Ivlev, A. V.; Dogiel, V. A.; Chernyshov, D. O.; Caselli, P.; Ko, C.-M.; Cheng, K. S.

    2018-03-01

    A flux of cosmic rays (CRs) propagating through a diffuse ionized gas can excite MHD waves, thus generating magnetic disturbances. We propose a generic model of CR penetration into molecular clouds through their diffuse envelopes, and identify the leading physical processes controlling their transport on the way from a highly ionized interstellar medium to the dense interior of the cloud. The model allows us to describe a transition between a free streaming of CRs and their diffusive propagation, determined by the scattering on the self-generated disturbances. A self-consistent set of equations, governing the diffusive transport regime in an envelope and the MHD turbulence generated by the modulated CR flux, is characterized by two dimensionless numbers. We demonstrate a remarkable mutual complementarity of different mechanisms leading to the onset of the diffusive regime, which results in a universal energy spectrum of the modulated CRs. In conclusion, we briefly discuss implications of our results for several fundamental astrophysical problems, such as the spatial distribution of CRs in the Galaxy as well as the ionization, heating, and chemistry in dense molecular clouds. This paper is dedicated to the memory of Prof. Vadim Tsytovich.

  5. Further studies of the role of dense molecular clouds around outflow sources

    International Nuclear Information System (INIS)

    Verdes-Montenegro, L.; Torrelles, J.M.; Rodriguez, L.F.; Anglada, G.; Lopez, R.

    1989-01-01

    The (J,K) = (1,1) and (2,2) ammonia inversion transitions toward six regions with active star formation and evidence of gas outflows have been observed. Ammonia emission has been detected and mapped in five of these regions: AFGL 5142, AFGL 5157, AFGL 6366S, HHL 73, and S140N. NH3 (2,2) emission was detected toward the peak of the NH3 (1,1) core of AFGL 5157 and S140N. A rotational temperature of T(R) (2,2;1,1) = about 16 K was estimated for the two regions. Two new H2O masers of intense emission, S(nu) greater or equal 40 Jy, were detected toward the ammonia cores of AFGL 5142 and AFGL 5157. It is clear that the dense NH3 gas is closely associated with the star formation activities, since the ammonia cores in all peak close to the centers of activity. In particular, the AFGL 5157 ammonia condensation coincides with the geometrical center of a bipolar molecular outflow, suggesting that the exciting source is embedded in the ammonia core. In contrast, the molecular outflow in the AFGL 6366S region is located at the southeast edge of the NH3 condensation, suggesting that the exciting source is outside the ammonia core and that the morphology of the outflow may be influenced by the interaction with the dense ambient gas. 52 refs

  6. Transport coefficients for dense hard-disk systems

    NARCIS (Netherlands)

    García-Rojo, R.; Luding, S.; Brey, J.J.

    2006-01-01

    A study of the transport coefficients of a system of elastic hard disks based on the use of Helfand-Einstein expressions is reported. The self-diffusion, the viscosity, and the heat conductivity are examined with averaging techniques especially appropriate for event-driven molecular dynamics

  7. Quantum molecular dynamics of warm dense iron and a five-phase equation of state

    Science.gov (United States)

    Sjostrom, Travis; Crockett, Scott

    2018-05-01

    Through quantum molecular dynamics (QMD), utilizing both Kohn-Sham (orbital-based) and orbital-free density functional theory, we calculate the equation of state of warm dense iron in the density range 7 -30 g/cm 3 and temperatures from 1 to 100 eV. A critical examination of the iron pseudopotential is made, from which we find a significant improvement at high pressure to the previous QMD calculations of Wang et al. [Phys. Rev. E 89, 023101 (2014), 10.1103/PhysRevE.89.023101]. Our results also significantly extend the ranges of density and temperature that were attempted in that prior work. We calculate the shock Hugoniot and find very good agreement with experimental results to pressures over 20 TPa. These results are then incorporated with previous studies to generate a five-phase equation of state for iron.

  8. KINETIC TEMPERATURES OF THE DENSE GAS CLUMPS IN THE ORION KL MOLECULAR CORE

    International Nuclear Information System (INIS)

    Wang, K.-S.; Kuan, Y.-J.; Liu, S.-Y.; Charnley, Steven B.

    2010-01-01

    High angular-resolution images of the J = 18 K -17 K emission of CH 3 CN in the Orion KL molecular core were observed with the Submillimeter Array (SMA). Our high-resolution observations clearly reveal that CH 3 CN emission originates mainly from the Orion Hot Core and the Compact Ridge, both within ∼15'' of the warm and dense part of Orion KL. The clumpy nature of the molecular gas in Orion KL can also be readily seen from our high-resolution SMA images. In addition, a semi-open cavity-like kinematic structure is evident at the location between the Hot Core and the Compact Ridge. We performed excitation analysis with the 'population diagram' method toward the Hot Core, IRc7, and the northern part of the Compact Ridge. Our results disclose a non-uniform temperature structure on small scales in Orion KL, with a range of temperatures from 190-620 K in the Hot Core. Near the Compact Ridge, the temperatures are found to be 170-280 K. Comparable CH 3 CN fractional abundances of 10 -8 to 10 -7 are found around both in the Hot Core and the Compact Ridge. Such high abundances require that a hot gas phase chemistry, probably involving ammonia released from grain mantles, plays an important role in forming these CH 3 CN molecules.

  9. A comparison between integral equation theory and molecular dynamics simulations of dense, flexible polymer liquids

    International Nuclear Information System (INIS)

    Curro, J.G.; Schweizer, K.S.; Grest, G.S.; Kremer, K.; Corporate Research Science Laboratory, Exxon Research and Engineering Company, Annandale, New Jersey 08801; Institut fur Festkorperforschung der Kernforschungsanlage Julich, D-5170 Julich, Federal Republic of Germany)

    1989-01-01

    Recently we (J.G.C. and K.S.S.) formulated a tractable ''reference interaction site model'' (RISM) integral equation theory of flexible polymer liquids. The purpose of this paper is to compare the results of the theory with recent molecular dynamics simulations (G.S.G. and K.K.) on dense chain liquids of degree of polymerization N=50 and 200. Specific comparisons were made between theory and simulation for the intramolecular structure factor ω(k) and the intermolecular radial distribution function g(r) in the liquid. In particular it was possible to independently test the assumptions inherent in the RISM theory and the additional ideality approximation that was made in the initial application of the theory. This comparison was accomplished by calculating the intermolecular g(r) using the simulated intramolecular structure factor, as well as, ω(k) derived from a freely jointed chain model.The RISM theory results, using the simulated ω(k), were found to be in excellent agreement, over all length scales, with the g(r) from molecular dynamics simulations. The theoretical predictions using the ''ideal'' intramolecular structure factor tended to underestimate g(r) near contact, indicating local intramolecular expansion of the chains. This local expansion can be incorporated into the theory self consistently by including the effects of the ''medium induced'' potential on the intramolecular structure

  10. DENSE GAS IN MOLECULAR CORES ASSOCIATED WITH PLANCK GALACTIC COLD CLUMPS

    Energy Technology Data Exchange (ETDEWEB)

    Yuan, Jinghua; Li, Jin Zeng; Liu, Hong-Li [National Astronomical Observatories, Chinese Academy of Sciences, 20A Datun Road, Chaoyang District, Beijing 100012 (China); Wu, Yuefang; Chen, Ping; Hu, Runjie [Department of Astronomy, Peking University, 100871 Beijing (China); Liu, Tie [Korea Astronomy and Space Science Institute 776, Daedeokdae-ro, Yuseong-gu, Daejeon, 305-348 (Korea, Republic of); Zhang, Tianwei [Peking University Health Science Center, Xueyuan Road 38th, Haidian District, Beijing 100191 (China); Meng, Fanyi [Physikalisches Institut, Universität zu Köln, Zülpicher Str. 77, D-50937 (Germany); Wang, Ke, E-mail: ywu@pku.edu.cn [European Southern Observatory, Karl-Schwarzschild-Str. 2, D-85748 Garching bei München (Germany)

    2016-03-20

    We present the first survey of dense gas toward Planck Galactic Cold Clumps (PGCCs). Observations in the J = 1–0 transitions of HCO{sup +} and HCN toward 621 molecular cores associated with PGCCs were performed using the Purple Mountain Observatory’s 13.7 m telescope. Among them, 250 sources were detected, including 230 cores detected in HCO{sup +} and 158 in HCN. Spectra of the J = 1–0 transitions from {sup 12}CO, {sup 13}CO, and C{sup 18}O at the centers of the 250 cores were extracted from previous mapping observations to construct a multi-line data set. The significantly low detection rate of asymmetric double-peaked profiles, together with the good consistency among central velocities of CO, HCO{sup +}, and HCN spectra, suggests that the CO-selected Planck cores are more quiescent than classical star-forming regions. The small difference between line widths of C{sup 18}O and HCN indicates that the inner regions of CO-selected Planck cores are no more turbulent than the exterior. The velocity-integrated intensities and abundances of HCO{sup +} are positively correlated with those of HCN, suggesting that these two species are well coupled and chemically connected. The detected abundances of both HCO{sup +} and HCN are significantly lower than values in other low- to high-mass star-forming regions. The low abundances may be due to beam dilution. On the basis of an inspection of the parameters given in the PGCC catalog, we suggest that there may be about 1000 PGCC objects that have a sufficient reservoir of dense gas to form stars.

  11. Magnetic diffusion and ionization fractions in dense molecular clouds: The role of charged grains

    International Nuclear Information System (INIS)

    Elmegreen, B.G.

    1979-01-01

    The ionization fraction is determined for dense molecular clouds by considering charge exchange, dissociative recombination, radiative recombination, and collisions between grains and charged species. The inclusion of grains tends to lower the ionization fraction for a given cosmic-ray ionization rate zeta and metal depletion delta. The observed values of the ionization fractions in dense cloud cores (i.e., -8 ) are obtained for reasonable values of zeta=10 -17 s -1 and delta=0.1.For temperatures less than 30 K, each grain alternates in charge between -e and 0. The resulting motion of the grains in a self-graviting cloud that contains a magnetic field will be periodic; their response to electromagnetic forces will depend on their instantaneous charge. This complex motion is calculated in order to determine the average viscous force between the grains and the neutral molecules in the cloud. The grain-neutral viscous force combines with the ion-neutral viscous force to regulate the motion of the neutral molecules relative to the magnetic field. The resultant The result neutral drift leads to a diffusion of the magnetic field out of the cloud. The time scale for this diffusion is calculated. Grain-related viscous forces dominate ion-related forces for ionization fractions less than 5 x 10 -8 . The magnetic diffusion time in a self-gravitating cloud that is supported by an internal magnetic field is shown to be at least 10 times larger thanthe free-fall time even when the ionization fraction is much less than 10 -8

  12. Seeing the Forest Through the Trees: The Distribution and Properties of Dense Molecular Gas in the Milky Way Galaxy

    Science.gov (United States)

    Ellsworth-Bowers, Timothy P.

    The Milky Way Galaxy serves as a vast laboratory for studying the dynamics and evolution of the dense interstellar medium and the processes of and surrounding massive star formation. From our vantage point within the Galactic plane, however, it has been extremely difficult to construct a coherent picture of Galactic structure; we cannot see the forest for the trees. The principal difficulties in studying the structure of the Galactic disk have been obscuration by the ubiquitous dust and molecular gas and confusion between objects along a line of sight. Recent technological advances have led to large-scale blind surveys of the Galactic plane at (sub-)millimeter wavelengths, where Galactic dust is generally optically thin, and have opened a new avenue for studying the forest. The Bolocam Galactic Plane Survey (BGPS) observed over 190 deg 2 of the Galactic plane in dust continuum emission near lambda = 1.1 mm, producing a catalog of over 8,000 dense molecular cloud structures across a wide swath of the Galactic disk. Deriving the spatial distribution and physical properties of these objects requires knowledge of distance, a component lacking in the data themselves. This thesis presents a generalized Bayesian probabilistic distance estimation method for dense molecular cloud structures, and demonstrates it with the BGPS data set. Distance probability density functions (DPDFs) are computed from kinematic distance likelihoods (which may be double- peaked for objects in the inner Galaxy) and an expandable suite of prior information to produce a comprehensive tally of our knowledge (and ignorance) of the distances to dense molecular cloud structures. As part of the DPDF formalism, this thesis derives several prior DPDFs for resolving the kinematic distance ambiguity in the inner Galaxy. From the collection of posterior DPDFs, a set of objects with well-constrained distance estimates is produced for deriving Galactic structure and the physical properties of dense molecular

  13. Transport coefficients for dense hard-disk systems.

    Science.gov (United States)

    García-Rojo, Ramón; Luding, Stefan; Brey, J Javier

    2006-12-01

    A study of the transport coefficients of a system of elastic hard disks based on the use of Helfand-Einstein expressions is reported. The self-diffusion, the viscosity, and the heat conductivity are examined with averaging techniques especially appropriate for event-driven molecular dynamics algorithms with periodic boundary conditions. The density and size dependence of the results are analyzed, and comparison with the predictions from Enskog's theory is carried out. In particular, the behavior of the transport coefficients in the vicinity of the fluid-solid transition is investigated and a striking power law divergence of the viscosity with density is obtained in this region, while all other examined transport coefficients show a drop in that density range in relation to the Enskog's prediction. Finally, the deviations are related to shear band instabilities and the concept of dilatancy.

  14. Molecular Line Studies of Ballistic Stellar Interlopers Burrowing through Dense Interstellar Clouds

    Science.gov (United States)

    Rosen, Anna; Sahai, R.; Claussen, M.; Morris, M.

    2010-01-01

    When an intermediate-mass star speeds through a dense interstellar cloud at a high velocity, it can produce a cometary or bow shock structure due to the cloud being impacted by the intense stellar wind. This class of objects, recently discovered in an HST imaging survey, has been dubbed "ballistic stellar interlopers" (Sahai et al. 2009). Using the ARO's 12m and SMT 10m millimeter-wave dishes, we have obtained molecular line emission data towards 10 stellar interloper sources, in order to identify and characterize the dense clouds with which the interlopers are interacting. We have made small "on-the-fly" maps in the 12CO (J=2-1) and 13CO (J=2-1) lines for each cloud, and obtained spectra of high-density tracers such as N2H+ (J=3-2), HCO+ (J=3-2), CN(N=2-1), and SO(J=5-4), which probe a range of physical conditions in the interstellar clouds being impacted by the interlopers. The data have been reduced and analyzed, and preliminary estimates of the cloud temperatures (9-22 K) and 13CO optical depths (0.18-0.37) have been made. The maps, which show the emission as a function of radial velocity and spatial offset from the location of the interlopers, have helped us distinguish between the clouds interacting with the interlopers, and those which are unrelated but happen to lie along the line of sight. These data will now enable us to carry out high-resolution mm-wave interferometric observations of the interlopers in the future. This research was performed at JPL under the Minority Education Initiatives program. RS and MM were funded by a Long Term Space Astrophysics award from NASA for this work. The National Radio Astronomy Observatory is a facility of the National Science Foundation operated under cooperative agreement by Associated Universities, Inc. Special thanks goes to John Bieging and Bill Peters of the Arizona Radio Observatory.

  15. Observation of visible emission from the molecular helium ion in the afterglow of a dense helium Z-pinch plasma

    International Nuclear Information System (INIS)

    Tucker, J.E.; Brake, M.L.; Gilgenbach, R.M.

    1986-01-01

    The authors present the results of axial and radial time resolved visible emission spectroscopy from the afterglow of a dense helium Z-pinch. These results show that the visible emissions in the pinch afterglow are dominated by line emissions from molecular helium and He II. Axial spectroscopy measurements show the occurrence of several absorption bands which cannot be identified as molecular or atomic helium nor impurities from the discharge chamber materials. The authors believe that these absorption bands are attributable to the molecular helium ion which is present in the discharge. The molecular ion has been observed by others in low pressure and temperature helium discharges directly by means of mass spectrometry and indirectly by the presence of helium atoms in the 2/sup 3/S state, (the He 2/sup 3/S state is believed to result from molecular helium ion recombination). However, the molecular helium ion has not previously been observed spectroscopically

  16. Large Area, High Resolution N2H+ studies of dense gas in the Perseus and Serpens Molecular Clouds

    Science.gov (United States)

    Storm, Shaye; Mundy, Lee

    2014-07-01

    Star formation in molecular clouds occurs over a wide range of spatial scales and physical densities. Understanding the origin of dense cores thus requires linking the structure and kinematics of gas and dust from cloud to core scales. The CARMA Large Area Star Formation Survey (CLASSy) is a CARMA Key Project that spectrally imaged five diverse regions of the Perseus and Serpens Molecular Clouds in N2H+ (J=1-0), totaling over 800 square arcminutes. The observations have 7’’ angular resolution (~0.01 pc spatial resolution) to probe dense gas down to core scales, and use combined interferometric and single-dish data to fully recover line emission up to parsec scales. CLASSy observations are complete, and this talk will focus on three science results. First, the dense gas in regions with existing star formation has complex hierarchical structure. We present a non-binary dendrogram analysis for all regions and show that dense gas hierarchy correlates with star formation activity. Second, well-resolved velocity information for each dendrogram-identified structure allows a new way of looking at linewidth-size relations in clouds. Specifically, we find that non-thermal line-of-sight velocity dispersion varies weakly with structure size, while rms variation in the centroid velocity increases strongly with structure size. We argue that the typical line-of-sight depth of a cloud can be estimated from these relations, and that our regions have depths that are several times less than their extent on the plane of the sky. This finding is consistent with numerical simulations of molecular cloud turbulence that show that high-density sheets are a generic result. Third, N2H+ is a good tracer of cold, dense gas in filaments; we resolve multiple beams across many filaments, some of which are narrower than 0.1 pc. The centroid velocity fields of several filaments show gradients perpendicular to their major axis, which is a common feature in filaments formed from numerical

  17. Carbon molecular sieve dense film membranes derived from Matrimid® for ethylene/ethane separation

    KAUST Repository

    Rungta, Meha

    2012-04-01

    Development of dense film carbon molecular sieve (CMS) membranes for ethylene/ethane (C 2H 4/C 2H 6) separation is reported. A commercial polyimide, Matrimid®, was pyrolyzed under vacuum and inert argon atmosphere, and the resultant CMS films were characterized using pure C 2H 4 and C 2H 6 permeation at 35 °C, 50 psia feed pressure. The effects on C 2H 4/C 2H 6 separation caused by different final vacuum pyrolysis temperatures from 500 to 800 °C are reported. For all pyrolysis temperatures separation surpassed the estimated \\'upper bound\\' solution processable polymer line for C 2H 4 permeability vs. C 2H 4/C 2H 6 selectivity. C 2H 4 permeability decreased and selectivity increased with increasing pyrolysis temperature until 650-675 °C where an optimum combination of C 2H 4 permeability ∼14-15 Barrer with C 2H 4/C 2H 6 selectivity ∼12 was observed. A modified heating rate protocol for 675 °C showed further increase in permeability with no selectivity loss. CMS films produced from argon pyrolysis showed results comparable to vacuum pyrolysis. Further, mixed gas (63.2 mol% C 2H 4 + 36.8 mol% C 2H 6) permeation showed a slightly lower C 2H 4 permeability with C 2H 4/C 2H 6 selectivity increase rather than a decrease that is often seen with polymers. The high selectivity of these membranes was shown to arise from a high \\'entropic selection\\' indicating that the \\'slimmer\\' ethylene molecule has significant advantage over ethane in passing through the rigid \\'slit-shaped\\' CMS pore structure. © 2011 Elsevier Ltd. All rights reserved.

  18. Synergetics of molecular systems

    CERN Document Server

    Lupichev, Lev N; Kadantsev, Vasiliy N

    2014-01-01

    Synergetics is the quantitative study of multicomponent systems that exhibit nonlinear dynamics and cooperativity. This book specifically considers basic models of the nonlinear dynamics of molecular systems and discusses relevant applications in biological physics and the polymer sciences.Emphasis is placed on specific solutions to the dynamical equations that correspond to the coherent formation of spatial-temporal structures, such as solitons, kinks and breathers, in particular. The emergence of these patterns in molecular structures provides a variety of information on their structural pro

  19. Novel OSNR Monitoring Technique in Dense WDM Systems using Inherently Generated CW Monitoring Channels

    DEFF Research Database (Denmark)

    Petersen, Martin Nordal

    2007-01-01

    We present a simple, yet effective OSNR monitoring technique based on an inherent effect in the optical modulator. Highly accurate OSNR monitoring is demonstrated in a 40 Gb/s dense WDM system with 50 GHz channel spacing.......We present a simple, yet effective OSNR monitoring technique based on an inherent effect in the optical modulator. Highly accurate OSNR monitoring is demonstrated in a 40 Gb/s dense WDM system with 50 GHz channel spacing....

  20. Multi-charge-state molecular dynamics and self-diffusion coefficient in the warm dense matter regime

    Science.gov (United States)

    Fu, Yongsheng; Hou, Yong; Kang, Dongdong; Gao, Cheng; Jin, Fengtao; Yuan, Jianmin

    2018-01-01

    We present a multi-ion molecular dynamics (MIMD) simulation and apply it to calculating the self-diffusion coefficients of ions with different charge-states in the warm dense matter (WDM) regime. First, the method is used for the self-consistent calculation of electron structures of different charge-state ions in the ion sphere, with the ion-sphere radii being determined by the plasma density and the ion charges. The ionic fraction is then obtained by solving the Saha equation, taking account of interactions among different charge-state ions in the system, and ion-ion pair potentials are computed using the modified Gordon-Kim method in the framework of temperature-dependent density functional theory on the basis of the electron structures. Finally, MIMD is used to calculate ionic self-diffusion coefficients from the velocity correlation function according to the Green-Kubo relation. A comparison with the results of the average-atom model shows that different statistical processes will influence the ionic diffusion coefficient in the WDM regime.

  1. Implementing a New Dense Symmetric Eigensolver on Multicore Systems

    KAUST Repository

    Sukkari, Dalal E.

    2013-07-01

    We present original advanced architecture implementations of the QDWHeig algo- rithm for solving dense symmetric eigenproblems. The algorithm (Y. Nakatsukasa and N. J. Higham, 2012) performs a spectral divide-and-conquer, which recursively divides the matrix into smaller submatrices by finding an invariant subspace for a subset of the spectrum. The main contribution of this thesis is to enhance the per- formance of QDWHeig algorithm by relying on a high performance kernels from PLASMA [1] and LAPACK [2]. We demonstrate the quality of the eigenpairs that are computed with the QDWHeig algorithm for many matrix types with different eigenvalue clustering. We then implement QDWHeig using kernels from LAPACK and PLASMA, and compare its performance against other divide-and-conquer sym- metric eigensolvers. The main part of QDWHeig is finding a polar decomposition. We introduce mixed precision to enhance the performance in finding the polar decom- position. Our evaluation considers speed and accuracy of the computed eigenvalues. Some applications require finding only a subspectrum of the eigenvalues; therefore we modify the algorithm to find the eigenpairs in a given interval of interest. An ex- perimental study shows significant improvement on the performance of our algorithm using mixed precision and PLASMA routines.

  2. Dense Molecular Gas and H2O Maser Emission in Galaxies F ...

    Indian Academy of Sciences (India)

    2School of Physics and Telecommunication Engineering, South China Normal University,. Guangzhou 510006, China. ∗ e-mail: jszhang@gzhu.edu.cn. Abstract. Extragalactic H2O masers have been found in dense gas cir- cumstance in off-nuclear star formation regions or within parsecs of. Active Galactic Nuclei (AGNs).

  3. The influence of molecular complexity on expanding flows of ideal and dense gases

    NARCIS (Netherlands)

    Harinck, J.; Guardone, A.; Colonna, P.

    2009-01-01

    This paper presents an investigation about the effect of the complexity of a fluid molecule on the fluid dynamic quantities sound speed, velocity, and Mach number in isentropic expansions. Ideal-gas and dense-gas expansions are analyzed, using the polytropic ideal gas and Van der Waals thermodynamic

  4. Equation of state of dense plasmas: Orbital-free molecular dynamics as the limit of quantum molecular dynamics for high-Z elements

    Energy Technology Data Exchange (ETDEWEB)

    Danel, J.-F.; Blottiau, P.; Kazandjian, L.; Piron, R.; Torrent, M. [CEA, DAM, DIF, 91297 Arpajon (France)

    2014-10-15

    The applicability of quantum molecular dynamics to the calculation of the equation of state of a dense plasma is limited at high temperature by computational cost. Orbital-free molecular dynamics, based on a semiclassical approximation and possibly on a gradient correction, is a simulation method available at high temperature. For a high-Z element such as lutetium, we examine how orbital-free molecular dynamics applied to the equation of state of a dense plasma can be regarded as the limit of quantum molecular dynamics at high temperature. For the normal mass density and twice the normal mass density, we show that the pressures calculated with the quantum approach converge monotonically towards those calculated with the orbital-free approach; we observe a faster convergence when the orbital-free approach includes the gradient correction. We propose a method to obtain an equation of state reproducing quantum molecular dynamics results up to high temperatures where this approach cannot be directly implemented. With the results already obtained for low-Z plasmas, the present study opens the way for reproducing the quantum molecular dynamics pressure for all elements up to high temperatures.

  5. Diamonds in dense molecular clouds - A challenge to the standard interstellar medium paradigm

    Science.gov (United States)

    Allamandola, L. J.; Sandford, S. A.; Tielens, A. G. G. M.; Herbst, T. M.

    1993-01-01

    Observations of a newly discovered infrared C-H stretching band indicate that interstellar diamond-like material appears to be characteristic of dense clouds. In sharp contrast, the spectral signature of dust in the diffuse interstellar medium is dominated by -CH2- and -CH3 groups. This dichotomy in the aliphatic organic component between the dense and diffuse media challenges standard assumptions about the processes occurring in, and interactions between, these two media. The ubiquity of this interstellar diamond-like material rules out models for meteoritic diamond formation in unusual circumstellar environments and implies that the formation of the diamond-like material is associated with common interstellar processes or stellar types.

  6. Transport Coefficients for dense hard-disk systems

    NARCIS (Netherlands)

    Garcia-Rojo, R.; Luding, Stefan; Brey, J. Javier; Ooms, G.; Hoogendoorn, C.J.

    2007-01-01

    A study of the transport coefficients of a system of elastic hard disks, based on the use of Helfand-Einstein expressions is reported. The pressure, the viscosity, and the heat conductivity are examined for different density and system-size. While most transport coefficients agree with Enskog theory

  7. Molecular characterization of thymidine kinase mutants of human cells induced by densely ionizing radiation

    Energy Technology Data Exchange (ETDEWEB)

    Kronenberg, A; Little, J B

    1989-04-01

    In order to characterize the nature of mutants induced by densely ionizing radiations at an autosomal locus, the authors have isolated a series of 99 thymidine kinase (tk) mutants of human TK6 lymphoblastoid cells iraadiated with either fast neutrons or accelerated argon ions. Individual muant clones were examined for alterations in their restriction fragment pattern after hybridization with a human cDNA probe for tk. A restriction fragment length polymorphism (RFLP) allowed identification of the active tk allele. Among the neutron-induced mutants, 34/52 exhibited loss of the previously active allele while 6/52 exhibited intragenic rearrangements. Among the argon-induced mutants 27/46 exhibited allele loses and 10/46 showed rearrangements within the tk locus. The remaining mutants had restriction patterns indistinguishable from the TK6 parent. Each of the mutant clones was further examined for structural alterations within the c-erbAl locus which has been localized to chromosome 17q11-q22, at some unknown distance from the human tk locus at chromosome 17q21-q22. A substantial proportion (54%) of tk mutants induced by densely ionizing radiation showed loss of the c-erb locus on the homologous chromosome, suggesting that the mutations involve large-scale genetic changes. (author). 51 refs.; 2 figs.; 6 tabs.

  8. Ice Chemistry in Interstellar Dense Molecular Clouds, Protostellar Disks, and Comets

    Science.gov (United States)

    Sandford, Scott A.

    2015-01-01

    Despite the low temperatures (T less than 20K), low pressures, and low molecular densities found in much of the cosmos, considerable chemistry is expected to occur in many astronomical environments. Much of this chemistry happens in icy grain mantles on dust grains and is driven by ionizing radiation. This ionizing radiation breaks chemical bonds of molecules in the ices and creates a host of ions and radicals that can react at the ambient temperature or when the parent ice is subsequently warmed. Experiments that similar these conditions have demonstrated a rich chemistry associated with these environments that leads to a wide variety of organic products. Many of these products are of considerable interest to astrobiology. For example, the irradiation of simple ices has been shown to abiotically produce amino acids, nucleobases, quinones, and amphiphiles, all compounds that play key roles in modern biochemistry. This suggests extraterrestrial chemistry could have played a role in the origin of life on Earth and, by extension, do so on planets in other stellar systems.

  9. Statistical properties of the dense hydrogen plasma: An ab initio molecular dynamics investigation

    International Nuclear Information System (INIS)

    Kohanoff, J.; Hansen, J.P.

    1995-12-01

    The hydrogen plasma is studied in the very high density (atomic and metallic) regime by extensive ab initio Molecular Dynamics simulations. Protons are treated classically, and electrons in the Born-Oppenheimer framework, within the local density approximation (LDA). Densities and temperatures studied fall within the strong coupling regime of the protons. We address the question of the validity of linear screening, and we find it to yield a reasonably good description up to r s approx. 0.5, but already too crude for r s = 1 (with r s = (3/4πρ) 1/3 the ion sphere radius). Finite-size and Brillouin zone sampling effects in metallic systems are studied and shown to be very delicate also in the fluid (liquid metal) phase. We analyse the low-temperature phase diagram and the melting transition. A remarkably fast decrease of the melting temperature with decreasing density is found, up to a point when it becomes comparable to the Fermi temperature of the protons. The possible vicinity of a triple point bcc-hcp(fcc)- liquid is discussed in the region of r s approx. 1.1 and T approx. 100 - 200K. The fluid phase is studied in detail for several temperatures. Proton-electron correlations show a weak temperature dependence, and proton-proton correlations exhibit a well-defined first coordination shell, thus characterizing fluid H in this regime as an atomic liquid. Diffusion coefficients are compared to the values for the one-component plasma. Vibrational densities of states (VDOS) show a plasmon renormalization due to electron screening, and the presence of a plasmon-coupled single-particle mode up to very high temperatures. Collective modes are studied through dynamical structure factors. In close relationship with the VDOS, the simulations reveal the remarkable persistent of a weakly damped high-frequency ion acoustic mode, even under conditions of strong electron screening. The possibility of using this observation as a diagnostic for the plasma phase transition to the

  10. High-Spatial-Multiplicity Multicore Fibers for Future Dense Space-Division-Multiplexing Systems

    DEFF Research Database (Denmark)

    Matsuo, Shoichiro; Takenaga, Katsuhiro; Sasaki, Yusuke

    2016-01-01

    Multicore fibers and few-mode fibers have potential application in realizing dense-space-division multiplexing systems. However, there are some tradeoff requirements for designing the fibers. In this paper, the tradeoff requirements such as spatial channel count, crosstalk, differential mode dela...

  11. Structure and properties of simple molecular systems at very high density

    International Nuclear Information System (INIS)

    LeSar, R.

    1989-01-01

    The use of computer simulations in the study of molecular systems at very high density is reviewed. Applications to the thermodynamics of dense fluid nitrogen and phase transitions in solid oxygen are presented. The effects of changes in the atomic electronic structure on the equation of state of very dense helium are discussed. 19 refs., 2 figs

  12. Direct coupling of a dense (supercritical) gas chromatograph to a mass spectrometer using a supersonic molecular beam interface

    International Nuclear Information System (INIS)

    Randall, L.G.; Wahrhaftig, A.L.

    1981-01-01

    A detecting mass spectrometer has been successfully coupled to a dense gas (supercritical fluid) chromatograph to produce an instrument (DGC/MS) that may be an alternative to high performance liquid chromatograph/mass spectrometer instruments (HPLC/MS) and gas chromatograph/mass spectrometer instruments (GC/MS) for analysis of involatile and/or thermally labile compounds. The mobile phase in DGC is a gas held at temperatures above the critical temperature and at pressures sufficient to obtain nearly liquid-like densities. DGC combines advantages of GC and HPLC: rapid separations, moderate operating temperatures, and analysis of involatile compounds. An advantage unique to DGC is the solvent power dependence upon pressure. While several groups have studied DGC, its development has been limited by the lack of a sensitive and selective detector. Hence, work has been directed towards the design and construction of a DGC/MS resulting in a trial instrument capable of chromatographic pressures of at least 300 atm and temperatures from 10 0 to 60 0 C. The DGC/MS coupling has been accomplished by the use of a supersonic molecular beam interface. This application of molecular beam formation appears to be unique in its requirements of a large pressure ratio (approx.10 8 ), low flow rates, and low final pressures. The authors outline characteristics of supersonic jets and molecular beams pertinent to the design of such an instrument. The interface which uses pumping speeds of 2400 and 1200 l/s in the beam forming chambers is described in detail, while the other components: the detecting mass spectrometer, the dense gas supply, and the DGC: are briefly described. Preliminary work with this instrument has established the feasibility of DGC/MS as an analytical technique and further development is recommended

  13. TWO MASS DISTRIBUTIONS IN THE L 1641 MOLECULAR CLOUDS: THE HERSCHEL CONNECTION OF DENSE CORES AND FILAMENTS IN ORION A

    International Nuclear Information System (INIS)

    Polychroni, D.; Schisano, E.; Elia, D.; Molinari, S.; Turrini, D.; Rygl, K. L. J.; Benedettini, M.; Busquet, G.; Di Giorgio, A. M.; Pestalozzi, M.; Pezzuto, S.; Roy, A.; André, Ph.; Hennemann, M.; Hill, T.; Könyves, V.; Martin, P.; Di Francesco, J.; Arzoumanian, D.; Bontemps, S.

    2013-01-01

    We present Herschel survey maps of the L 1641 molecular clouds in Orion A. We extracted both the filaments and dense cores in the region. We identified which of the dense sources are proto- or pre-stellar, and studied their association with the identified filaments. We find that although most (71%) of the pre-stellar sources are located on filaments there, is still a significant fraction of sources not associated with such structures. We find that these two populations (on and off the identified filaments) have distinctly different mass distributions. The mass distribution of the sources on the filaments is found to peak at 4 M ☉ and drives the shape of the core mass function (CMF) at higher masses, which we fit with a power law of the form dN/dlogM∝M –1.4±0.4 . The mass distribution of the sources off the filaments, on the other hand, peaks at 0.8 M ☉ and leads to a flattening of the CMF at masses lower than ∼4 M ☉ . We postulate that this difference between the mass distributions is due to the higher proportion of gas that is available in the filaments, rather than in the diffuse cloud

  14. TWO MASS DISTRIBUTIONS IN THE L 1641 MOLECULAR CLOUDS: THE HERSCHEL CONNECTION OF DENSE CORES AND FILAMENTS IN ORION A

    Energy Technology Data Exchange (ETDEWEB)

    Polychroni, D. [Department of Astrophysics, University of Athens, Astronomy and Mechanics, Faculty of Physics, Panepistimiopolis, 15784 Zografos, Athens (Greece); Schisano, E.; Elia, D.; Molinari, S.; Turrini, D.; Rygl, K. L. J.; Benedettini, M.; Busquet, G.; Di Giorgio, A. M.; Pestalozzi, M.; Pezzuto, S. [Istituto di Astrofisica e Planetologia Spaziali (INAF-IAPS), via del Fosso del Cavaliere 100, I-00133 Roma (Italy); Roy, A.; André, Ph.; Hennemann, M.; Hill, T.; Könyves, V. [Laboratoire AIM, CEA/IRFU CNRS/INSU Université Paris Diderot, Paris-Saclay, F-91191 Gif-sur-Yvette (France); Martin, P. [Canadian Institute for Theoretical Astrophysics, University of Toronto, 60 St. George Street, Toronto, ON M5S 3H8 (Canada); Di Francesco, J. [National Research Council Canada, 5071 West Saanich Road, Victoria, BC V9E 2E7 (Canada); Arzoumanian, D. [IAS, CNRS (UMR 8617), Université Paris-Sud, Bâtiment 121, F-91400 Orsay (France); Bontemps, S., E-mail: dpolychroni@phys.uoa.gr [Université de Bordeaux, Laboratoire d' Astrophysique de Bordeaux, CNRS/INSU, UMR 5804, BP 89, F-33271, Floirac Cedex (France); and others

    2013-11-10

    We present Herschel survey maps of the L 1641 molecular clouds in Orion A. We extracted both the filaments and dense cores in the region. We identified which of the dense sources are proto- or pre-stellar, and studied their association with the identified filaments. We find that although most (71%) of the pre-stellar sources are located on filaments there, is still a significant fraction of sources not associated with such structures. We find that these two populations (on and off the identified filaments) have distinctly different mass distributions. The mass distribution of the sources on the filaments is found to peak at 4 M {sub ☉} and drives the shape of the core mass function (CMF) at higher masses, which we fit with a power law of the form dN/dlogM∝M {sup –1.4±0.4}. The mass distribution of the sources off the filaments, on the other hand, peaks at 0.8 M {sub ☉} and leads to a flattening of the CMF at masses lower than ∼4 M {sub ☉}. We postulate that this difference between the mass distributions is due to the higher proportion of gas that is available in the filaments, rather than in the diffuse cloud.

  15. Directly calculated electrical conductivity of hot dense hydrogen from molecular dynamics simulation beyond Kubo-Greenwood formula

    Science.gov (United States)

    Ma, Qian; Kang, Dongdong; Zhao, Zengxiu; Dai, Jiayu

    2018-01-01

    Electrical conductivity of hot dense hydrogen is directly calculated by molecular dynamics simulation with a reduced electron force field method, in which the electrons are represented as Gaussian wave packets with fixed sizes. Here, the temperature is higher than electron Fermi temperature ( T > 300 eV , ρ = 40 g / cc ). The present method can avoid the Coulomb catastrophe and give the limit of electrical conductivity based on the Coulomb interaction. We investigate the effect of ion-electron coupled movements, which is lost in the static method such as density functional theory based Kubo-Greenwood framework. It is found that the ionic dynamics, which contributes to the dynamical electrical microfield and electron-ion collisions, will reduce the conductivity significantly compared with the fixed ion configuration calculations.

  16. Diagnostic system for EUV radiation measurements from dense xenon plasma generated by MPC

    International Nuclear Information System (INIS)

    Petrov, Yu.V.; Garkusha, I.E.; Solyakov, D.G.; Marchenko, A.K.; Chebotarev, V.V.; Ladygina, M.S.; Staltsov, V.V.; Yelisyeyev, D.V.; Hassanein, A.

    2011-01-01

    Magnetoplasma compressor (MPC) of compact geometry has been designed and tested as a source of EUV radiation. In present paper diagnostic system for registration of EUV radiation is described. It was applied for radiation measurements in different operation modes of MPC. The registration system was designed on the base of combination of different types of AXUV photodiodes. Possibility to minimize the influence of electrons and ions flows from dense plasma stream on AXUV detector performance and results of the measurements has been discussed.

  17. Ballistic near-field heat transport in dense many-body systems

    Science.gov (United States)

    Latella, Ivan; Biehs, Svend-Age; Messina, Riccardo; Rodriguez, Alejandro W.; Ben-Abdallah, Philippe

    2018-01-01

    Radiative heat transport mediated by near-field interactions is known to be superdiffusive in dilute, many-body systems. Here we use a generalized Landauer theory of radiative heat transfer in many-body planar systems to demonstrate a nonmonotonic transition from superdiffusive to ballistic transport in dense systems. We show that such a transition is associated to a change of the polarization of dominant modes. Our findings are complemented by a quantitative study of the relaxation dynamics of the system in the different regimes of heat transport. This result could have important consequences on thermal management at nanoscale of many-body systems.

  18. Determination of the friction coefficient via the force autocorrelation function. A molecular dynamics investigation for a dense Lennard-Jones fluid

    International Nuclear Information System (INIS)

    Vogelsang, R.; Hoheisel, C.

    1987-01-01

    For a large region of dense fluid states of a Lennard-Jones system, they have calculated the friction coefficient by the force autocorrelation function of a Brownian-type particle by molecular dynamics (MD). The time integral over the force autocorrelation function showed an interesting behavior and the expected plateau value when the mass of the Brownian particle was chosen to be about a factor of 100 larger than the mass of the fluid particle. Sufficient agreement was found for the friction coefficient calculated by this way and that obtained by calculations of the self-diffusion coefficient using the common relation between these coefficients. Furthermore, a modified friction coefficient was determined by integration of the force autocorrelation function up to the first maximum. This coefficient can successfully be used to derive a reasonable soft part of the friction coefficient necessary for the Rice-Allnatt approximation for the shear velocity and simple liquids

  19. The electronic and optical properties of warm dense nitrous oxide using quantum molecular dynamics simulations

    International Nuclear Information System (INIS)

    Zhang Yujuan; Wang Cong; Zhang Ping

    2012-01-01

    First-principles molecular-dynamics simulations based on density-functional theory have been used to study the electronic and optical properties of fluid nitrous oxide under extreme conditions. Systematic descriptions of pair-correlation function, atomic structure, and the charge density distribution are used to investigate the dissociation of fluid nitrous oxide. The electrical and optical properties are derived from the Kubo-Greenwood formula. It is found that the nonmetal-metal transition for fluid nitrous oxide can be directly associated to the dissociation and has significant influence on the optical properties of the fluid.

  20. Quantum molecular dynamics simulations of warm dense lithium hydride: Examination of mixing rules

    International Nuclear Information System (INIS)

    Horner, D. A.; Kress, J. D.; Collins, L. A.

    2008-01-01

    We have performed a systematic study of lithium hydride (LiH) in a density range from half to twice solid for temperatures from 0.5 to 3.0 eV using quantum molecular dynamics (QMD) methods and have tested density and pressure mixing rules for obtaining equations of state and optical properties such as frequency-dependent absorption coefficients and Rosseland mean opacities. The QMD simulations for the full LiH fluid served as a benchmark against which to assess the rules. In general, the mixing rule based on the pressure matching produces superior equations of state and mean opacities for the mixture except at the very lowest temperatures and densities. However, the frequency-dependent absorption coefficients displayed considerable differences in some frequency ranges except at the highest temperatures and densities

  1. Shear viscosity for dense plasmas by equilibrium molecular dynamics in asymmetric Yukawa ionic mixtures

    Science.gov (United States)

    Haxhimali, Tomorr; Rudd, Robert E.; Cabot, William H.; Graziani, Frank R.

    2015-11-01

    We present molecular dynamics (MD) calculations of shear viscosity for asymmetric mixed plasma for thermodynamic conditions relevant to astrophysical and inertial confinement fusion plasmas. Specifically, we consider mixtures of deuterium and argon at temperatures of 100-500 eV and a number density of 1025 ions/cc. The motion of 30 000-120 000 ions is simulated in which the ions interact via the Yukawa (screened Coulomb) potential. The electric field of the electrons is included in this effective interaction; the electrons are not simulated explicitly. Shear viscosity is calculated using the Green-Kubo approach with an integral of the shear stress autocorrelation function, a quantity calculated in the equilibrium MD simulations. We systematically study different mixtures through a series of simulations with increasing fraction of the minority high-Z element (Ar) in the D-Ar plasma mixture. In the more weakly coupled plasmas, at 500 eV and low Ar fractions, results from MD compare very well with Chapman-Enskog kinetic results. In the more strongly coupled plasmas, the kinetic theory does not agree well with the MD results. We develop a simple model that interpolates between classical kinetic theories at weak coupling and the Murillo Yukawa viscosity model at higher coupling. This hybrid kinetics-MD viscosity model agrees well with the MD results over the conditions simulated, ranging from moderately weakly coupled to moderately strongly coupled asymmetric plasma mixtures.

  2. Study of shear viscosity for dense plasmas by equilibrium molecular dynamics in asymmetric Yukawa ionic mixtures

    Science.gov (United States)

    Haxhimali, Tomorr; Rudd, Robert; Cabot, William; Graziani, Frank

    2015-11-01

    We present molecular dynamics (MD) calculations of shear viscosity for asymmetric mixed plasma for thermodynamic conditions relevant to astrophysical and Inertial Confinement Fusion plasmas. Specifically, we consider mixtures of deuterium and argon at temperatures of 100-500 eV and a number density of 1025 ions/cc. The motion of 30000-120000 ions is simulated in which the ions interact via the Yukawa (screened Coulomb) potential. The electric field of the electrons is included in this effective interaction. Shear viscosity is calculated using the Green-Kubo approach with an integral of the shear stress autocorrelation function, a quantity calculated in the equilibrium MD simulations. We study different mixtures with increasing fraction of the minority high-Z element (Ar) in the D-Ar plasma mixture. In the more weakly coupled plasmas, at 500 eV and low Ar fractions, results from MD compare very well with Chapman-Enskog kinetic results. We introduce a model that interpolates between a screened-plasma kinetic theory at weak coupling and the Murillo Yukawa viscosity model at higher coupling. This hybrid kinetics-MD viscosity model agrees well with the MD results over the conditions simulated. This work was performed under the auspices of the US Dept. of Energy by Lawrence Livermore National Security, LLC under Contract DE-AC52-07NA27344.

  3. A Systematic Method of Interconnection Optimization for Dense-Array Concentrator Photovoltaic System

    Science.gov (United States)

    Siaw, Fei-Lu

    2013-01-01

    This paper presents a new systematic approach to analyze all possible array configurations in order to determine the most optimal dense-array configuration for concentrator photovoltaic (CPV) systems. The proposed method is fast, simple, reasonably accurate, and very useful as a preliminary study before constructing a dense-array CPV panel. Using measured flux distribution data, each CPV cells' voltage and current values at three critical points which are at short-circuit, open-circuit, and maximum power point are determined. From there, an algorithm groups the cells into basic modules. The next step is I-V curve prediction, to find the maximum output power of each array configuration. As a case study, twenty different I-V predictions are made for a prototype of nonimaging planar concentrator, and the array configuration that yields the highest output power is determined. The result is then verified by assembling and testing of an actual dense-array on the prototype. It was found that the I-V curve closely resembles simulated I-V prediction, and measured maximum output power varies by only 1.34%. PMID:24453823

  4. A Systematic Method of Interconnection Optimization for Dense-Array Concentrator Photovoltaic System

    Directory of Open Access Journals (Sweden)

    Fei-Lu Siaw

    2013-01-01

    Full Text Available This paper presents a new systematic approach to analyze all possible array configurations in order to determine the most optimal dense-array configuration for concentrator photovoltaic (CPV systems. The proposed method is fast, simple, reasonably accurate, and very useful as a preliminary study before constructing a dense-array CPV panel. Using measured flux distribution data, each CPV cells’ voltage and current values at three critical points which are at short-circuit, open-circuit, and maximum power point are determined. From there, an algorithm groups the cells into basic modules. The next step is I-V curve prediction, to find the maximum output power of each array configuration. As a case study, twenty different I-V predictions are made for a prototype of nonimaging planar concentrator, and the array configuration that yields the highest output power is determined. The result is then verified by assembling and testing of an actual dense-array on the prototype. It was found that the I-V curve closely resembles simulated I-V prediction, and measured maximum output power varies by only 1.34%.

  5. A systematic method of interconnection optimization for dense-array concentrator photovoltaic system.

    Science.gov (United States)

    Siaw, Fei-Lu; Chong, Kok-Keong

    2013-01-01

    This paper presents a new systematic approach to analyze all possible array configurations in order to determine the most optimal dense-array configuration for concentrator photovoltaic (CPV) systems. The proposed method is fast, simple, reasonably accurate, and very useful as a preliminary study before constructing a dense-array CPV panel. Using measured flux distribution data, each CPV cells' voltage and current values at three critical points which are at short-circuit, open-circuit, and maximum power point are determined. From there, an algorithm groups the cells into basic modules. The next step is I-V curve prediction, to find the maximum output power of each array configuration. As a case study, twenty different I-V predictions are made for a prototype of nonimaging planar concentrator, and the array configuration that yields the highest output power is determined. The result is then verified by assembling and testing of an actual dense-array on the prototype. It was found that the I-V curve closely resembles simulated I-V prediction, and measured maximum output power varies by only 1.34%.

  6. THE BLAST SURVEY OF THE VELA MOLECULAR CLOUD: PHYSICAL PROPERTIES OF THE DENSE CORES IN VELA-D

    International Nuclear Information System (INIS)

    Olmi, Luca; Angles-Alcazar, Daniel; Ade, Peter A. R.; Griffin, Matthew; Hargrave, Peter C.; Bock, James J.; Chapin, Edward L.; Halpern, Mark; Marsden, Gaelen; De Luca, Massimo; Devlin, Mark J.; Dicker, Simon; Klein, Jeff; Elia, Davide; Fazio, Giovanni G.; Marengo, Massimo; Giannini, Teresa; Lorenzetti, Dario; Gundersen, Joshua O.; Hughes, David H.

    2009-01-01

    The Balloon-borne Large-Aperture Submillimeter Telescope (BLAST) carried out a 250, 350, and 500 μm survey of the galactic plane encompassing the Vela Molecular Ridge, with the primary goal of identifying the coldest dense cores possibly associated with the earliest stages of star formation. Here, we present the results from observations of the Vela-D region, covering about 4 deg 2 , in which we find 141 BLAST cores. We exploit existing data taken with the Spitzer MIPS, IRAC, and SEST-SIMBA instruments to constrain their (single-temperature) spectral energy distributions, assuming a dust emissivity index β = 2.0. This combination of data allows us to determine the temperature, luminosity, and mass of each BLAST core, and also enables us to separate starless from protostellar sources. We also analyze the effects that the uncertainties on the derived physical parameters of the individual sources have on the overall physical properties of starless and protostellar cores, and we find that there appear to be a smooth transition from the pre- to the protostellar phase. In particular, for protostellar cores we find a correlation between the MIPS24 flux, associated with the central protostar, and the temperature of the dust envelope. We also find that the core mass function of the Vela-D cores has a slope consistent with other similar (sub)millimeter surveys.

  7. The Effects of Stellar Dynamics on the Evolution of Young, Dense Stellar Systems

    Science.gov (United States)

    Belkus, H.; van Bever, J.; Vanbeveren, D.

    In this paper, we report on first results of a project in Brussels in which we study the effects of stellar dynamics on the evolution of young dense stellar systems using 3 decades of expertise in massive-star evolution and our population (number and spectral) synthesis code. We highlight an unconventionally formed object scenario (UFO-scenario) for Wolf Rayet binaries and study the effects of a luminous blue variable-type instability wind mass-loss formalism on the formation of intermediate-mass black holes.

  8. Parametric dense stereovision implementation on a system-on chip (SoC).

    Science.gov (United States)

    Gardel, Alfredo; Montejo, Pablo; García, Jorge; Bravo, Ignacio; Lázaro, José L

    2012-01-01

    This paper proposes a novel hardware implementation of a dense recovery of stereovision 3D measurements. Traditionally 3D stereo systems have imposed the maximum number of stereo correspondences, introducing a large restriction on artificial vision algorithms. The proposed system-on-chip (SoC) provides great performance and efficiency, with a scalable architecture available for many different situations, addressing real time processing of stereo image flow. Using double buffering techniques properly combined with pipelined processing, the use of reconfigurable hardware achieves a parametrisable SoC which gives the designer the opportunity to decide its right dimension and features. The proposed architecture does not need any external memory because the processing is done as image flow arrives. Our SoC provides 3D data directly without the storage of whole stereo images. Our goal is to obtain high processing speed while maintaining the accuracy of 3D data using minimum resources. Configurable parameters may be controlled by later/parallel stages of the vision algorithm executed on an embedded processor. Considering hardware FPGA clock of 100 MHz, image flows up to 50 frames per second (fps) of dense stereo maps of more than 30,000 depth points could be obtained considering 2 Mpix images, with a minimum initial latency. The implementation of computer vision algorithms on reconfigurable hardware, explicitly low level processing, opens up the prospect of its use in autonomous systems, and they can act as a coprocessor to reconstruct 3D images with high density information in real time.

  9. Extended application of Kohn-Sham first-principles molecular dynamics method with plane wave approximation at high energy—From cold materials to hot dense plasmas

    International Nuclear Information System (INIS)

    Zhang, Shen; Kang, Wei; Wang, Hongwei; Zhang, Ping; He, X. T.

    2016-01-01

    An extended first-principles molecular dynamics (FPMD) method based on Kohn-Sham scheme is proposed to elevate the temperature limit of the FPMD method in the calculation of dense plasmas. The extended method treats the wave functions of high energy electrons as plane waves analytically and thus expands the application of the FPMD method to the region of hot dense plasmas without suffering from the formidable computational costs. In addition, the extended method inherits the high accuracy of the Kohn-Sham scheme and keeps the information of electronic structures. This gives an edge to the extended method in the calculation of mixtures of plasmas composed of heterogeneous ions, high-Z dense plasmas, lowering of ionization potentials, X-ray absorption/emission spectra, and opacities, which are of particular interest to astrophysics, inertial confinement fusion engineering, and laboratory astrophysics.

  10. Extended application of Kohn-Sham first-principles molecular dynamics method with plane wave approximation at high energy—From cold materials to hot dense plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Shen; Kang, Wei, E-mail: weikang@pku.edu.cn [Center for Applied Physics and Technology, HEDPS, Peking University, Beijing 100871 (China); College of Engineering, Peking University, Beijing 100871 (China); Wang, Hongwei [College of Engineering, Peking University, Beijing 100871 (China); Zhang, Ping, E-mail: zhang-ping@iapcm.ac.cn [Center for Applied Physics and Technology, HEDPS, Peking University, Beijing 100871 (China); LCP, Institute of Applied Physics and Computational Mathematics, Beijing 100088 (China); He, X. T., E-mail: xthe@iapcm.ac.cn [Center for Applied Physics and Technology, HEDPS, and IFSA Collaborative Innovation Center of MoE, Peking University, Beijing 100871 (China); Institute of Applied Physics and Computational Mathematics, Beijing 100088 (China)

    2016-04-15

    An extended first-principles molecular dynamics (FPMD) method based on Kohn-Sham scheme is proposed to elevate the temperature limit of the FPMD method in the calculation of dense plasmas. The extended method treats the wave functions of high energy electrons as plane waves analytically and thus expands the application of the FPMD method to the region of hot dense plasmas without suffering from the formidable computational costs. In addition, the extended method inherits the high accuracy of the Kohn-Sham scheme and keeps the information of electronic structures. This gives an edge to the extended method in the calculation of mixtures of plasmas composed of heterogeneous ions, high-Z dense plasmas, lowering of ionization potentials, X-ray absorption/emission spectra, and opacities, which are of particular interest to astrophysics, inertial confinement fusion engineering, and laboratory astrophysics.

  11. Sustainable energy policy for Asia: Mitigating systemic hurdles in a highly dense city

    International Nuclear Information System (INIS)

    Ng, Artie W.; Nathwani, Jatin

    2010-01-01

    Greenhouse gas emission (GHG) has been increasingly a sensitive issue that is across border and impacting global public interests. While the use of renewable energy technology is perceived as a means to enable delivery of emission-free solutions, its penetration into the energy market has not been timely and significant enough as projected in prior studies. This article aims to illustrate some of the critical hurdles as the policy makers start formulating environmentally friendly energy consumption means for the public in Asian economies. In particular, through analyzing the characteristics in the case of Hong Kong, the authors unveil the challenges for this highly dense city to reach a landscape of alternative energy resources for its transition into a sustainable economy. Education and engagement with the public about a sustainable future, alignment of stakeholders' economic interests and absorption capacity of emerging technologies are argued as the three main challenges and initiatives in mitigating the underlying systemic hurdles that remain to be overcome. Observing the current responses to the externalities by the policy makers in Hong Kong, this study articulates the critical challenges to mitigate these specific systemic hurdles embedded in the existing infrastructure of a highly dense city. Possible mitigating measures to enable deployment of integrative sustainable energy solutions in dealing with climate change are discussed. (author)

  12. Detuning-induced stimulated Raman adiabatic passage in dense two-level systems

    Science.gov (United States)

    Deng, Li; Lin, Gongwei; Niu, Yueping; Gong, Shangqing

    2018-05-01

    We investigate the coherence generation in dense two-level systems under detuning-induced stimulated Raman adiabatic passage (D-STIRAP). In the dense two-level system, the near dipole-dipole (NDD) interaction should be taken into consideration. With the increase in the strength of the NDD interaction, it is found that a switchlike transition of the generated coherence from maximum value to zero appears. Meanwhile, the adiabatic condition of the D-STIRAP is destroyed in the presence of the NDD interaction. In order to avoid the sudden decrease in the generated coherence and maintain the maximum value, we can use stronger detuning pulse or pump pulse, between which increasing the intensity of the detuning pulse is of more efficiency. Except for taking advantage of such maximum coherence in the high density case into areas like enhancing the four-wave mixing process, we also point out that the phenomenon of the coherence transition can be applied as an optical switch.

  13. Architecture of a modular, multichannel readout system for dense electrochemical biosensor microarrays

    International Nuclear Information System (INIS)

    Ramfos, Ioannis; Birbas, Alexios; Blionas, Spyridon

    2015-01-01

    The architecture of a modular, multichannel readout system for dense electrochemical microarrays, targeting Lab-on-a-Chip applications, is presented. This approach promotes efficient component reusability through a hybrid multiplexing methodology, maintaining high levels of sampling performance and accuracy. Two readout modes are offered, which can be dynamically interchanged following signal profiling, to cater for both rapid signal transitions and weak current responses. Additionally, functional extensions to the described architecture are discussed, which provide the system with multi-biasing capabilities. A prototype integrated circuit of the proposed architecture’s analog core and a supporting board were implemented to verify the working principles. The system was evaluated using standard loads, as well as electrochemical sensor arrays. Through a range of operating conditions and loads, the prototype exhibited a highly linear response and accurately delivered the readout of input signals with fast transitions and wide dynamic ranges. (paper)

  14. OBLIQUE MULTI-CAMERA SYSTEMS – ORIENTATION AND DENSE MATCHING ISSUES

    Directory of Open Access Journals (Sweden)

    E. Rupnik

    2014-03-01

    Full Text Available The use of oblique imagery has become a standard for many civil and mapping applications, thanks to the development of airborne digital multi-camera systems, as proposed by many companies (Blomoblique, IGI, Leica, Midas, Pictometry, Vexcel/Microsoft, VisionMap, etc.. The indisputable virtue of oblique photography lies in its simplicity of interpretation and understanding for inexperienced users allowing their use of oblique images in very different applications, such as building detection and reconstruction, building structural damage classification, road land updating and administration services, etc. The paper reports an overview of the actual oblique commercial systems and presents a workflow for the automated orientation and dense matching of large image blocks. Perspectives, potentialities, pitfalls and suggestions for achieving satisfactory results are given. Tests performed on two datasets acquired with two multi-camera systems over urban areas are also reported.

  15. Parallelized event chain algorithm for dense hard sphere and polymer systems

    International Nuclear Information System (INIS)

    Kampmann, Tobias A.; Boltz, Horst-Holger; Kierfeld, Jan

    2015-01-01

    We combine parallelization and cluster Monte Carlo for hard sphere systems and present a parallelized event chain algorithm for the hard disk system in two dimensions. For parallelization we use a spatial partitioning approach into simulation cells. We find that it is crucial for correctness to ensure detailed balance on the level of Monte Carlo sweeps by drawing the starting sphere of event chains within each simulation cell with replacement. We analyze the performance gains for the parallelized event chain and find a criterion for an optimal degree of parallelization. Because of the cluster nature of event chain moves massive parallelization will not be optimal. Finally, we discuss first applications of the event chain algorithm to dense polymer systems, i.e., bundle-forming solutions of attractive semiflexible polymers

  16. Densely crosslinked polycarbosiloxanes .2. Thermal and mechanical properties

    NARCIS (Netherlands)

    Flipsen, T.A C; Derks, R.; van der Vegt, H.A.; Stenekes, R.; Pennings, A.J; Hadziioannou, G

    1997-01-01

    The thermal and mechanical properties of two densely crosslinked polycarbosiloxane systems were investigated in relation to the molecular structure. The networks were prepared from functional branched prepolymers and crosslinked via a hydrosilylation curing reaction. The prepolymers having only

  17. Parametric Dense Stereovision Implementation on a System-on Chip (SoC

    Directory of Open Access Journals (Sweden)

    Pablo Montejo

    2012-02-01

    Full Text Available This paper proposes a novel hardware implementation of a dense recovery of stereovision 3D measurements. Traditionally 3D stereo systems have imposed the maximum number of stereo correspondences, introducing a large restriction on artificial vision algorithms. The proposed system-on-chip (SoC provides great performance and efficiency, with a scalable architecture available for many different situations, addressing real time processing of stereo image flow. Using double buffering techniques properly combined with pipelined processing, the use of reconfigurable hardware achieves a parametrisable SoC which gives the designer the opportunity to decide its right dimension and features. The proposed architecture does not need any external memory because the processing is done as image flow arrives. Our SoC provides 3D data directly without the storage of whole stereo images. Our goal is to obtain high processing speed while maintaining the accuracy of 3D data using minimum resources. Configurable parameters may be controlled by later/parallel stages of the vision algorithm executed on an embedded processor. Considering hardware FPGA clock of 100 MHz, image flows up to 50 frames per second (fps of dense stereo maps of more than 30,000 depth points could be obtained considering 2 Mpix images, with a minimum initial latency. The implementation of computer vision algorithms on reconfigurable hardware, explicitly low level processing, opens up the prospect of its use in autonomous systems, and they can act as a coprocessor to reconstruct 3D images with high density information in real time.

  18. Optical characterization of nonimaging dish concentrator for the application of dense-array concentrator photovoltaic system.

    Science.gov (United States)

    Tan, Ming-Hui; Chong, Kok-Keong; Wong, Chee-Woon

    2014-01-20

    Optimization of the design of a nonimaging dish concentrator (NIDC) for a dense-array concentrator photovoltaic system is presented. A new algorithm has been developed to determine configuration of facet mirrors in a NIDC. Analytical formulas were derived to analyze the optical performance of a NIDC and then compared with a simulated result obtained from a numerical method. Comprehensive analysis of optical performance via analytical method has been carried out based on facet dimension and focal distance of the concentrator with a total reflective area of 120 m2. The result shows that a facet dimension of 49.8 cm, focal distance of 8 m, and solar concentration ratio of 411.8 suns is the most optimized design for the lowest cost-per-output power, which is US$1.93 per watt.

  19. Multiple solutions to dense systems in radar scattering using a preconditioned block GMRES solver

    Energy Technology Data Exchange (ETDEWEB)

    Boyse, W.E. [Advanced Software Resources, Inc., Santa Clara, CA (United States)

    1996-12-31

    Multiple right-hand sides occur in radar scattering calculations in the computation of the simulated radar return from a body at a large number of angles. Each desired angle requires a right-hand side vector to be computed and the solution generated. These right-hand sides are naturally smooth functions of the angle parameters and this property is utilized in a novel way to compute solutions an order of magnitude faster than LINPACK The modeling technique addressed is the Method of Moments (MOM), i.e. a boundary element method for time harmonic Maxwell`s equations. Discretization by this method produces general complex dense systems of rank 100`s to 100,000`s. The usual way to produce the required multiple solutions is via LU factorization and solution routines such as found in LINPACK. Our method uses the block GMRES iterative method to directly iterate a subset of the desired solutions to convergence.

  20. Nonequilibrium mode-coupling theory for dense active systems of self-propelled particles.

    Science.gov (United States)

    Nandi, Saroj Kumar; Gov, Nir S

    2017-10-25

    The physics of active systems of self-propelled particles, in the regime of a dense liquid state, is an open puzzle of great current interest, both for statistical physics and because such systems appear in many biological contexts. We develop a nonequilibrium mode-coupling theory (MCT) for such systems, where activity is included as a colored noise with the particles having a self-propulsion force f 0 and a persistence time τ p . Using the extended MCT and a generalized fluctuation-dissipation theorem, we calculate the effective temperature T eff of the active fluid. The nonequilibrium nature of the systems is manifested through a time-dependent T eff that approaches a constant in the long-time limit, which depends on the activity parameters f 0 and τ p . We find, phenomenologically, that this long-time limit is captured by the potential energy of a single, trapped active particle (STAP). Through a scaling analysis close to the MCT glass transition point, we show that τ α , the α-relaxation time, behaves as τ α ∼ f 0 -2γ , where γ = 1.74 is the MCT exponent for the passive system. τ α may increase or decrease as a function of τ p depending on the type of active force correlations, but the behavior is always governed by the same value of the exponent γ. Comparison with the numerical solution of the nonequilibrium MCT and simulation results give excellent agreement with scaling analysis.

  1. Thunderstorm monitoring with VLF network and super dense meteorological observation system

    Science.gov (United States)

    Takahashi, Yukihiro; Sato, Mitsuteru

    2015-04-01

    It's not easy to understand the inside structure and developing process of thunderstorm only with existing meteorological instruments since its horizontal extent of the storm cell is sometimes smaller than an order of 10 km while one of the densest ground network in Japan, AMEDAS, consists of sites located every 17 km in average and the resolution of meteorological radar is 1-2 km in general. Even the X-band radar realizes the resolution of 250 m or larger. Here we suggest a thunderstorm monitoring system consisting of the network of VLF radio wave receivers and the super dense meteorological observation system with simple and low cost plate-type sensors that can be used for measurement both of raindrop and vertical electric field change caused by cloud-to-ground lightning discharge, adding to basic equipments for meteorological measurements. The plate-type sensor consists of two aluminum plates with a diameter of 10-20 cm. We carried out an observation campaign in summer of 2013 in the foothills of Mt. Yastugatake, Yamanashi and Nagano prefectures in Japan, installing 6 plate-type sensors at a distance of about 4 km. Horizontal location, height and charge amount of each lightning discharge are estimated successfully based on the information of electric field changes at several observing sites. Moreover, it was found that the thunderstorm has a very narrow structure smaller than 300 m that cannot be measured by any other ways, counting the positive and negative pulses caused by attachment of raindrop to the sensor plate, respectively. We plan to construct a new super dense observation network in the north Kanto region, Japan, where the lightning activity is most prominent in summer Japan and surrounded by our VLF systems developed for detecting sferics from lightning discharge, distributing more than several tens of sensors at every 4 km or shorter, such as an order of 100 m at minimum. This kind of new type network will reveal the unknown fine structures of

  2. An antilock molecular braking system.

    Science.gov (United States)

    Sun, Wei-Ting; Huang, Shou-Ling; Yao, Hsuan-Hsiao; Chen, I-Chia; Lin, Ying-Chih; Yang, Jye-Shane

    2012-08-17

    A light-driven molecular brake displaying an antilock function is constructed by introducing a nonradiative photoinduced electron transfer (PET) decay channel to compete with the trans (brake-off) → cis (brake-on) photoisomerization. A fast release of the brake can be achieved by deactivating the PET process through addition of protons. The cycle of irradiation-protonation-irradiation-deprotonation conducts the brake function and mimics the antilock braking system (ABS) of vehicles.

  3. High-Resolution Imaging of Dense Gas Structure and Kinematics in Nearby Molecular Clouds with the CARMA Large Area Star Formation Survey

    Science.gov (United States)

    Storm, Shaye

    This thesis utilizes new observations of dense gas in molecular clouds to develop an empirical framework for how clouds form structures which evolve into young cores and stars. Previous observations show the general turbulent and hierarchical nature of clouds. However, current understanding of the star formation pathway is limited by existing data that do not combine angular resolution needed to resolve individual cores with area coverage required to capture entire star-forming regions and with tracers that can resolve gas motions. The original contributions of this thesis to astrophysical research are the creation and analysis of the largest-area high-angular-resolution maps of dense gas in molecular clouds to-date, and the development of a non-binary dendrogram algorithm to quantify the hierarchical nature and three-dimensional morphology of cloud structure. I first describe the CARMA Large Area Star Formation Survey, which provides spectrally imaged N2H+, HCO+, and HCN (J = 1→0) emission across diverse regions of the Perseus and Serpens Molecular Clouds. I then present a detailed analysis of the Barnard 1 and L1451 regions in Perseus. A non-binary dendrogram analysis of Barnard 1 N2H emission and all L1451 emission shows that the most hierarchically complex gas corresponds with sub-regions actively forming young stars. I estimate the typical depth of molecular emission in each region using the spatial and kinematic properties of dendrogram-identified structures. Barnard 1 appears to be a sheet-like region at the largest scales with filamentary substructure, while the L1451 region is composed of more spatially distinct ellipsoidal structures. I then do a uniform comparison of the hierarchical structure and young stellar content of all five regions. The more evolved regions with the most young stellar objects (YSOs) and strongest emission have formed the most hierarchical levels. However, all regions show similar mean branching properties at each level

  4. A dense cell retention culture system using stirred ceramic membrane reactor.

    Science.gov (United States)

    Suzuki, T; Sato, T; Kominami, M

    1994-11-20

    A novel reactor design incorporating porous ceramic tubes into a stirred jar fermentor was developed. The stirred ceramic membrane reactor has two ceramic tubular membrane units inside the vessel and maintains high filtration flux by alternating use for filtering and recovering from clogging. Each filter unit was linked for both extraction of culture broth and gas sparging. High permeability was maintained for long periods by applying the periodical control between filtering and air sparging during the stirred retention culture of Saccharomyces cerevisiae. The ceramic filter aeration system increased the k(L)a to about five times that of ordinary gas sparing. Using the automatic feeding and filtering system, cell mass concentration reached 207 g/L in a short time, while it was 64 g/L in a fed-batch culture. More than 99% of the growing cells were retained in the fermentor by the filtering culture. Both yield and productivity of cells were also increased by controlling the feeding of fresh medium and filtering the supernatant of the dense cells culture. (c) 1994 John Wiley & Sons, Inc.

  5. Investigating the Composite Step Biconjugate A-Orthogonal Residual Method for Non-Hermitian Dense Linear Systems in Electromagnetics

    NARCIS (Netherlands)

    Jing, Yan-Fei; Huang, Ting-Zhu; Carpentieri, Bruno; Duan, Yong

    An interesting stabilizing variant of the biconjugate A-orthogonal residual (BiCOR) method is investigated for solving dense complex non-Hermitian systems of linear equations arising from the Galerlcin discretization of surface integral equations in electromagnetics. The novel variant is naturally

  6. Optimizing contaminant desorption and bioavailability in dense slurry systems. 2. PAH bioavailability and rates of degradation.

    Science.gov (United States)

    Kim, Han S; Weber, Walter J

    2005-04-01

    The effects of mechanical mixing on rates of polycyclic aromatic hydrocarbon (PAH) biodegradation in dense geosorbent slurry (67% solids content, w/w) systems were evaluated using laboratory-scale intermittently mixed batch bioreactors. A PAH-contaminated soil and a phenanthrene-sorbed mineral sorbent (alpha-Al2O3) were respectively employed as slurry solids in aerobic and anaerobic biodegradation studies. Both slurries exhibited a characteristic behavior of pseudoplastic non-Newtonian fluids, and the impeller revolution rate and its diameter had dramatic impacts on power and torque requirements in their laminar flow mixing. Rates of phenanthrene biodegradation were markedly enhanced by relatively low-level auger mixing under both aerobic and anaerobic (denitrifying) conditions. Parameters for empirical models correlating biodegradation rate coefficient (k(b)) values to the degree of mixing were similar to those for correlations between mass transfer (desorption) rate coefficient (k(r)) values for rapidly desorbing fractions of soil organic matter and degree of mixing reported in a companion study, supporting a conclusion that performance-efficient and cost-effective enhancements of PAH mass transfer (desorption) and its biodegradation processes can be achieved by the introduction of optimal levels of reactor-scale mechanical mixing.

  7. Information theory of molecular systems

    CERN Document Server

    Nalewajski, Roman F

    2006-01-01

    As well as providing a unified outlook on physics, Information Theory (IT) has numerous applications in chemistry and biology owing to its ability to provide a measure of the entropy/information contained within probability distributions and criteria of their information ""distance"" (similarity) and independence. Information Theory of Molecular Systems applies standard IT to classical problems in the theory of electronic structure and chemical reactivity. The book starts by introducing the basic concepts of modern electronic structure/reactivity theory based upon the Density Functional Theory

  8. PREFACE: Many-body correlations from dilute to dense nuclear systems

    Science.gov (United States)

    Otsuka, Takaharu; Urban, Michael; Yamada, Taiichi

    2011-09-01

    The International EFES-IN2P3 conference on "Many body correlations from dilute to dense nuclear systems" was held at the Institut Henri Poincaré (IHP), Paris, France, from 15-18 February 2011, on the occasion of the retirement of our colleague Peter Schuck. Correlations play a decisive role in various many-body systems such as nuclear systems, condensed matter and quantum gases. Important examples include: pairing correlations (Cooper pairs) which give rise to nuclear superfluidity (analogous to superconductivity in condensed matter); particle-hole (RPA) correlations in the description of the ground state beyond mean-field theory; clusters; and α-particle correlations in certain nuclei. Also, the nucleons themselves can be viewed as clusters of three quarks. During the past few years, researchers have started to study how the character of these correlations changes with the variation of the density. For instance, the Cooper pairs in dense matter can transform into a Bose-Einstein condensate (BEC) of true bound states at low density (this is the BCS-BEC crossover studied in ultracold Fermi gases). Similar effects play a role in neutron matter at low density, e.g., in the "neutron skin" of exotic nuclei. The α-cluster correlation becomes particularly important at lower density, such as in the excited states of some nuclei (e.g., the α-condensate-like structure in the Hoyle state of 12C) or in the formation of compact stars. In addition to nuclear physics, topics from astrophysics (neutron stars), condensed matter, and quantum gases were discussed in 48 talks and 19 posters, allowing the almost 90 participants from different communities to exchange their ideas, experiences and methods. The conference dinner took place at the Musée d'Orsay, and all the participants enjoyed the very pleasant atmosphere. One session of the conference was dedicated to the celebration of Peter's retirement. We would like to take this opportunity to wish Peter all the best and we hope

  9. THE BOLOCAM GALACTIC PLANE SURVEY. XII. DISTANCE CATALOG EXPANSION USING KINEMATIC ISOLATION OF DENSE MOLECULAR CLOUD STRUCTURES WITH {sup 13}CO(1-0)

    Energy Technology Data Exchange (ETDEWEB)

    Ellsworth-Bowers, Timothy P.; Glenn, Jason [CASA, University of Colorado, UCB 389, Boulder, CO 80309 (United States); Rosolowsky, Erik [Department of Physics, 4-183 CCIS, University of Alberta, Edmonton, AB T6G 2E1 (Canada); Ginsburg, Adam [European Southern Observatory, Karl-Schwarzschild-Straße 2, D-85748 Garching bei München (Germany); Evans II, Neal J. [Department of Astronomy, University of Texas, 2515 Speedway, Stop C1400, Austin, TX 78712 (United States); Battersby, Cara [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Shirley, Yancy L.; Svoboda, Brian, E-mail: timothy.ellsworthbowers@colorado.edu [Steward Observatory, University of Arizona, 933 North Cherry Avenue, Tucson, AZ 85721 (United States)

    2015-01-20

    We present an expanded distance catalog for 1710 molecular cloud structures identified in the Bolocam Galactic Plane Survey (BGPS) version 2, representing a nearly threefold increase over the previous BGPS distance catalog. We additionally present a new method for incorporating extant data sets into our Bayesian distance probability density function (DPDF) methodology. To augment the dense-gas tracers (e.g., HCO{sup +}(3-2), NH{sub 3}(1,1)) used to derive line-of-sight velocities for kinematic distances, we utilize the Galactic Ring Survey (GRS) {sup 13}CO(1-0) data to morphologically extract velocities for BGPS sources. The outline of a BGPS source is used to select a region of the GRS {sup 13}CO data, along with a reference region to subtract enveloping diffuse emission, to produce a line profile of {sup 13}CO matched to the BGPS source. For objects with a HCO{sup +}(3-2) velocity, ≈95% of the new {sup 13}CO(1-0) velocities agree with that of the dense gas. A new prior DPDF for kinematic distance ambiguity (KDA) resolution, based on a validated formalism for associating molecular cloud structures with known objects from the literature, is presented. We demonstrate this prior using catalogs of masers with trigonometric parallaxes and H II regions with robust KDA resolutions. The distance catalog presented here contains well-constrained distance estimates for 20% of BGPS V2 sources, with typical distance uncertainties ≲ 0.5 kpc. Approximately 75% of the well-constrained sources lie within 6 kpc of the Sun, concentrated in the Scutum-Centaurus arm. Galactocentric positions of objects additionally trace out portions of the Sagittarius, Perseus, and Outer arms in the first and second Galactic quadrants, and we also find evidence for significant regions of interarm dense gas.

  10. The description of dense hydrogen with Wave Packet Molecular Dynamics (WPMD) simulations; Die Beschreibung von dichtem Wasserstoff mit der Methode der Wellenpaket-Molekulardynamik (WPMD)

    Energy Technology Data Exchange (ETDEWEB)

    Jakob, B.

    2006-10-10

    In this work the wave packet molecular dynamics (WPMD) is presented and applied to dense hydrogen. In the WPMD method the electrons are described by a slater determinant of periodic Gaussian wave packets. Each single particle wave function can parametrised through 8 coordinates which can be interpreted as the position and momentum, the width and its conjugate momentum. The equation of motion for these coordinates can be derived from a time depended variational principle. Properties of the equilibrium can be ascertained by a Monte Carlo simulation. With the now completely implemented antisymmetrisation the simulation yields a fundamental different behavior for dense hydrogen compare to earlier simplified models. The results show a phase transition to metallic hydrogen with a higher density than in the molecular phase. This behavior has e.g. a large implication to the physics of giant planets. This work describes the used model and explains in particular the calculation of the energy and forces. The periodicity of the wave function leads to a description in the Fourier space. The antisymmetrisation is done by Matrix operations. Moreover the numerical implementation is described in detail to allow the further development of the code. The results provided in this work show the equation of state in the temperature range 300K - 50000K an density 10{sup 23}-10{sup 24} cm{sup -3}, according a pressure 1 GPa-1000 GPa. In a phase diagram the phase transition to metallic hydrogen can be red off. The electrical conductivity of both phases is destined. (orig.)

  11. ALMA 0.1–0.2 arcsec resolution imaging of the NGC 1068 Nucleus: compact dense molecular gas emission at the putative AGN location

    Energy Technology Data Exchange (ETDEWEB)

    Imanishi, Masatoshi [Subaru Telescope, 650 North A’ohoku Place, Hilo, HI 96720 (United States); Nakanishi, Kouichiro [National Astronomical Observatory of Japan, 2-21-1 Osawa, Mitaka, Tokyo 181-8588 (Japan); Izumi, Takuma, E-mail: masa.imanishi@nao.ac.jp [Institute of Astronomy, School of Science, The University of Tokyo, 2-21-1 Osawa, Mitaka, Tokyo 181-0015 (Japan)

    2016-05-01

    We present the results of our ALMA Cycle 2 high angular resolution (0.″1–0.″2) observations of the nuclear region of the nearby well-studied type-2 active galactic nucleus (AGN), NGC 1068, at HCN J = 3–2 and HCO{sup +} J = 3–2 emission lines. For the first time, due to a higher angular resolution than previous studies, we clearly detected dense molecular gas emission at the putative AGN location, identified as a ∼1.1 mm (∼266 GHz) continuum emission peak, by separating this emission from brighter emission located at 0.″5–2.″0 on the eastern and western sides of the AGN. The estimated intrinsic molecular emission size and dense molecular mass, which are thought to be associated with the putative dusty molecular torus around an AGN, were ∼10 pc and ∼several × 10{sup 5} M {sub ⊙}, respectively. HCN-to-HCO{sup +} J = 3–2 flux ratios substantially higher than unity were found throughout the nuclear region of NGC 1068. The continuum emission displayed an elongated morphology along the direction of the radio jet located at the northern side of the AGN, as well as a weak spatially-resolved component at ∼2.″0 on the southwestern side of the AGN. The latter component most likely originated from star formation, with the estimated luminosity more than one order of magnitude lower than the luminosity of the central AGN. No vibrationally excited ( v {sub 2} = 1f) J = 3–2 emission lines were detected for HCN and HCO{sup +} across the field of view.

  12. Electron scattering in dense atomic and molecular gases: An empirical correlation of polarizability and electron scattering length

    International Nuclear Information System (INIS)

    Rupnik, K.; Asaf, U.; McGlynn, S.P.

    1990-01-01

    A linear correlation exists between the electron scattering length, as measured by a pressure shift method, and the polarizabilities for He, Ne, Ar, Kr, and Xe gases. The correlative algorithm has excellent predictive capability for the electron scattering lengths of mixtures of rare gases, simple molecular gases such as H 2 and N 2 and even complex molecular entities such as methane, CH 4

  13. Effects of Noise and Vibration on the Solid to Liquid Fluidization Transition in Small Dense Granular Systems Under Shear

    Science.gov (United States)

    Melhus, Martin Frederic

    2011-07-01

    Granular materials exhibit bulk properties that are distinct from conventional solids, liq- uids, and gases, due to the dissipative nature of the inter-granular forces. Understanding the fundamentals of granular materials draws upon and gives insight into many fields at the current frontiers of physics, such as plasticity of solids, fracture and friction, com- plex systems such as colloids, foams and suspensions, and a variety of biological systems. Particulate flows are widespread in geophysics, and are also essential to many industries. Despite the importance of these phenomena, we lack a theoretical model that explains most behaviors of granular materials. Since granular assemblies are highly dissipative, they are often far from mechanical equilibrium, making most classical analyses inappli- cable. A theory for dilute granular systems exists, but for dense granular systems (by far the majority of granular systems in the real world) no comparable theory is accepted. We approach this problem by examining the fluidization, or transition from solid to liquid, in dense granular systems. In this study, the separate effects of random noise and vibration on the static to flowing transition of a dense granular assembly under planar shear is studied numerically using soft contact particle dynamics simulations in two dimensions. We focus on small systems in a thin planar Couette cell, examining the bistable region while increasing shear, with varying amounts of random noise or vibration, and determine the statistics of the shear required for the onset of flow. We find that the applied power is the key parameter in determining the magnitude of the effects of the noise or vibration, with vibration frequency also having an influence. Similarities and differences between noise and vibration are determined, and the results compare favorably with a two phase model for dense granular flow.

  14. On the dynamics of polymers in dense systems - Results of neutron spin echo spectroscopy

    International Nuclear Information System (INIS)

    Richter, D.

    1997-01-01

    One of the basic problems in the dynamics of polymers concerns the importance of geometrical or topological interactions which are directly related to the large scale molecular structures. In the famous reptation model these constraints are pictured in terms of a tube of localization following the average chain profile and confining the chain motion to the curve-linear tube. Recently studying the dynamic structure factor of a single labeled chain in a polymer melt by means of neutron spin echo spectroscopy (NSE) led to a direct observation of these tube constraints. Here I shall summarize these neutron spin echo experiments. I shall address the NSE technique, present results on the entropy driven segmental chain dynamics, discuss the dynamics of single chains in the melt where the chain length is increased through the transition to 'reptation' dynamics and display NSE measurements on long chain systems which revealed the molecular existence of the entanglement distance. Their magnitudes agree very well with tube diameters derived from dynamical mechanical measurements on the basis of the reptation model proving thereby the basic assumption of this Nobel Price winning concept

  15. Dense range map reconstruction from a versatile robotic sensor system with an active trinocular vision and a passive binocular vision.

    Science.gov (United States)

    Kim, Min Young; Lee, Hyunkee; Cho, Hyungsuck

    2008-04-10

    One major research issue associated with 3D perception by robotic systems is the creation of efficient sensor systems that can generate dense range maps reliably. A visual sensor system for robotic applications is developed that is inherently equipped with two types of sensor, an active trinocular vision and a passive stereo vision. Unlike in conventional active vision systems that use a large number of images with variations of projected patterns for dense range map acquisition or from conventional passive vision systems that work well on specific environments with sufficient feature information, a cooperative bidirectional sensor fusion method for this visual sensor system enables us to acquire a reliable dense range map using active and passive information simultaneously. The fusion algorithms are composed of two parts, one in which the passive stereo vision helps active vision and the other in which the active trinocular vision helps the passive one. The first part matches the laser patterns in stereo laser images with the help of intensity images; the second part utilizes an information fusion technique using the dynamic programming method in which image regions between laser patterns are matched pixel-by-pixel with help of the fusion results obtained in the first part. To determine how the proposed sensor system and fusion algorithms can work in real applications, the sensor system is implemented on a robotic system, and the proposed algorithms are applied. A series of experimental tests is performed for a variety of configurations of robot and environments. The performance of the sensor system is discussed in detail.

  16. Bistable behaviour of biexciton population in a dense exciton-biexciton system in semiconductors

    International Nuclear Information System (INIS)

    Nguyen Ba An.

    1986-05-01

    The steady state bistable behaviour of biexciton population in a dense exciton-biexciton semiconductor is considered. The intrinsic optical feedback is provided by the recombination mechanism. The exciton-biexciton and biexciton-biexciton interactions play the role of non-linearity responsible for biexciton bistability to occur. The conditions leading to the effect of bistability are obtained and two-parameter phase transition diagrams are drawn for both intensity and frequency bistable phenomena. (author)

  17. Photometric and spectroscopic evidence for a dense ring system around Centaur Chariklo

    Science.gov (United States)

    Duffard, R.; Pinilla-Alonso, N.; Ortiz, J. L.; Alvarez-Candal, A.; Sicardy, B.; Santos-Sanz, P.; Morales, N.; Colazo, C.; Fernández-Valenzuela, E.; Braga-Ribas, F.

    2014-08-01

    Context. A stellar occultation observed on 3rd June 2013 revealed the presence of two dense and narrow rings separated by a small gap around the Centaur object (10 199) Chariklo. The composition of these rings is not known. We suspect that water ice is present in the rings, as is the case for Saturn and other rings around the giant planets. Aims: In this work, we aim to determine if the variability in the absolute magnitude of Chariklo and the temporal variation of the spectral ice feature, even when it disappeared in 2007, can be explained by an icy ring system whose aspect angle changes with time. Methods: We explained the variations on the absolute magnitude of Chariklo and its ring by modeling the light reflected by a system as the one described above. Using X-shooter at VLT, we obtained a new reflectance spectra. We compared this new set of data with the ones available in the literature. We showed how the water ice feature is visible in 2013 in accordance with the ring configuration, which had an opening angle of nearly 34° in 2013. Finally, we also used models of light scattering to fit the visible and near-infrared spectra that shows different characteristics to obtain information on the composition of Chariklo and its rings. Results: We showed that absolute photometry of Chariklo from the literature and new photometric data that we obtained in 2013 can be explained by a ring of particles whose opening angle changes as a function of time. We used the two possible pole solutions for the ring system and found that only one of them, α = 151.30 ± 0.5, δ = 41.48 ± 0.2° (λ = 137.9 ± 0.5, β = 27.7 ± 0.2°), provides the right variation of the aspect angle with time to explain the photometry, whereas the other possible pole solution fails to explain the photometry. From spectral modeling, we derived the composition of the Chariklo surface and that of the rings using the result on the pole solution. Chariklo surface is composed with about 60% of amorphous

  18. Experimental study on direct-contact liquid film cooling simulated dense-array solar cells in high concentrating photovoltaic system

    International Nuclear Information System (INIS)

    Wang, Yiping; Shi, Xusheng; Huang, Qunwu; Cui, Yong; Kang, Xue

    2017-01-01

    Highlights: • Direct-contact liquid film cooling dense-array solar cells was first proposed. • Average temperature was controlled well below 80 °C. • The maximum temperature difference was less than 10 °C. • The heat transfer coefficient reached up to 11.91 kW/(m"2·K) under 589X. - Abstract: This paper presented a new method of cooling dense-array solar cells in high concentrating photovoltaic system by direct-contact liquid film, and water was used as working fluid. An electric heating plate was designed to simulate the dense-array solar cells in high concentrating photovoltaic system. The input power of electric heating plate simulated the concentration ratios. By heat transfer experiments, the effect of water temperatures and flow rates on heat transfer performance was investigated. The results indicated that: the average temperature of simulated solar cells was controlled well below 80 °C under water temperature of 30 °C and flow rate of 300 L/h when concentration ratio ranged between 300X and 600X. The maximum temperature difference among temperature measurement points was less than 10 °C, which showed the temperature distribution was well uniform. The heat transfer coefficient reached up to 11.91 kW/(m"2·K) under concentration ratio of 589X. To improve heat transfer performance and obtain low average temperature of dense-array solar cells, lower water temperature and suitable water flow rate are preferred.

  19. ALMA OBSERVATIONS OF THE SUBMILLIMETER DENSE MOLECULAR GAS TRACERS IN THE LUMINOUS TYPE-1 ACTIVE NUCLEUS OF NGC 7469

    International Nuclear Information System (INIS)

    Izumi, Takuma; Kohno, Kotaro; Ikarashi, Soh; Aalto, Susanne; Doi, Akihiro; Espada, Daniel; Fathi, Kambiz; Harada, Nanase; Hsieh, Pei-Ying; Matsushita, Satoki; Hatsukade, Bunyo; Hattori, Takashi; Imanishi, Masatoshi; Iono, Daisuke; Ishizuki, Sumio; Nagai, Hiroshi; Krips, Melanie; Martín, Sergio; Meier, David S.; Nakai, Naomasa

    2015-01-01

    We present Atacama Large Millimeter/submillimeter Array (ALMA) Cycle 1 observations of the central kiloparsec region of the luminous type 1 Seyfert galaxy NGC 7469 with unprecedented high resolution (0.″5 ×0.″4 = 165 × 132 pc) at submillimeter wavelengths. Utilizing the wide bandwidth of ALMA, we simultaneously obtained HCN(4–3), HCO + (4–3), CS(7–6), and partially CO(3–2) line maps, as well as the 860 μm continuum. The region consists of the central ∼1″ component and the surrounding starburst ring with a radius of ∼1.″5–2.″5. Several structures connect these components. Except for CO(3–2), these dense gas tracers are significantly concentrated toward the central ∼1″, suggesting their suitability to probe the nuclear regions of galaxies. Their spatial distribution resembles well those of centimeter and mid-infrared continuum emissions, but it is anticorrelated with the optical one, indicating the existence of dust-obscured star formation. The integrated intensity ratios of HCN(4–3)/HCO + (4–3) and HCN(4–3)/CS(7–6) are higher at the active galactic nucleus (AGN) position than at the starburst ring, which is consistent with our previous findings (submillimeter-HCN enhancement). However, the HCN(4–3)/HCO + (4–3) ratio at the AGN position of NGC 7469 (1.11 ± 0.06) is almost half of the corresponding value of the low-luminosity type 1 Seyfert galaxy NGC 1097 (2.0 ± 0.2), despite the more than two orders of magnitude higher X-ray luminosity of NGC 7469. But the ratio is comparable to that of the close vicinity of the AGN of NGC 1068 (∼1.5). Based on these results, we speculate that some heating mechanisms other than X-ray (e.g., mechanical heating due to an AGN jet) can contribute significantly for shaping the chemical composition in NGC 1097

  20. ALMA OBSERVATIONS OF THE SUBMILLIMETER DENSE MOLECULAR GAS TRACERS IN THE LUMINOUS TYPE-1 ACTIVE NUCLEUS OF NGC 7469

    Energy Technology Data Exchange (ETDEWEB)

    Izumi, Takuma; Kohno, Kotaro; Ikarashi, Soh [Institute of Astronomy, School of Science, The University of Tokyo, 2-21-1 Osawa, Mitaka, Tokyo 181-0015 (Japan); Aalto, Susanne [Department of Earth and Space Sciences, Chalmers University of Technology, Onsala Observatory, SE-439 94 Onsala (Sweden); Doi, Akihiro [Institute of Space and Astronautical Science, 3-1-1 Yoshinodai, Chuo-ku, Sagamihara 252-5210 (Japan); Espada, Daniel [Joint ALMA Observatory, Alonso de Córdova, 3107, Vitacura, Santiago 763-0355 (Chile); Fathi, Kambiz [Stockholm Observatory, Department of Astronomy, Stockholm University, AlbaNova Centre, SE-106 91 Stockholm (Sweden); Harada, Nanase; Hsieh, Pei-Ying; Matsushita, Satoki [Academia Sinica, Institute of Astronomy and Astrophysics, P.O. Box 23-141, Taipei 10617, Taiwan (China); Hatsukade, Bunyo; Hattori, Takashi; Imanishi, Masatoshi; Iono, Daisuke; Ishizuki, Sumio; Nagai, Hiroshi [National Astronomical Observatory of Japan, 2-21-1 Osawa, Mitaka, Tokyo 181-8588 (Japan); Krips, Melanie; Martín, Sergio [Institut de Radio Astronomie Millimétrique, 300 rue de la Piscine, Domaine Universitaire, F-38406 St. Martin d’Hères (France); Meier, David S. [Department of Physics, New Mexico Institute of Mining and Technology, 801 Leroy Place, Soccoro, NM 87801 (United States); Nakai, Naomasa, E-mail: takumaizumi@ioa.s.u-tokyo.ac.jp [Department of Physics, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8571 (Japan); and others

    2015-09-20

    We present Atacama Large Millimeter/submillimeter Array (ALMA) Cycle 1 observations of the central kiloparsec region of the luminous type 1 Seyfert galaxy NGC 7469 with unprecedented high resolution (0.″5 ×0.″4 = 165 × 132 pc) at submillimeter wavelengths. Utilizing the wide bandwidth of ALMA, we simultaneously obtained HCN(4–3), HCO{sup +}(4–3), CS(7–6), and partially CO(3–2) line maps, as well as the 860 μm continuum. The region consists of the central ∼1″ component and the surrounding starburst ring with a radius of ∼1.″5–2.″5. Several structures connect these components. Except for CO(3–2), these dense gas tracers are significantly concentrated toward the central ∼1″, suggesting their suitability to probe the nuclear regions of galaxies. Their spatial distribution resembles well those of centimeter and mid-infrared continuum emissions, but it is anticorrelated with the optical one, indicating the existence of dust-obscured star formation. The integrated intensity ratios of HCN(4–3)/HCO{sup +}(4–3) and HCN(4–3)/CS(7–6) are higher at the active galactic nucleus (AGN) position than at the starburst ring, which is consistent with our previous findings (submillimeter-HCN enhancement). However, the HCN(4–3)/HCO{sup +}(4–3) ratio at the AGN position of NGC 7469 (1.11 ± 0.06) is almost half of the corresponding value of the low-luminosity type 1 Seyfert galaxy NGC 1097 (2.0 ± 0.2), despite the more than two orders of magnitude higher X-ray luminosity of NGC 7469. But the ratio is comparable to that of the close vicinity of the AGN of NGC 1068 (∼1.5). Based on these results, we speculate that some heating mechanisms other than X-ray (e.g., mechanical heating due to an AGN jet) can contribute significantly for shaping the chemical composition in NGC 1097.

  1. Environmental Catastrophes in the Earth's History Due to Solar Systems Encounters with Giant Molecular Clouds

    Science.gov (United States)

    Pavlov, Alexander A.

    2011-01-01

    In its motion through the Milky Way galaxy, the solar system encounters an average density (>=330 H atoms/cubic cm) giant molecular cloud (GMC) approximately every 108 years, a dense (approx 2 x 103 H atoms/cubic cm) GMC every approx 109 years and will inevitably encounter them in the future. However, there have been no studies linking such events with severe (snowball) glaciations in Earth history. Here we show that dramatic climate change can be caused by interstellar dust accumulating in Earth's atmosphere during the solar system's immersion into a dense (approx ,2 x 103 H atoms/cubic cm) GMC. The stratospheric dust layer from such interstellar particles could provide enough radiative forcing to trigger the runaway ice-albedo feedback that results in global snowball glaciations. We also demonstrate that more frequent collisions with less dense GMCs could cause moderate ice ages.

  2. Model Intercomparison Study to Investigate a Dense Contaminant Plume in a Complex Hydrogeologic System

    International Nuclear Information System (INIS)

    Williams, Mark D.; Cole, Charles R.; Foley, Michael G.; Zinina, Galina A.; Zinin, Alexander I.; Vasil'Kova, Nelly A.; Samsonova, Lilia M.

    2001-01-01

    A joint Russian and U.S. model intercomparison study was undertaken for developing more realistic contaminant transport models of the Mayak Site, Southern Urals. The test problems were developed by the Russian Team based on their experience modeling contaminant migration near Lake Karachai. The intercomparison problems were designed to address lake and contaminant plume interactions, as well as river interactions and plume density effects. Different numerical codes were used. Overall there is good agreement between the results of both models. Features shown by both models include (1) the sinking of the plume below the lake, (2) the raising of the water table in the fresh water adjacent to the lake in response to the increased pressure from the dense plume, and (3) the formation of a second sinking plume in an area where evapotranspiration exceeded infiltration, thus increasing the solute concentrations above the source (i.e., lake) values

  3. Effect of electron degeneracy on fast-particles energy deposition in dense plasma systems

    International Nuclear Information System (INIS)

    Johzaki, T.; Nakao, Y.; Nakashima, H.; Kudo, K.

    1997-01-01

    The effects of electron degeneracy on fast-particles energy deposition in dense plasmas are investigated by making transport calculations for the fast particles. It is found that the degeneracy substantially affects the profiles of energy deposition of 3.52-MeV α-particles. On the other hand, the effect on the energy deposition of 14.1-MeV neutrons is negligibly small because the recoil ions, which transfer the neutron energy to the plasma constituents, are produced in a whole plasma volume due to the long mean-free-path of neutrons. The coupled transport-hydrodynamic calculations show that these effects of degeneracy are negligible in the ignition and burn characteristics of central ignition D-T targets. (author)

  4. Radiation transport in dense interstellar dust clouds. II. Infrared emission from molecular clouds associated with H II regions

    International Nuclear Information System (INIS)

    Leung, C.M.

    1976-01-01

    Theoretical models are constructed to study the distribution of grain temperature (T/sub d/) and infrared emission from molecular clouds associated with H II regions (with embedded O: B stars). The effects of the following parameters on the temperature structure and the emergent spectrum are studied: grain type (graphite, silicate, and core-mantle grains), optical depth, density inhomogeneity, cloud size, anisotropic scattering, radiation field anisotropy, and characteristics of central heat source. T/sub d/ varies from approximately-greater-than100 K to approximately-less-than20 K throughout the major portion of a cloud, and dielectric grains attain lower temperatures. Due to an inward increase in T/sub d/, the radiation field is strongly forward-peaking, thereby producing a pronounced limb-darkening in the surface brightness. Important features of the computed emission spectra from typical models are compared with available observations, and the importance of beam dilution is emphasized. Theoretical surface brightnesses at selected infrared wavelengths are also presented. The outward radiation pressure on the dust grains is found to exceed the self-gravitational force of the gas over a large portion of a cloud, thus possibly causing the gas in the inner region to expand. Assumptions commonly used in the analysis of infrared observations are examined. Finally, observational methods of deriving the temperature structure (from color and brightness temperatures in the far-infrared), density distribution (from surface brightness at lambdaapproximately-greater-than1 mm), and optical depth (from multiaperture photometry) for the dust component in simple sources are discussed

  5. Power Generation from Concentration Gradient by Reverse Electrodialysis in Dense Silica Membranes for Microfluidic and Nanofluidic Systems

    Directory of Open Access Journals (Sweden)

    Sang Woo Lee

    2016-01-01

    Full Text Available In this study, we investigate power generation by reverse electrodialysis in a dense silica membrane that is between two NaCl solutions with various combinations of concentrations. Each silica membrane is fabricated by depositing a silica layer on a porous alumina substrate via chemical vapor deposition. The measured potential-current (V-I characteristics of the silica membrane are used to obtain the transference number, diffusion potential, and electrical resistance. We develop empirical correlations for the transference number and the area-specific resistance, and present the results of power generation by reverse electrodialysis using the fabricated silica membranes. The highest measured power density is 0.98 mW/m2. In addition, we develop a contour map of the power density as a function of NaCl concentrations on the basis of the empirical correlations. The contour map shows that a power output density of 1.2 mW/m2 is achievable with the use of silica membranes and is sufficient to drive nanofluidic and microfluidic systems. The dense silica membrane has the potential for use in micro power generators in nanofluidic and microfluidic systems.

  6. Molecular motor assembly of a biomimetic system

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@ Active biological molecules and functional structures can be fabricated into a bio-mimetic system by using molecular assembly method. Such materials can be used for the drug delivery, disease diagnosis and therapy, and new nanodevice construction.

  7. Improved thermodynamics of the dense solar plasma and molecular-dynamics simulations of the nuclear-reaction rates

    Science.gov (United States)

    Mao, Dan

    available, there is no alternative source. The official OPAL tables, however, have disadvantages. First, they are inflexible regarding the chemical mix, which is set once and for all by the producers of the tables. Our equation of state will allow the user to choose, in principle, an arbitrary mix. Second, the OPAL tables by their very nature are limited by the errors of interpolation within tables. The second equation of state model is a density expansion based on the Feynman-Kac path-integral formalism. By making use of the equivalence of quantum Hamiltonian matrix and the classical action of closed and open filaments (paths), an analytic formalism of equation of state. Although the character of density expansion limits its application, the formalism can still be valid in most region in the Sun. Our work provides the link between the abstract theoretical formalism that was developed in the 1990s and a numerically smooth realization that can be used in solar and stellar models. Since it is so far the most exact and systematic approach for an EOS, it provides another way to study the influence of different very fine physical effects, despite considerable limitations in its domain of applicability. In the nuclear-reaction part of the thesis, we have used a molecular-dynamics method to simulate the motion of protons in a hydrogen plasma (which is a good approximation for this purpose). Quantum tunneling explains why nuclear fusion can occur in the first place, considering the "low" temperature in the solar core. It is well known that this tunneling is enhanced (which leads to higher nuclear reaction rates) in the presence of Coulomb screening. In the 1950, Salpeter formulated a theory based on the static-screened Coulomb potential, as derived by Debye and H=FCckel in the 1920s. As expected, Salpeter obtained enhanced reaction rates. But from our simulation, we confirmed the results of a recent controversy about the existence of a dynamic effect. Since the bulk of fusion

  8. A system for household enumeration and re-identification in densely populated slums to facilitate community research, education, and advocacy.

    Directory of Open Access Journals (Sweden)

    Dana R Thomson

    Full Text Available We devised and implemented an innovative Location-Based Household Coding System (LBHCS appropriate to a densely populated informal settlement in Mumbai, India.LBHCS codes were designed to double as unique household identifiers and as walking directions; when an entire community is enumerated, LBHCS codes can be used to identify the number of households located per road (or lane segment. LBHCS was used in community-wide biometric, mental health, diarrheal disease, and water poverty studies. It also facilitated targeted health interventions by a research team of youth from Mumbai, including intensive door-to-door education of residents, targeted follow-up meetings, and a full census. In addition, LBHCS permitted rapid and low-cost preparation of GIS mapping of all households in the slum, and spatial summation and spatial analysis of survey data.LBHCS was an effective, easy-to-use, affordable approach to household enumeration and re-identification in a densely populated informal settlement where alternative satellite imagery and GPS technologies could not be used.

  9. THE BOLOCAM GALACTIC PLANE SURVEY. X. A COMPLETE SPECTROSCOPIC CATALOG OF DENSE MOLECULAR GAS OBSERVED TOWARD 1.1 mm DUST CONTINUUM SOURCES WITH 7.°5 ≤ l ≤ 194°

    International Nuclear Information System (INIS)

    Shirley, Yancy L.; Svoboda, Brian; Ellsworth-Bowers, Timothy P.; Schlingman, Wayne M.; Ginsburg, Adam; Battersby, Cara; Stringfellow, Guy; Glenn, Jason; Bally, John; Rosolowsky, Erik; Gerner, Thomas; Mairs, Steven; Dunham, Miranda K.

    2013-01-01

    The Bolocam Galactic Plane Survey (BGPS) is a 1.1 mm continuum survey of dense clumps of dust throughout the Galaxy covering 170 deg 2 . We present spectroscopic observations using the Heinrich Hertz Submillimeter Telescope of the dense gas tracers, HCO + and N 2 H + 3-2, for all 6194 sources in the BGPS v1.0.1 catalog between 7.°5 ≤ l ≤ 194°. This is the largest targeted spectroscopic survey of dense molecular gas in the Milky Way to date. We find unique velocities for 3126 (50.5%) of the BGPS v1.0.1 sources observed. Strong N 2 H + 3-2 emission (T mb > 0.5 K) without HCO + 3-2 emission does not occur in this catalog. We characterize the properties of the dense molecular gas emission toward the entire sample. HCO + is very sub-thermally populated and the 3-2 transitions are optically thick toward most BGPS clumps. The median observed line width is 3.3 km s –1 consistent with supersonic turbulence within BGPS clumps. We find strong correlations between dense molecular gas integrated intensities and 1.1 mm peak flux and the gas kinetic temperature derived from previously published NH 3 observations. These intensity correlations are driven by the sensitivity of the 3-2 transitions to excitation conditions rather than by variations in molecular column density or abundance. We identify a subset of 113 sources with stronger N 2 H + than HCO + integrated intensity, but we find no correlations between the N 2 H + /HCO + ratio and 1.1 mm continuum flux density, gas kinetic temperature, or line width. Self-absorbed profiles are rare (1.3%)

  10. THE BOLOCAM GALACTIC PLANE SURVEY. X. A COMPLETE SPECTROSCOPIC CATALOG OF DENSE MOLECULAR GAS OBSERVED TOWARD 1.1 mm DUST CONTINUUM SOURCES WITH 7.°5 ≤ l ≤ 194°

    Energy Technology Data Exchange (ETDEWEB)

    Shirley, Yancy L.; Svoboda, Brian [Steward Observatory, 933 North Cherry Avenue, Tucson, AZ 85721 (United States); Ellsworth-Bowers, Timothy P.; Schlingman, Wayne M.; Ginsburg, Adam; Battersby, Cara; Stringfellow, Guy; Glenn, Jason; Bally, John [CASA, University of Colorado, CB 389, Boulder, CO 80309 (United States); Rosolowsky, Erik [Department of Physics, University of Alberta, 4-181 CCIS Edmonton AB T6G 2E1 (Canada); Gerner, Thomas [Max-Planck-Institut für Astronomie (MPIA), Knigstuhl 17, D-69117 Heidelberg (Germany); Mairs, Steven [Department of Physics and Astronomy, University of Victoria, P.O. Box 3055, STN CSC, Victoria, BC V8W 3P6 (Canada); Dunham, Miranda K. [Department of Astronomy, Yale University, P.O. Box 208101, New Haven, CT 06520 (United States)

    2013-11-01

    The Bolocam Galactic Plane Survey (BGPS) is a 1.1 mm continuum survey of dense clumps of dust throughout the Galaxy covering 170 deg{sup 2}. We present spectroscopic observations using the Heinrich Hertz Submillimeter Telescope of the dense gas tracers, HCO{sup +} and N{sub 2}H{sup +} 3-2, for all 6194 sources in the BGPS v1.0.1 catalog between 7.°5 ≤ l ≤ 194°. This is the largest targeted spectroscopic survey of dense molecular gas in the Milky Way to date. We find unique velocities for 3126 (50.5%) of the BGPS v1.0.1 sources observed. Strong N{sub 2}H{sup +} 3-2 emission (T {sub mb} > 0.5 K) without HCO{sup +} 3-2 emission does not occur in this catalog. We characterize the properties of the dense molecular gas emission toward the entire sample. HCO{sup +} is very sub-thermally populated and the 3-2 transitions are optically thick toward most BGPS clumps. The median observed line width is 3.3 km s{sup –1} consistent with supersonic turbulence within BGPS clumps. We find strong correlations between dense molecular gas integrated intensities and 1.1 mm peak flux and the gas kinetic temperature derived from previously published NH{sub 3} observations. These intensity correlations are driven by the sensitivity of the 3-2 transitions to excitation conditions rather than by variations in molecular column density or abundance. We identify a subset of 113 sources with stronger N{sub 2}H{sup +} than HCO{sup +} integrated intensity, but we find no correlations between the N{sub 2}H{sup +}/HCO{sup +} ratio and 1.1 mm continuum flux density, gas kinetic temperature, or line width. Self-absorbed profiles are rare (1.3%)

  11. Spatially resolved chemistry in nearby galaxies. III. Dense molecular gas in the inner disk of the LIRG IRAS 04296+2923

    Energy Technology Data Exchange (ETDEWEB)

    Meier, David S. [Department of Physics, New Mexico Institute of Mining and Technology, 801 Leroy Place, Socorro, NM 87801 (United States); Turner, Jean L. [Department of Physics and Astronomy, UCLA, Los Angeles, CA 90095-1547 (United States); Beck, Sara C., E-mail: dmeier@nmt.edu, E-mail: turner@astro.ucla.edu, E-mail: sara@wise.tau.ac.il [Department of Physics and Astronomy, Tel Aviv University, 69978 Ramat Aviv (Israel)

    2014-11-10

    We present a survey of 3 mm molecular lines in IRAS 04296+2923, one of the brightest known molecular-line emitting galaxies, and one of the closest luminous infrared galaxies (LIRGs). Data are from the Owens Valley and CARMA millimeter interferometers. Species detected at ≲ 4'' resolution include C{sup 18}O, HCN, HCO{sup +}, HNC, CN, CH{sub 3}OH, and, tentatively, HNCO. Along with existing CO, {sup 13}CO, and radio continuum data, these lines constrain the chemical properties of the inner disk. Dense molecular gas in the nucleus fuels a star formation rate ≳10 M {sub ☉} yr{sup –1} and is traced by lines of HCN, HCO{sup +}, HNC, and CN. A correlation between HCN and star formation rate is observed on sub-kiloparsec scales, consistent with global relations. Toward the nucleus, CN abundances are similar to those of HCN, indicating emission comes from a collection (∼40-50) of moderate visual extinction, photon-dominated-region clouds. The CO isotopic line ratios are unusual: CO(1-0)/{sup 13}CO(1-0) and CO(1-0)/C{sup 18}O(1-0) line ratios are large toward the starburst, as is commonly observed in LIRGs, but farther out in the disk these ratios are remarkably low (≲ 3). {sup 13}CO/C{sup 18}O abundance ratios are lower than in Galactic clouds, possibly because the C{sup 18}O is enriched by massive star ejecta from the starburst. {sup 13}CO is underabundant relative to CO. Extended emission from CH{sub 3}OH indicates that dynamical shocks pervade both the nucleus and the inner disk. The unusual CO isotopologue ratios, the CO/HCN intensity ratio versus L {sub IR}, the HCN/CN abundance ratio, and the gas consumption time versus inflow rate all indicate that the starburst in IRAS 04296+2923 is in an early stage of development.

  12. Collective dynamics in dense fluid mixtures

    International Nuclear Information System (INIS)

    Sinha, S.

    1992-01-01

    This thesis deals with the short wavelength collective dynamics of dense binary fluid mixtures. The analysis shows that at the level of linearized generalized hydrodynamics, the longitudinal modes of the system separates essentially into two parts - one involves the coupling of partial density fluctuations of the two species and the other involves coupling of longitudinal momentum and temperature fluctuations. The authors have shown that the coupling of longitudinal momentum and temperature fluctuations leads to an adequate description of sound propagation in such systems. In particular, they show that structural disorder controls the trapping of sound waves in dense mixtures. The coupling of the partial density fluctuations of the two species leads to a simple description of the partial dynamic structure factors. The results are in agreement with the molecular dynamics simulations of soft sphere mixtures. The partial density fluctuations are the slowest decaying fluctuations on molecular length scales and it turns out that nonlinear coupling of these slow modes leads to important corrections to the long time behavior of the time correlation functions determining the shear viscosity in dense mixtures

  13. Reaction dynamics in polyatomic molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.

  14. Primary Systemic Amyloidosis Presenting as Swollen Dense Breast: A Case Report

    International Nuclear Information System (INIS)

    Lee, Byung Hoon; Kim, Mi Young; Kim, Su Young; Hwang, Yoon Joon; Han, Yoon Hee; Seo, Jung Wook; Kim, Yong Hoon; Cha, Soon Joo; Hur, Gham; Joo, Mee

    2006-01-01

    Breast involvement of primary systemic amyloidosis is rare. This is a rare case of breast amyloidosis presenting as a diffuse infiltrative lesion. We present the mammographic, ultrasound, and MR findings of a systemic primary amyloidosis involving the breast with diffuse infiltrative pattern

  15. Propulsion and Power Generation Capabilities of a Dense Plasma Focus (DPF) Fusion System for Future Military Aerospace Vehicles

    International Nuclear Information System (INIS)

    Knecht, Sean D.; Mead, Franklin B.; Thomas, Robert E.; Miley, George H.; Froning, David

    2006-01-01

    The objective of this study was to perform a parametric evaluation of the performance and interface characteristics of a dense plasma focus (DPF) fusion system in support of a USAF advanced military aerospace vehicle concept study. This vehicle is an aerospace plane that combines clean 'aneutronic' dense plasma focus (DPF) fusion power and propulsion technology, with advanced 'lifting body'-like airframe configurations utilizing air-breathing MHD propulsion and power technology within a reusable single-stage-to-orbit (SSTO) vehicle. The applied approach was to evaluate the fusion system details (geometry, power, T/W, system mass, etc.) of a baseline p-11B DPF propulsion device with Q = 3.0 and thruster efficiency, ηprop = 90% for a range of thrust, Isp and capacitor specific energy values. The baseline details were then kept constant and the values of Q and ηprop were varied to evaluate excess power generation for communication systems, pulsed-train plasmoid weapons, ultrahigh-power lasers, and gravity devices. Thrust values were varied between 100 kN and 1,000 kN with Isp of 1,500 s and 2,000 s, while capacitor specific energy was varied from 1 - 15 kJ/kg. Q was varied from 3.0 to 6.0, resulting in gigawatts of excess power. Thruster efficiency was varied from 0.9 to 1.0, resulting in hundreds of megawatts of excess power. Resulting system masses were on the order of 10's to 100's of metric tons with thrust-to-weight ratios ranging from 2.1 to 44.1, depending on capacitor specific energy. Such a high thrust/high Isp system with a high power generation capability would allow military versatility in sub-orbital space, as early as 2025, and beyond as early as 2050. This paper presents the results that coincide with a total system mass between 15 and 20 metric tons

  16. A semantic autonomous video surveillance system for dense camera networks in Smart Cities.

    Science.gov (United States)

    Calavia, Lorena; Baladrón, Carlos; Aguiar, Javier M; Carro, Belén; Sánchez-Esguevillas, Antonio

    2012-01-01

    This paper presents a proposal of an intelligent video surveillance system able to detect and identify abnormal and alarming situations by analyzing object movement. The system is designed to minimize video processing and transmission, thus allowing a large number of cameras to be deployed on the system, and therefore making it suitable for its usage as an integrated safety and security solution in Smart Cities. Alarm detection is performed on the basis of parameters of the moving objects and their trajectories, and is performed using semantic reasoning and ontologies. This means that the system employs a high-level conceptual language easy to understand for human operators, capable of raising enriched alarms with descriptions of what is happening on the image, and to automate reactions to them such as alerting the appropriate emergency services using the Smart City safety network.

  17. System for deuterium-tritium mixture filling the working chamber of a dense plasma focus device

    International Nuclear Information System (INIS)

    Bondar', A.I.; Vyskubov, V.P.; Gerasimov, S.A.

    1981-01-01

    A gas-vacuum system designed for filling the gas-discharge chamber of a plasma focus device with equal-coaponent deuterium-tritium mixture is described. The system consists of a unit for gaseous mixture prepa ration and a unit for mixture absorption and device evacuation. The system provides the gaseous mixture purification of O 2 and N 2 impurities. Final tritium content in the gas-discharge chamber after tritium removal is not greater than 2x10 8 Bq/l. Tritium content in a sealed box in which the device is placed does not exceed 30 Bq/l that is less than limiting safe value. The conclusion is made that the described system design gives an opportunity to begin experimental studies at plasma focus devices with deuterium-tritium mixture [ru

  18. A Semantic Autonomous Video Surveillance System for Dense Camera Networks in Smart Cities

    Directory of Open Access Journals (Sweden)

    Antonio Sánchez-Esguevillas

    2012-08-01

    Full Text Available This paper presents a proposal of an intelligent video surveillance system able to detect and identify abnormal and alarming situations by analyzing object movement. The system is designed to minimize video processing and transmission, thus allowing a large number of cameras to be deployed on the system, and therefore making it suitable for its usage as an integrated safety and security solution in Smart Cities. Alarm detection is performed on the basis of parameters of the moving objects and their trajectories, and is performed using semantic reasoning and ontologies. This means that the system employs a high-level conceptual language easy to understand for human operators, capable of raising enriched alarms with descriptions of what is happening on the image, and to automate reactions to them such as alerting the appropriate emergency services using the Smart City safety network.

  19. Marandu palisade grass intercropped with densely spaced teak in silvopastoral system

    Directory of Open Access Journals (Sweden)

    Carlos Eduardo Avelino Cabral

    2017-08-01

    Full Text Available This study was conducted to evaluate two systems of production: integration between teak and forage (silvopastoral system and forage only (monoculture. The forage species used was Marandu palisade grass (Urochloa brizantha cv. Marandu. In January 2009, part of the pasture was desiccated and the teak (Tectona grandis was implemented in a 3 × 4 m spacing arrangement, and at every five rows, a space between rows of 6 m was established, providing a population of 750 trees per hectare. Alongside the development of the trees, the Marandu palisade grass pasture was reestablished. In February 2015, the animals were removed from the experimental area and, in March, the pasture degradation, the density and the mass of tillers was assessed. The following variables were evaluated: sward height; forage mass, percentage of leaf blade, stem+sheath and senescent material; leaf blade:stem+sheath ratio; and live:dead material ratio. The experimental design was completely randomized, with 12 replicates. Treatments consisted of two systems (silvopastoral and monoculture. The total forage accumulation was higher in the monoculture system. The sward height and the percentage of stem+sheath were higher in the integrated system, while the percentage of leaf blade and the leaf blade:stem+sheath ratio were higher in the system exclusively with forage. In conclusion, Marandu palisade grass tolerates shading in a high density spacing silvopastoral system, but the degradation process is more intense compared to grass in monoculture, and the use of Marandu palisade grass in silvopastoral systems changes the forage mass and the structure of the produced forage.

  20. In-service crosstalk monitoring for dense space division multiplexed multi-core fiber transmission systems

    DEFF Research Database (Denmark)

    Mizuno, T.; Isoda, A.; Shibahara, K.

    2017-01-01

    We present in-service inter-core crosstalk monitoring for MCF transmission systems. We transmit 54-WDM PDM-16QAM signals over 111.6-km 32-core DSDM transmission line incorporating cladding-pumped 32-core MC-EYDFA, and demonstrate -30 dB crosstalk monitoring without affecting transmission...

  1. ASAP: A MAC Protocol for Dense and Time-Constrained RFID Systems

    Directory of Open Access Journals (Sweden)

    Kyounghwan Lee

    2007-08-01

    Full Text Available We introduce a novel medium access control (MAC protocol for radio frequency identification (RFID systems which exploits the statistical information collected at the reader. The protocol, termed adaptive slotted ALOHA protocol (ASAP, is motivated by the need to significantly improve the total read time performance of the currently suggested MAC protocols for RFID systems. In order to accomplish this task, ASAP estimates the dynamic tag population and adapts the frame size in the subsequent round via a simple policy that maximizes an appropriately defined efficiency function. We demonstrate that ASAP provides significant improvement in total read time performance over the current RFID MAC protocols. We next extend the design to accomplish reliable performance of ASAP in realistic scenarios such as the existence of constraints on frame size, and mobile RFID systems where tags move at constant velocity in the reader's field. We also consider the case where tags may fail to respond because of a physical breakdown or a temporary malfunction, and show the robustness in those scenarios as well.

  2. Improved modeling of two-dimensional transitions in dense phases on crystalline surfaces. Krypton-graphite system.

    Science.gov (United States)

    Ustinov, E A

    2015-02-21

    This paper presents a refined technique to describe two-dimensional phase transitions in dense fluids adsorbed on a crystalline surface. Prediction of parameters of 2D liquid-solid equilibrium is known to be an extremely challenging problem, which is mainly due to a small difference in thermodynamic functions of coexisting phases and lack of accuracy of numerical experiments in case of their high density. This is a serious limitation of various attempts to circumvent this problem. To improve this situation, a new methodology based on the kinetic Monte Carlo method was applied. The methodology involves analysis of equilibrium gas-liquid and gas-solid systems undergoing an external potential, which allows gradual shifting parameters of the phase coexistence. The interrelation of the chemical potential and tangential pressure for each system is then treated with the Gibbs-Duhem equation to obtain the point of intersection corresponding to the liquid/solid-solid equilibrium coexistence. The methodology is demonstrated on the krypton-graphite system below and above the 2D critical temperature. Using experimental data on the liquid-solid and the commensurate-incommensurate transitions in the krypton monolayer derived from adsorption isotherms, the Kr-graphite Lennard-Jones parameters have been corrected resulting in a higher periodic potential modulation.

  3. Light redirecting system using sine-wave based panels for dense urban areas

    Science.gov (United States)

    Mohamed, Mohamed W. N.; Mashaly, Islam A.; Mohamed, Osama N.; El-Henawy, Sally I.; Galal, Ola; Taha, Iman; Nassar, Khaled; Safwat, Amr M. E.

    2014-09-01

    Cities and towns around the world are becoming more condensed due to the shrinking amount of buildable areas, which significantly reduces the amount of light that occupants have access to. This lack of natural lighting results in health, safety and quality of life degradation. This paper presents a new technique of transmitting sunlight downward into narrow alleys and streets, by using a daylighting guiding acrylic panel that is capable of changing the direction and distribution of the incident light. The core of the proposed daylight guidance system is made up of light transmission panels with high quality. The corrugations have sine wave shaped cross-section so that the panel functions as an optical diffuser perpendicular to the direction of sunlight propagation. The day lighting system consists of the corrugated panels and a lattice frame, which supports the panel. The proposed system is to be mounted on the building roof facing the sun so as to redirect the incident sunlight downward into the narrow alleys or streets. Since building sizes and orientations are different the frame is arranged such that substantially deep light penetration and high luminance level can be achieved. Simulation results show that the proposed panel improves the illuminance values by more than 200% and 400% in autumn and winter, respectively, provides fan-out angle that exceeds 80° for certain solar altitudes and the transmitted power percentage varies from 40% to 90% as the solar altitude varies from 10° to 80°. Experimental results are in a good agreement with the simulations.

  4. Balancing Energy and Performance in Dense Linear System Solvers for Hybrid ARM+GPU platforms

    Directory of Open Access Journals (Sweden)

    Juan P. Silva

    2016-04-01

    Full Text Available The high performance computing community has traditionally focused uniquely on the reduction of execution time, though in the last years, the optimization of energy consumption has become a main issue. A reduction of energy usage without a degradation of performance requires the adoption of energy-efficient hardware platforms accompanied by the development of energy-aware algorithms and computational kernels. The solution of linear systems is a key operation for many scientific and engineering problems. Its relevance has motivated an important amount of work, and consequently, it is possible to find high performance solvers for a wide variety of hardware platforms. In this work, we aim to develop a high performance and energy-efficient linear system solver. In particular, we develop two solvers for a low-power CPU-GPU platform, the NVIDIA Jetson TK1. These solvers implement the Gauss-Huard algorithm yielding an efficient usage of the target hardware as well as an efficient memory access. The experimental evaluation shows that the novel proposal reports important savings in both time and energy-consumption when compared with the state-of-the-art solvers of the platform.

  5. Scalable Molecular Dynamics for Large Biomolecular Systems

    Directory of Open Access Journals (Sweden)

    Robert K. Brunner

    2000-01-01

    Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.

  6. Coulomb interactions in dense two-dimensional electron systems in a magnetic field

    International Nuclear Information System (INIS)

    Cheng, Szucheng.

    1988-01-01

    The simplest model of a two-dimensional system ignores the Coulomb interactions between the electrons. In this approximation, the electrons occupy the Landau levels, broadened by impurities and irregularities in the lattice. This independent electron approximation has usually been used to discuss observations for electron densities ρ and magnetic fields B where bar ν > 1 (bar ν triple-bond the number of Landau levels occupied). The most famous example is the theory of the integral Quantum Hall effect. However, when bar ν 1, electron-electron interactions should become important through the mixing of Landau levels. This thesis describes calculations for bar ν > 1 on phenomena which should be sensitive to electron-electron interactions: Wigner crystallization, the stability of the Landau levels under electron-electron interactions, the existence of quasiparticles and quasiholes, and the densities of states. The main results obtained concern: (1) The values of ρ and B where crystallization should occur when bar ν > 1. (2) The effect of electron-electron interactions in broadening the individual Landau levels, and in distributing the amplitudes for the excitation of independent electrons over many Landau levels. (3) The existence of quasiparticles and quasiholes whose lifetime is infinite near the Fermi level

  7. Applications of Extensive Green-roof Systems in Contributing to Sustainable Development in Densely Populated Cities: a Hong Kong Study

    Directory of Open Access Journals (Sweden)

    Xiaoling Zhang

    2011-03-01

    Full Text Available Developed cities such as Hong Kong are usually densely populated. Since the land is limited, high-rise buildings are constructed. When the building height becomes higher, air flow is reduced and heat is trapped among high-rise buildings. Air temperature will be greatly increased and air pollution becomes a serious problem. This creates a walled building problem. To reduce air temperature caused by the wall-effects, various methods have been developed in the previous studies. One typical method is the use of green roof systems. The application of extensive green roofs on the existing building rooftops has been recommended in Hong Kong since 2001. The advantage of this practice is that no additional floor area is required and it can also improve urban greenery. Although a green roof system has been introduced and adopted in Hong Kong since 2001, the emphasis is mainly given to the application of intensive green roofs for podium garden instead of extensive green roofs. It is considered valuable and necessary of the extensive green roofs for the buildings. This paper investigates the current practice of using extensive green roofs in Hong Kong. The constraints in applying extensive green roofs are investigated, which leads to studying the solutions for mitigating these constraints and improving the future development of the implementation.

  8. DENSE MULTIPHASE FLOW SIMULATION: CONTINUUM MODEL FOR POLY-DISPERSED SYSTEMS USING KINETIC THEORY

    Energy Technology Data Exchange (ETDEWEB)

    Moses Bogere

    2011-08-31

    The overall objective of the project was to verify the applicability of the FCMOM approach to the kinetic equations describing the particle flow dynamics. For monodispersed systems the fundamental equation governing the particle flow dynamics is the Boltzmann equation. During the project, the FCMOM was successfully applied to several homogeneous and in-homogeneous problems in different flow regimes, demonstrating that the FCMOM has the potential to be used to solve efficiently the Boltzmann equation. However, some relevant issues still need to be resolved, i.e. the homogeneous cooling problem (inelastic particles cases) and the transition between different regimes. In this report, the results obtained in homogeneous conditions are discussed first. Then a discussion of the validation results for in-homogeneous conditions is provided. And finally, a discussion will be provided about the transition between different regimes. Alongside the work on development of FCMOM approach studies were undertaken in order to provide insights into anisotropy or particles kinetics in riser hydrodynamics. This report includes results of studies of multiphase flow with unequal granular temperatures and analysis of momentum re-distribution in risers due to particle-particle and fluid-particle interactions. The study of multiphase flow with unequal granular temperatures entailed both simulation and experimental studies of two particles sizes in a riser and, a brief discussion of what was accomplished will be provided. And finally, a discussion of the analysis done on momentum re-distribution of gas-particles flow in risers will be provided. In particular a discussion of the remaining work needed in order to improve accuracy and predictability of riser hydrodynamics based on two-fluid models and how they can be used to model segregation in risers.

  9. Dynamics of dense particle disks

    International Nuclear Information System (INIS)

    Araki, S.; Tremaine, S.; Toronto Univ., Canada)

    1986-01-01

    The present investigation of mechanical equilibrium and collisional transport processes in dense, differentially rotating particle disks is based on the Enskog (1922) theory of dense, hard sphere gases, with the single exception that the spheres are inelastic. The viscous instability suggested as a source of Saturn B ring structure does not arise in the models presented, although the ring may be subject to a phase transition analogous to the liquid-solid transition observed in molecular dynamics simulations of elastic hard spheres. In such a case, the ring would alternately exhibit zero-shear, or solid, and high shear, or liquid, zones. 29 references

  10. Efficient parallel iterative solvers for the solution of large dense linear systems arising from the boundary element method in electromagnetism

    Energy Technology Data Exchange (ETDEWEB)

    Alleon, G. [EADS-CCR, 31 - Blagnac (France); Carpentieri, B.; Du, I.S.; Giraud, L.; Langou, J.; Martin, E. [Cerfacs, 31 - Toulouse (France)

    2003-07-01

    The boundary element method has become a popular tool for the solution of Maxwell's equations in electromagnetism. It discretizes only the surface of the radiating object and gives rise to linear systems that are smaller in size compared to those arising from finite element or finite difference discretizations. However, these systems are prohibitively demanding in terms of memory for direct methods and challenging to solve by iterative methods. In this paper we address the iterative solution via preconditioned Krylov methods of electromagnetic scattering problems expressed in an integral formulation, with main focus on the design of the pre-conditioner. We consider an approximate inverse method based on the Frobenius-norm minimization with a pattern prescribed in advance. The pre-conditioner is constructed from a sparse approximation of the dense coefficient matrix, and the patterns both for the pre-conditioner and for the coefficient matrix are computed a priori using geometric information from the mesh. We describe the implementation of the approximate inverse in an out-of-core parallel code that uses multipole techniques for the matrix-vector products, and show results on the numerical scalability of our method on systems of size up to one million unknowns. We propose an embedded iterative scheme based on the GMRES method and combined with multipole techniques, aimed at improving the robustness of the approximate inverse for large problems. We prove by numerical experiments that the proposed scheme enables the solution of very large and difficult problems efficiently at reduced computational and memory cost. Finally we perform a preliminary study on a spectral two-level pre-conditioner to enhance the robustness of our method. This numerical technique exploits spectral information of the preconditioned systems to build a low rank-update of the pre-conditioner. (authors)

  11. Efficient parallel iterative solvers for the solution of large dense linear systems arising from the boundary element method in electromagnetism

    International Nuclear Information System (INIS)

    Alleon, G.; Carpentieri, B.; Du, I.S.; Giraud, L.; Langou, J.; Martin, E.

    2003-01-01

    The boundary element method has become a popular tool for the solution of Maxwell's equations in electromagnetism. It discretizes only the surface of the radiating object and gives rise to linear systems that are smaller in size compared to those arising from finite element or finite difference discretizations. However, these systems are prohibitively demanding in terms of memory for direct methods and challenging to solve by iterative methods. In this paper we address the iterative solution via preconditioned Krylov methods of electromagnetic scattering problems expressed in an integral formulation, with main focus on the design of the pre-conditioner. We consider an approximate inverse method based on the Frobenius-norm minimization with a pattern prescribed in advance. The pre-conditioner is constructed from a sparse approximation of the dense coefficient matrix, and the patterns both for the pre-conditioner and for the coefficient matrix are computed a priori using geometric information from the mesh. We describe the implementation of the approximate inverse in an out-of-core parallel code that uses multipole techniques for the matrix-vector products, and show results on the numerical scalability of our method on systems of size up to one million unknowns. We propose an embedded iterative scheme based on the GMRES method and combined with multipole techniques, aimed at improving the robustness of the approximate inverse for large problems. We prove by numerical experiments that the proposed scheme enables the solution of very large and difficult problems efficiently at reduced computational and memory cost. Finally we perform a preliminary study on a spectral two-level pre-conditioner to enhance the robustness of our method. This numerical technique exploits spectral information of the preconditioned systems to build a low rank-update of the pre-conditioner. (authors)

  12. Laboratory Information Systems in Molecular Diagnostics: Why Molecular Diagnostics Data are Different.

    Science.gov (United States)

    Lee, Roy E; Henricks, Walter H; Sirintrapun, Sahussapont J

    2016-03-01

    Molecular diagnostic testing presents new challenges to information management that are yet to be sufficiently addressed by currently available information systems for the molecular laboratory. These challenges relate to unique aspects of molecular genetic testing: molecular test ordering, informed consent issues, diverse specimen types that encompass the full breadth of specimens handled by traditional anatomic and clinical pathology information systems, data structures and data elements specific to molecular testing, varied testing workflows and protocols, diverse instrument outputs, unique needs and requirements of molecular test reporting, and nuances related to the dissemination of molecular pathology test reports. By satisfactorily addressing these needs in molecular test data management, a laboratory information system designed for the unique needs of molecular diagnostics presents a compelling reason to migrate away from the current paper and spreadsheet information management that many molecular laboratories currently use. This paper reviews the issues and challenges of information management in the molecular diagnostics laboratory.

  13. Long-Haul Dense Space Division Multiplexed Transmission over Low-Crosstalk Heterogeneous 32-Core Transmission Line Using Partial Recirculating Loop System

    DEFF Research Database (Denmark)

    Mizuno, Takayuki; Shibahara, Kohki; Ye, Feihong

    2017-01-01

    In this paper, we present long-haul 32-core dense space division multiplexed (DSDM) unidirectional transmission over a single-mode multicore transmission line. We developed a low-crosstalk heterogeneous 32-core fiber with a square lattice arrangement, and a novel partial recirculating loop system...

  14. High sensitivity optical molecular imaging system

    Science.gov (United States)

    An, Yu; Yuan, Gao; Huang, Chao; Jiang, Shixin; Zhang, Peng; Wang, Kun; Tian, Jie

    2018-02-01

    Optical Molecular Imaging (OMI) has the advantages of high sensitivity, low cost and ease of use. By labeling the regions of interest with fluorescent or bioluminescence probes, OMI can noninvasively obtain the distribution of the probes in vivo, which play the key role in cancer research, pharmacokinetics and other biological studies. In preclinical and clinical application, the image depth, resolution and sensitivity are the key factors for researchers to use OMI. In this paper, we report a high sensitivity optical molecular imaging system developed by our group, which can improve the imaging depth in phantom to nearly 5cm, high resolution at 2cm depth, and high image sensitivity. To validate the performance of the system, special designed phantom experiments and weak light detection experiment were implemented. The results shows that cooperated with high performance electron-multiplying charge coupled device (EMCCD) camera, precision design of light path system and high efficient image techniques, our OMI system can simultaneously collect the light-emitted signals generated by fluorescence molecular imaging, bioluminescence imaging, Cherenkov luminance and other optical imaging modality, and observe the internal distribution of light-emitting agents fast and accurately.

  15. Formation and fragmentation of protostellar dense cores

    International Nuclear Information System (INIS)

    Maury, Anaelle

    2009-01-01

    Stars form in molecular clouds, when they collapse and fragment to produce protostellar dense cores. These dense cores are then likely to contract under their own gravity, and form young protostars, that further evolve while accreting their circumstellar mass, until they reach the main sequence. The main goal of this thesis was to study the formation and fragmentation of protostellar dense cores. To do so, two main studies, described in this manuscript, were carried out. First, we studied the formation of protostellar cores by quantifying the impact of protostellar outflows on clustered star formation. We carried out a study of the protostellar outflows powered by the young stellar objects currently formed in the NGc 2264-C proto-cluster, and we show that protostellar outflows seem to play a crucial role as turbulence progenitors in clustered star forming regions, although they seem unlikely to significantly modify the global infall processes at work on clump scales. Second, we investigated the formation of multiple systems by core fragmentation, by using high - resolution observations that allow to probe the multiplicity of young protostars on small scales. Our results suggest that the multiplicity rate of protostars on small scales increase while they evolve, and thus favor dynamical scenarios for the formation of multiple systems. Moreover, our results favor magnetized scenarios of core collapse to explain the small-scale properties of protostars at the earliest stages. (author) [fr

  16. Intense, ultrashort light and dense, hot matter

    Indian Academy of Sciences (India)

    tiphoton and tunneling ionization, the physics of plasma formed in dense matter is .... A typical Gaussian laser pulse of 100 fs dura- .... J range) – and finally it is compressed back to its .... bond-hardening, molecular orientation and reori-.

  17. Nuclear molecular structure in heavy mass systems

    International Nuclear Information System (INIS)

    Arctaedius, T.; Bargholtz, C.

    1989-04-01

    A study is made of nuclear molecular configurations involving one heavy mass partner. The stability of these configurations to mass flow and to fission is investigated as well as their population in fusion reactions. It is concluded that shell effects in combination with the effects of angular momentum may be important in stabilizing certain configurations. A possible relation of these configurations to the so called superdeformed states is pointed out. The spectrum of rotational and vibrational trasitions within molecular configurations is investigated. For sufficiently mass-asymmetric systems the engergies of vibrational transitions are comparable to the neutron separation energy. Gamma radiation from such transitions may then be observable above the background of statistical transitions. The gamma spectrum and the directional distribution of the radioation following fusion reactions with 12 C and 16 O are calculated. (authors)

  18. Molecular Simulation of Reacting Systems; TOPICAL

    International Nuclear Information System (INIS)

    THOMPSON, AIDAN P.

    2002-01-01

    The final report for a Laboratory Directed Research and Development project entitled, Molecular Simulation of Reacting Systems is presented. It describes efforts to incorporate chemical reaction events into the LAMMPS massively parallel molecular dynamics code. This was accomplished using a scheme in which several classes of reactions are allowed to occur in a probabilistic fashion at specified times during the MD simulation. Three classes of reaction were implemented: addition, chain transfer and scission. A fully parallel implementation was achieved using a checkerboarding scheme, which avoids conflicts due to reactions occurring on neighboring processors. The observed chemical evolution is independent of the number of processors used. The code was applied to two test applications: irreversible linear polymerization and thermal degradation chemistry

  19. Molecular ecology of anaerobic reactor systems

    DEFF Research Database (Denmark)

    Hofman-Bang, H. Jacob Peider; Zheng, D.; Westermann, Peter

    2003-01-01

    Anaerobic reactor systems are essential for the treatment of solid and liquid wastes and constitute a core facility in many waste treatment plants. Although much is known about the basic metabolism in different types of anaerobic reactors, little is known about the microbes responsible for these ......Anaerobic reactor systems are essential for the treatment of solid and liquid wastes and constitute a core facility in many waste treatment plants. Although much is known about the basic metabolism in different types of anaerobic reactors, little is known about the microbes responsible...... to the abundance of each microbe in anaerobic reactor systems by rRNA probing. This chapter focuses on various molecular techniques employed and problems encountered when elucidating the microbial ecology of anaerobic reactor systems. Methods such as quantitative dot blot/fluorescence in-situ probing using various...

  20. Microelectromechanical systems integrating molecular spin crossover actuators

    Energy Technology Data Exchange (ETDEWEB)

    Manrique-Juarez, Maria D. [LCC, CNRS and Université de Toulouse, UPS, INP, F-31077 Toulouse (France); LAAS, CNRS and Université de Toulouse, INSA, UPS, F-31077 Toulouse (France); Rat, Sylvain; Salmon, Lionel; Molnár, Gábor; Bousseksou, Azzedine, E-mail: liviu.nicu@laas.fr, E-mail: azzedine.bousseksou@lcc-toulouse.fr [LCC, CNRS and Université de Toulouse, UPS, INP, F-31077 Toulouse (France); Mathieu, Fabrice; Saya, Daisuke; Séguy, Isabelle; Leïchlé, Thierry; Nicu, Liviu, E-mail: liviu.nicu@laas.fr, E-mail: azzedine.bousseksou@lcc-toulouse.fr [LAAS, CNRS and Université de Toulouse, INSA, UPS, F-31077 Toulouse (France)

    2016-08-08

    Silicon MEMS cantilevers coated with a 200 nm thin layer of the molecular spin crossover complex [Fe(H{sub 2}B(pz){sub 2}){sub 2}(phen)] (H{sub 2}B(pz){sub 2} = dihydrobis(pyrazolyl)borate and phen = 1,10-phenantroline) were actuated using an external magnetic field and their resonance frequency was tracked by means of integrated piezoresistive detection. The light-induced spin-state switching of the molecules from the ground low spin to the metastable high spin state at 10 K led to a well-reproducible shift of the cantilever's resonance frequency (Δf{sub r} = −0.52 Hz). Control experiments at different temperatures using coated as well as uncoated devices along with simple calculations support the assignment of this effect to the spin transition. This latter translates into changes in mechanical behavior of the cantilever due to the strong spin-state/lattice coupling. A guideline for the optimization of device parameters is proposed so as to efficiently harness molecular scale movements for large-scale mechanical work, thus paving the road for nanoelectromechanical systems (NEMS) actuators based on molecular materials.

  1. The Optical Bichromatic Force in Molecular Systems

    Science.gov (United States)

    Aldridge, Leland; Galica, Scott; Eyler, E. E.

    2015-05-01

    The optical bichromatic force has been demonstrated to be useful for slowing atomic beams much more rapidly than radiative forces. Through numerical simulations, we examine several aspects of applying the bichromatic force to molecular beams. One is the unavoidable existence of out-of-system radiative decay, requiring one or more repumping beams. We find that the average deceleration varies strongly with the repumping intensity, but when using optimal parameters, the force approaches the limiting value allowed by population statistics. Another consideration is the effect of fine and hyperfine structure. We examine a simplified multlevel model based on the B X transition in calcium monofluoride. To circumvent optical pumping into coherent dark states, we include two possible schemes: (1) a skewed dc magnetic field, and (2) rapid optical polarization switching. Our results indicate that the bichromatic force remains a viable option for creating large forces in molecular beams, with a reduction in the peak force by approximately an order of magnitude compared to a two-level atom, but little effect on the velocity range over which the force is effective. We also describe our progress towards experimental tests of the bichromatic force on a molecular beam of CaF. Supported by the National Science Foundation.

  2. Molecular marker systems for Oenothera genetics.

    Science.gov (United States)

    Rauwolf, Uwe; Golczyk, Hieronim; Meurer, Jörg; Herrmann, Reinhold G; Greiner, Stephan

    2008-11-01

    The genus Oenothera has an outstanding scientific tradition. It has been a model for studying aspects of chromosome evolution and speciation, including the impact of plastid nuclear co-evolution. A large collection of strains analyzed during a century of experimental work and unique genetic possibilities allow the exchange of genetically definable plastids, individual or multiple chromosomes, and/or entire haploid genomes (Renner complexes) between species. However, molecular genetic approaches for the genus are largely lacking. In this study, we describe the development of efficient PCR-based marker systems for both the nuclear genome and the plastome. They allow distinguishing individual chromosomes, Renner complexes, plastomes, and subplastomes. We demonstrate their application by monitoring interspecific exchanges of genomes, chromosome pairs, and/or plastids during crossing programs, e.g., to produce plastome-genome incompatible hybrids. Using an appropriate partial permanent translocation heterozygous hybrid, linkage group 7 of the molecular map could be assigned to chromosome 9.8 of the classical Oenothera map. Finally, we provide the first direct molecular evidence that homologous recombination and free segregation of chromosomes in permanent translocation heterozygous strains is suppressed.

  3. Developing Off-site Emergency Preparedness and Response Model (OEPRM) for Severe Accident of NPP in a Densely Populated Country Using System Dynamics Approach

    Energy Technology Data Exchange (ETDEWEB)

    Hossena, Muhammed Mufazzal; Kang, Kyoung Ho; Song, Jin Ho [KAERI, Deajeon (Korea, Republic of)

    2016-05-15

    The main objectives of this study are to find the influencing factors of systems and sub-systems of OEPRM, to find the interdependency among the influencing factors, and to develop a conceptual qualitative OEPRM for densely populated NPP country in case of SA using system dynamics (SD). NPP accidents are classified as nuclear accidents and incidents depending on the severity. Severe accident (SA) is certain low probability accident that are beyond design basis accident which may arise due to multiple failures of safety systems leading to significant core degradation and jeopardize the integrity of many or all of the barriers to the release of radioactive material. The weakness to the off-site emergency response in the time of Fukushima accident was observed. So, it is crucial to develop an off-site emergency preparedness and responses model (OEPRM) for radiological emergency in densely populated country from the Fukushima emergency response lesson. In this study, an OEPRM is developed for densely populated NPP country to mitigate radiological effects in case of SA using SD approach. Besides, this study focuses the weakness of emergency response in Fukushima accident and proposed solution approach. The development of OEPRM in case of SA of NPP is very complex because of the involvement of various organization and it requires highly specialized agencies and technical experts. Moreover, if the country is agriculture based, it will make completely sophisticated.

  4. Developing Off-site Emergency Preparedness and Response Model (OEPRM) for Severe Accident of NPP in a Densely Populated Country Using System Dynamics Approach

    International Nuclear Information System (INIS)

    Hossena, Muhammed Mufazzal; Kang, Kyoung Ho; Song, Jin Ho

    2016-01-01

    The main objectives of this study are to find the influencing factors of systems and sub-systems of OEPRM, to find the interdependency among the influencing factors, and to develop a conceptual qualitative OEPRM for densely populated NPP country in case of SA using system dynamics (SD). NPP accidents are classified as nuclear accidents and incidents depending on the severity. Severe accident (SA) is certain low probability accident that are beyond design basis accident which may arise due to multiple failures of safety systems leading to significant core degradation and jeopardize the integrity of many or all of the barriers to the release of radioactive material. The weakness to the off-site emergency response in the time of Fukushima accident was observed. So, it is crucial to develop an off-site emergency preparedness and responses model (OEPRM) for radiological emergency in densely populated country from the Fukushima emergency response lesson. In this study, an OEPRM is developed for densely populated NPP country to mitigate radiological effects in case of SA using SD approach. Besides, this study focuses the weakness of emergency response in Fukushima accident and proposed solution approach. The development of OEPRM in case of SA of NPP is very complex because of the involvement of various organization and it requires highly specialized agencies and technical experts. Moreover, if the country is agriculture based, it will make completely sophisticated

  5. DENSE MEDIUM CYCLONE OPTIMIZATON

    Energy Technology Data Exchange (ETDEWEB)

    Gerald H. Luttrell; Chris J. Barbee; Peter J. Bethell; Chris J. Wood

    2005-06-30

    Dense medium cyclones (DMCs) are known to be efficient, high-tonnage devices suitable for upgrading particles in the 50 to 0.5 mm size range. This versatile separator, which uses centrifugal forces to enhance the separation of fine particles that cannot be upgraded in static dense medium separators, can be found in most modern coal plants and in a variety of mineral plants treating iron ore, dolomite, diamonds, potash and lead-zinc ores. Due to the high tonnage, a small increase in DMC efficiency can have a large impact on plant profitability. Unfortunately, the knowledge base required to properly design and operate DMCs has been seriously eroded during the past several decades. In an attempt to correct this problem, a set of engineering tools have been developed to allow producers to improve the efficiency of their DMC circuits. These tools include (1) low-cost density tracers that can be used by plant operators to rapidly assess DMC performance, (2) mathematical process models that can be used to predict the influence of changes in operating and design variables on DMC performance, and (3) an expert advisor system that provides plant operators with a user-friendly interface for evaluating, optimizing and trouble-shooting DMC circuits. The field data required to develop these tools was collected by conducting detailed sampling and evaluation programs at several industrial plant sites. These data were used to demonstrate the technical, economic and environmental benefits that can be realized through the application of these engineering tools.

  6. Molecular Imaging with Activatable Reporter Systems

    Directory of Open Access Journals (Sweden)

    Gang Niu, Xiaoyuan Chen

    2012-01-01

    Full Text Available Molecular imaging is a newly emerged multiple disciplinary field that aims to visualize, characterize and quantitatively measure biological processes at cellular and molecular levels in humans and other living systems. A reporter gene is a piece of DNA encoding reporter protein, which presents as a readily measurable phenotype that can be distinguished easily from the background of endogenous protein. After being transferred into cells of organ systems (transgenes, the reporter gene can be utilized to visualize transcriptional and posttranscriptional regulation of gene expression, protein-protein interactions, or trafficking of proteins or cells in living subjects. Herein, we review previous classification of reporter genes and regroup the reporter gene based imaging as basic, inducible and activatable, based on the regulation of reporter gene transcription and post-translational modification of reporter proteins. We then focus on activatable reporters, in which the signal can be activated at the posttranslational level for visualizing protein-protein interactions, protein phosphorylation or tertiary structure changes. The applications of several types of activatable reporters will also be summarized. We conclude that activatable reporter imaging can benefit both basic biomedical research and drug development.

  7. Energy transformation in molecular electronic systems

    International Nuclear Information System (INIS)

    Kasha, M.

    1985-01-01

    Our new optical pumping spectroscopy (steady state, and double-laser pulse) allows the production and study of the unstable rare tautomer in its ground and excited states, including picosecond dynamic studies. Molecules under study here included 7-azaindole (model for biological purines), 3-hydroxyflavone (model for plant flavones), lumichrome, and other heterocyclics. New detailed molecular mechanisms for proton transfer are derived, especially with catalytic assisting molecules. A new proton-transfer laser of extraordinary efficiency has become a side dividend, possibly worth of industrial development. The excited and highly reactive singlet molecular oxygen species 1 Δ/sub g/) has proven to be ubiquitous in chemical peroxide systems and in physically excited sensitizer-oxygen systems. Hyperbaric oxygen mechanisms in biology probably involve singlet oxygen. We have undertaken a spectroscopic study of tris - dibenzoylmethane chelates of Al, Gd, Eu, and Yb trivalent ions. These chelates offer a variety of electronic behaviors, from Z-effects on π-electron spin-orbital coupling (Al, Gd) to Weissman intramolecular energy transfer to 4f mestable levels (Eu, Gd). Elegant new spectroscopic resolution at 77K permits separation of tautomeric, parasitic self-absorption, dissociation, and cage effects to be resolved. 18 refs., 4 figs

  8. Systems Pharmacology in Small Molecular Drug Discovery

    Directory of Open Access Journals (Sweden)

    Wei Zhou

    2016-02-01

    Full Text Available Drug discovery is a risky, costly and time-consuming process depending on multidisciplinary methods to create safe and effective medicines. Although considerable progress has been made by high-throughput screening methods in drug design, the cost of developing contemporary approved drugs did not match that in the past decade. The major reason is the late-stage clinical failures in Phases II and III because of the complicated interactions between drug-specific, human body and environmental aspects affecting the safety and efficacy of a drug. There is a growing hope that systems-level consideration may provide a new perspective to overcome such current difficulties of drug discovery and development. The systems pharmacology method emerged as a holistic approach and has attracted more and more attention recently. The applications of systems pharmacology not only provide the pharmacodynamic evaluation and target identification of drug molecules, but also give a systems-level of understanding the interaction mechanism between drugs and complex disease. Therefore, the present review is an attempt to introduce how holistic systems pharmacology that integrated in silico ADME/T (i.e., absorption, distribution, metabolism, excretion and toxicity, target fishing and network pharmacology facilitates the discovery of small molecular drugs at the system level.

  9. Atoms in dense plasmas

    International Nuclear Information System (INIS)

    More, R.M.

    1986-01-01

    Recent experiments with high-power pulsed lasers have strongly encouraged the development of improved theoretical understanding of highly charged ions in a dense plasma environment. This work examines the theory of dense plasmas with emphasis on general rules which govern matter at extreme high temperature and density. 106 refs., 23 figs

  10. Atoms in dense plasmas

    Energy Technology Data Exchange (ETDEWEB)

    More, R.M.

    1986-01-01

    Recent experiments with high-power pulsed lasers have strongly encouraged the development of improved theoretical understanding of highly charged ions in a dense plasma environment. This work examines the theory of dense plasmas with emphasis on general rules which govern matter at extreme high temperature and density. 106 refs., 23 figs.

  11. Predicting diffusivities in dense fluid mixtures

    Directory of Open Access Journals (Sweden)

    C. DARIVA

    1999-09-01

    Full Text Available In this work the Enskog solution of the Boltzmann equation, as corrected by Speedy, together with the Weeks-Chandler-Andersen (WCA perturbation theory of liquids is employed in correlating and predicting self-diffusivities of dense fluids. Afterwards this theory is used to estimate mutual diffusion coefficients of solutes at infinite dilution in sub and supercritical solvents. We have also investigated the behavior of Fick diffusion coefficients in the proximity of a binary vapor-liquid critical point since this subject is of great interest for extraction purposes. The approach presented here, which makes use of a density and temperature dependent hard-sphere diameter, is shown to be excellent for predicting diffusivities in dense pure fluids and fluid mixtures. The calculations involved highly nonideal mixtures as well as systems with high molecular asymmetry. The predicted diffusivities are in good agreement with the experimental data for the pure and binary systems. The methodology proposed here makes only use of pure component information and density of mixtures. The simple algebraic relations are proposed without any binary adjustable parameters and can be readily used for estimating diffusivities in multicomponent mixtures.

  12. Well-posed two-temperature constitutive equations for stable dense fluid shock waves using molecular dynamics and generalizations of Navier-Stokes-Fourier continuum mechanics.

    Science.gov (United States)

    Hoover, Wm G; Hoover, Carol G

    2010-04-01

    Guided by molecular dynamics simulations, we generalize the Navier-Stokes-Fourier constitutive equations and the continuum motion equations to include both transverse and longitudinal temperatures. To do so we partition the contributions of the heat transfer, the work done, and the heat flux vector between the longitudinal and transverse temperatures. With shockwave boundary conditions time-dependent solutions of these equations converge to give stationary shockwave profiles. The profiles include anisotropic temperature and can be fitted to molecular dynamics results, demonstrating the utility and simplicity of a two-temperature description of far-from-equilibrium states.

  13. New Compensation Technique for Fiber Impairments in Ultra High Capacity Super channel Based on (QDPASK Dense wavelength division multiplex (DWDM systems

    Directory of Open Access Journals (Sweden)

    Ibrahim A.Murdas

    2017-07-01

    Full Text Available In this paper we want to increase the data rate and to get larger transmission distance, therefore we use the Advanced modulation technique QDPASK in DWDM system with low channels space. In case of long transmission distance and multi channels system both giving rise to inter channel crosstalk induced by fiber nonlinearities as a result the use of advanced modulation technique becomes difficult. In this paper Quaternary differential phase amplitude shift keying (QDPASK is designed for 32 dense wavelength division multiplexing (DWDM channels, therefore we proposed a new cascade compensation system consist of optical and digital back propagation techniques (ODBP for compensate the linear and nonlinear effects . A performance of the system was reported using QDPASK DWDM fiber-optic system for various system parameters. The research is tested in VPI maker environment.

  14. Computer modeling of properties of complex molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Kulkova, E.Yu. [Moscow State University of Technology “STANKIN”, Vadkovsky per., 1, Moscow 101472 (Russian Federation); Khrenova, M.G.; Polyakov, I.V. [Lomonosov Moscow State University, Chemistry Department, Leninskie Gory 1/3, Moscow 119991 (Russian Federation); Nemukhin, A.V. [Lomonosov Moscow State University, Chemistry Department, Leninskie Gory 1/3, Moscow 119991 (Russian Federation); N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow 119334 (Russian Federation)

    2015-03-10

    Large molecular aggregates present important examples of strongly nonhomogeneous systems. We apply combined quantum mechanics / molecular mechanics approaches that assume treatment of a part of the system by quantum-based methods and the rest of the system with conventional force fields. Herein we illustrate these computational approaches by two different examples: (1) large-scale molecular systems mimicking natural photosynthetic centers, and (2) components of prospective solar cells containing titan dioxide and organic dye molecules. We demonstrate that modern computational tools are capable to predict structures and spectra of such complex molecular aggregates.

  15. Common intersection points in dense fluids via equations of state

    International Nuclear Information System (INIS)

    Parsafar, G. A.; Noorian, R.

    2001-01-01

    Some new of state which are derived for dense fluids in recent years, namely the linear isotherm regularity, the dense system equation of state, Ihm-Song-Mason equation of state, and a newly derived semi-empirical equation of state have used to investigate the common intersection point of isobaric expansivity (α p ) in dense fluids. We have shown that the accuracy of these equations of state in predicting such a common intersection point is reduced from the new semi-imperial equation of state, dense system equation of state, linear isotherm regularity, to Ihm-Song-Mason equation of state. respectively. Form physical point of view, the van der Waals equation of state is used to investigate such an intersection point. It is shown that the van der Waals repulsion forces and temperature dependency of the effective molecular diameter are important for existence of this common point. Finally, we have shown that the common intersection points of the isotherms of thermal pressure coefficient, the isotherms of heat capacity at constant volume, and the iso chores of internal pressure for a fluid are related to each other. Also, the common intersection points of the reduced bulk modulus and 1/(Tα p ) for isotherms of a fluid both appear at the same density

  16. Nonlinear Absorption-Gain Response and Population Dynamics in a Laser-Driven Four-Level Dense Atomic System

    International Nuclear Information System (INIS)

    Li Jiahua; Liu Jibing; Luo Jinming; Xie Xiaotao

    2006-01-01

    We theoretically investigate the response of nonlinear absorption and population dynamics in optically dense media of four-level atoms driven by a single-mode probe laser, via taking the density-dependent near dipole-dipole (NDD) interactions into consideration. The influence of the NDD effects on the absorption of the probe field and population dynamics is predicted via numerical calculations. It is shown that the NDD effects can reduce gradually to transient absorption with the increase of the strengths of the NDD interactions, and transient amplification can be achieved. In the steady-state limit, the probe field exhibits transparency for strong NDD interactions. Alternatively, the population entirely remains at the ground state due to the NDD effects.

  17. Molecular communications and nanonetworks from nature to practical systems

    CERN Document Server

    Atakan, Barış

    2014-01-01

    In this book, the concepts of molecular communications and nanonetworks are introduced. Throughout the book, the existing molecular communication paradigms are categorized into two main groups. The first group includes the Passive Molecular Communication (PMC) paradigms in which molecules freely diffuse to transfer information from a transmitter to a receiver. The second group includes the Active Molecular Communication (AMC) paradigms in which molecules are carried or guided by some mediators such as molecular motors, gap junction channels and bacteria. In the book, after briefly discussing why molecular communication is needed for the sophisticated nano and biotechnology applications, the existing molecular communication systems are first presented. Then, the principles of diffusion phenomena and molecular reception with absorbers and the ligand-receptor binding mechanism are introduced. Based on these principles, the communication theories and techniques are given for the PMC. Then, the physical dynamics o...

  18. Warm Dense Matter: An Overview

    International Nuclear Information System (INIS)

    Kalantar, D H; Lee, R W; Molitoris, J D

    2004-01-01

    This document provides a summary of the ''LLNL Workshop on Extreme States of Materials: Warm Dense Matter to NIF'' which was held on 20, 21, and 22 February 2002 at the Wente Conference Center in Livermore, CA. The warm dense matter regime, the transitional phase space region between cold material and hot plasma, is presently poorly understood. The drive to understand the nature of matter in this regime is sparking scientific activity worldwide. In addition to pure scientific interest, finite temperature dense matter occurs in the regimes of interest to the SSMP (Stockpile Stewardship Materials Program). So that obtaining a better understanding of WDM is important to performing effective experiments at, e.g., NIF, a primary mission of LLNL. At this workshop we examined current experimental and theoretical work performed at, and in conjunction with, LLNL to focus future activities and define our role in this rapidly emerging research area. On the experimental front LLNL plays a leading role in three of the five relevant areas and has the opportunity to become a major player in the other two. Discussion at the workshop indicated that the path forward for the experimental efforts at LLNL were two fold: First, we are doing reasonable baseline work at SPLs, HE, and High Energy Lasers with more effort encouraged. Second, we need to plan effectively for the next evolution in large scale facilities, both laser (NIF) and Light/Beam sources (LCLS/TESLA and GSI) Theoretically, LLNL has major research advantages in areas as diverse as the thermochemical approach to warm dense matter equations of state to first principles molecular dynamics simulations. However, it was clear that there is much work to be done theoretically to understand warm dense matter. Further, there is a need for a close collaboration between the generation of verifiable experimental data that can provide benchmarks of both the experimental techniques and the theoretical capabilities. The conclusion of this

  19. Dense image correspondences for computer vision

    CERN Document Server

    Liu, Ce

    2016-01-01

    This book describes the fundamental building-block of many new computer vision systems: dense and robust correspondence estimation. Dense correspondence estimation techniques are now successfully being used to solve a wide range of computer vision problems, very different from the traditional applications such techniques were originally developed to solve. This book introduces the techniques used for establishing correspondences between challenging image pairs, the novel features used to make these techniques robust, and the many problems dense correspondences are now being used to solve. The book provides information to anyone attempting to utilize dense correspondences in order to solve new or existing computer vision problems. The editors describe how to solve many computer vision problems by using dense correspondence estimation. Finally, it surveys resources, code, and data necessary for expediting the development of effective correspondence-based computer vision systems.   ·         Provides i...

  20. Quantum dense key distribution

    International Nuclear Information System (INIS)

    Degiovanni, I.P.; Ruo Berchera, I.; Castelletto, S.; Rastello, M.L.; Bovino, F.A.; Colla, A.M.; Castagnoli, G.

    2004-01-01

    This paper proposes a protocol for quantum dense key distribution. This protocol embeds the benefits of a quantum dense coding and a quantum key distribution and is able to generate shared secret keys four times more efficiently than the Bennet-Brassard 1984 protocol. We hereinafter prove the security of this scheme against individual eavesdropping attacks, and we present preliminary experimental results, showing its feasibility

  1. Development of the Fragment Molecular Orbital Method for Calculating Nonlocal Excitations in Large Molecular Systems.

    Science.gov (United States)

    Fujita, Takatoshi; Mochizuki, Yuji

    2018-04-19

    We developed the fragment-based method for calculating nonlocal excitations in large molecular systems. This method is based on the multilayer fragment molecular orbital method and the configuration interaction single (CIS) wave function using localized molecular orbitals. The excited-state wave function for the whole system is described as a superposition of configuration state functions (CSFs) for intrafragment excitations and for interfragment charge-transfer excitations. The formulation and calculations of singlet excited-state Hamiltonian matrix elements in the fragment CSFs are presented in detail. The efficient approximation schemes for calculating the matrix elements are also presented. The computational efficiency and the accuracy were evaluated using the molecular dimers and molecular aggregates. We confirmed that absolute errors of 50 meV (relative to the conventional calculations) are achievable for the molecular systems in their equilibrium geometries. The perturbative electron correlation correction to the CIS excitation energies is also demonstrated. The present theory can compute a large number of excited states in large molecular systems; in addition, it allows for the systematic derivation of a model exciton Hamiltonian. These features are useful for studying excited-state dynamics in condensed molecular systems based on the ab initio electronic structure theory.

  2. Agent-Based Modeling in Molecular Systems Biology.

    Science.gov (United States)

    Soheilypour, Mohammad; Mofrad, Mohammad R K

    2018-06-08

    Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is still a need for methods that bridge the gap between spatially-detailed and computationally-efficient approaches. In this review, we summarize the capabilities of agent-based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease. © 2018 WILEY Periodicals, Inc.

  3. Remote Laser Evaporative Molecular Absorption Spectroscopy Sensor System

    Data.gov (United States)

    National Aeronautics and Space Administration — We propose a sensor system capable of remotely probing the molecular composition of cold solar system targets (asteroids, comets, planets, moons), such as from a...

  4. Logic circuits based on molecular spider systems.

    Science.gov (United States)

    Mo, Dandan; Lakin, Matthew R; Stefanovic, Darko

    2016-08-01

    Spatial locality brings the advantages of computation speed-up and sequence reuse to molecular computing. In particular, molecular walkers that undergo localized reactions are of interest for implementing logic computations at the nanoscale. We use molecular spider walkers to implement logic circuits. We develop an extended multi-spider model with a dynamic environment wherein signal transmission is triggered via localized reactions, and use this model to implement three basic gates (AND, OR, NOT) and a cascading mechanism. We develop an algorithm to automatically generate the layout of the circuit. We use a kinetic Monte Carlo algorithm to simulate circuit computations, and we analyze circuit complexity: our design scales linearly with formula size and has a logarithmic time complexity. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  5. Transport coefficients of dense fluids composed of globular molecules. Equilibrium molecular dynamics investigations using more-center Lennard-Jones potentials

    Science.gov (United States)

    Hoheisel, C.

    1988-09-01

    Equilibrium molecular dynamics calculations with constraints have been performed for model liquids SF6 and CF4. The computations were carried out with four- and six-center Lennard-Jones potentials and up to 2×105 integration steps. Shear, bulk viscosity and the thermal conductivity have been calculated with use of Green-Kubo relations in the formulation of ``molecule variables.'' Various thermodynamic states were investigated. For SF6, a detailed comparison with experimental data was possible. For CF4, the MD results could only be compared with experiment for one liquid state. For the latter liquid, a complementary comparison was performed using MD results obtained with a one-center Lennard-Jones potential. A limited test of the particle number dependence of the results is presented. Partial and total correlations functions are shown and discussed with respect to findings obtained for the one-center Lennard-Jones liquid.

  6. A FIRST LOOK AT THE AURIGA-CALIFORNIA GIANT MOLECULAR CLOUD WITH HERSCHEL AND THE CSO: CENSUS OF THE YOUNG STELLAR OBJECTS AND THE DENSE GAS

    Energy Technology Data Exchange (ETDEWEB)

    Harvey, Paul M. [Astronomy Department, University of Texas at Austin, 1 University Station C1400, Austin, TX 78712-0259 (United States); Fallscheer, Cassandra [Department of Physics and Astronomy, University of Victoria, 3800 Finnerty Road, Victoria, BC V8P 5C2 (Canada); Ginsburg, Adam [Center for Astrophysics and Space Astronomy, University of Colorado, 389 UCB, Boulder, CO 80309-0389 (United States); Terebey, Susan [Department of Physics and Astronomy PS315, 5151 State University Drive, California State University at Los Angeles, Los Angeles, CA 90032 (United States); Andre, Philippe; Koenyves, Vera [Laboratoire AIM, CEA/DSM-CNRS-Universite Paris Diderot, IRFU/Service d' Astrophysique, CEA Saclay, F-91191 Gif-sur-Yvette (France); Bourke, Tyler L. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Di Francesco, James; Matthews, Brenda C. [Herzberg Institute of Astrophysics, National Research Council of Canada, 5071 West Saanich Road, Victoria, BC V9E 2E7 (Canada); Peterson, Dawn E., E-mail: pmh@astro.as.utexas.edu, E-mail: Cassandra.Fallscheer@nrc-cnrc.gc.ca, E-mail: adam.ginsburg@colorado.edu, E-mail: sterebe@calstatela.edu, E-mail: pandre@cea.fr, E-mail: vera.konyves@cea.fr, E-mail: tbourke@cfa.harvard.edu, E-mail: James.DiFrancesco@nrc-cnrc.gc.ca, E-mail: Brenda.Matthews@nrc-cnrc.gc.ca, E-mail: dpeterson@spacescience.org [Space Science Institute, 4750 Walnut Street, Suite 205, Boulder, CO 80303 (United States)

    2013-02-20

    We have mapped the Auriga/California molecular cloud with the Herschel PACS and SPIRE cameras and the Bolocam 1.1 mm camera on the Caltech Submillimeter Observatory with the eventual goal of quantifying the star formation and cloud structure in this giant molecular cloud (GMC) that is comparable in size and mass to the Orion GMC, but which appears to be forming far fewer stars. We have tabulated 60 compact 70/160 {mu}m sources that are likely pre-main-sequence objects and correlated those with Spitzer and WISE mid-IR sources. At 1.1 mm, we find 18 cold, compact sources and discuss their properties. The most important result from this part of our study is that we find a modest number of additional compact young objects beyond those identified at shorter wavelengths with Spitzer. We also describe the dust column density and temperature structure derived from our photometric maps. The column density peaks at a few Multiplication-Sign 10{sup 22} cm{sup -2} (N {sub H2}) and is distributed in a clear filamentary structure along which nearly all of the pre-main-sequence objects are found. We compare the young stellar object surface density to the gas column density and find a strong nonlinear correlation between them. The dust temperature in the densest parts of the filaments drops to {approx}10 K from values {approx}14-15 K in the low-density parts of the cloud. We also derive the cumulative mass fraction and probability density function of material in the cloud, which we compare with similar data on other star-forming clouds.

  7. A FIRST LOOK AT THE AURIGA-CALIFORNIA GIANT MOLECULAR CLOUD WITH HERSCHEL AND THE CSO: CENSUS OF THE YOUNG STELLAR OBJECTS AND THE DENSE GAS

    International Nuclear Information System (INIS)

    Harvey, Paul M.; Fallscheer, Cassandra; Ginsburg, Adam; Terebey, Susan; André, Philippe; Könyves, Vera; Bourke, Tyler L.; Di Francesco, James; Matthews, Brenda C.; Peterson, Dawn E.

    2013-01-01

    We have mapped the Auriga/California molecular cloud with the Herschel PACS and SPIRE cameras and the Bolocam 1.1 mm camera on the Caltech Submillimeter Observatory with the eventual goal of quantifying the star formation and cloud structure in this giant molecular cloud (GMC) that is comparable in size and mass to the Orion GMC, but which appears to be forming far fewer stars. We have tabulated 60 compact 70/160 μm sources that are likely pre-main-sequence objects and correlated those with Spitzer and WISE mid-IR sources. At 1.1 mm, we find 18 cold, compact sources and discuss their properties. The most important result from this part of our study is that we find a modest number of additional compact young objects beyond those identified at shorter wavelengths with Spitzer. We also describe the dust column density and temperature structure derived from our photometric maps. The column density peaks at a few × 10 22 cm –2 (N H2 ) and is distributed in a clear filamentary structure along which nearly all of the pre-main-sequence objects are found. We compare the young stellar object surface density to the gas column density and find a strong nonlinear correlation between them. The dust temperature in the densest parts of the filaments drops to ∼10 K from values ∼14-15 K in the low-density parts of the cloud. We also derive the cumulative mass fraction and probability density function of material in the cloud, which we compare with similar data on other star-forming clouds.

  8. THE SPITZER c2d SURVEY OF NEARBY DENSE CORES: JET AND MOLECULAR OUTFLOW ASSOCIATED WITH A YOUNG STELLAR OBJECT IN CORE A OF L1251

    International Nuclear Information System (INIS)

    Lee, Jeong-Eun; Kim, Il-Suk; Choi, Yunhee; Lee, Ho-Gyu; Shinn, Jong-Ho; Dunham, Michael M.; Evans, Neal J.; Kim, Chang Hee; Bourke, Tyler L.

    2010-01-01

    A long infrared jet has been discovered by the Spitzer c2d Legacy Program in core A of L1251. It is associated with a very embedded Class 0 object with an accretion luminosity of about 0.9 L sun derived by radiative transfer model fitting to the observed spectral energy distribution. Comparing the observed Infrared Array Camera colors along the infrared jet with those calculated from a model of an admixture of gas with a power-law temperature distribution indicates that the jet is possibly created by a paraboloidal bow shock propagating into the ambient medium of n(H 2 ) = 10 5 cm -3 . In addition, the variation of the power-law index along the jet suggests that the portion of hot gas decreases with distance from the jet engine. The molecular outflow in this region has been mapped for the first time using CO data. From the calculated outflow momentum flux, a very strong lower limit to the average accretion luminosity is 3.6 sin i/cos 3 i L sun , indicative of a decrease in the accretion rate with time.

  9. Advances in study of molecular imaging reporte gene systems

    International Nuclear Information System (INIS)

    Wu Tao; An Rui

    2010-01-01

    The use of molecular imaging reporter gene systems has allowed gene therapy to move from the laboratory to the clinical application, which provides methodology to monitor the expression of therapeutic gene noninvasively and achieve quantitative outcome in vivo. Recently, the radionuclide reporter gene still is the focus many studies, but MRI and optical reporter gene have gradually played a important part in reporter gene systems. On the basis of combination of multi-subject, for example applied chemistry and molecular biology, more and more new modified reporter genes and molecular probes have spread out. This paper mainly introduces the advantages and disadvantages of reporter gene system and development trends. (authors)

  10. A New Molecular Surveillance System for Leishmaniasis

    Science.gov (United States)

    Pandey, Kishor; Pandey, Basu Dev; Mallik, Arun Kumar; Acharya, Jyoti; Kato, Kentaro; Kaneko, Osamu; Ferreira, Pedro Eduardo

    2014-01-01

    Abstract. Presently, global efforts are being made to control and eradicate the deadliest tropical diseases through the improvement of adequate interventions. A critical point for programs to succeed is the prompt and accurate diagnosis in endemic regions. Rapid diagnostic tests (RDTs) are being massively deployed and used to improve diagnosis in tropical countries. In the present report, we evaluated the hypothesis of, after use for diagnosis, the reuse of the Leishmania RDT kit as a DNA source, which can be used downstream as a molecular surveillance and/or quality control tool. As a proof of principle, a polymerase chain reaction-based method was used to detect Leishmania spp. minicircle kinetoplast DNA from leishmaniasis RDT kits. Our results show that Leishmania spp. DNA can be extracted from used RDTs and may constitute an important, reliable, and affordable tool to assist in future leishmaniasis molecular surveillance methods. PMID:24752687

  11. Electron-nuclear dynamics of molecular systems

    International Nuclear Information System (INIS)

    Diz, A.; Oehrn, Y.

    1994-01-01

    The content of an ab initio time-dependent theory of quantum molecular dynamics of electrons and atomic nuclei is presented. Employing the time-dependent variational principle and a family of approximate state vectors yields a set of dynamical equations approximating the time-dependent Schroedinger equation. These equations govern the time evolution of the relevant state vector parameters as molecular orbital coefficients, nuclear positions, and momenta. This approach does not impose the Born-Oppenheimer approximation, does not use potential energy surfaces, and takes into account electron-nuclear coupling. Basic conservation laws are fully obeyed. The simplest model of the theory employs a single determinantal state for the electrons and classical nuclei and is implemented in the computer code ENDyne. Results from this ab-initio theory are reported for ion-atom and ion-molecule collisions

  12. Immunodiagnosis and molecular validation of Toxoplasma gondii-recombinant dense granular (GRA) 7 protein for the detection of toxoplasmosis in patients with cancer.

    Science.gov (United States)

    Arab-Mazar, Zahra; Fallahi, Shirzad; Koochaki, Ameneh; Haghighi, Ali; Seyyed Tabaei, Seyyed Javad

    2016-02-01

    Serological assays for the diagnosis of toxoplasmosis mostly rely on the tachyzoite specific antigens of Toxoplasma gondii, which are difficult to produce by conventional methods. The aim of this study was to clone and express of GRA7 protein of T. gondii and evaluate its potential for immunodiagnosis of toxoplasmosis in cancer patients. As well as validate the results using a new molecular assay, LAMP technique. The GRA7 gene was successfully cloned, expressed and purified by affinity chromatography and the production was evaluated by SDS PAGE, dot blot and western blot analyses. The rGRA7 was used for developing an ELISA based on the rGRA7 using sera from patients with toxoplasmosis and healthy controls. Furthermore, 50 serum samples from leukemic children infected with toxoplasmosis and 50 seronegative controls were included to evaluate the sensitivity and specificity of rGRA7 based ELISA. Finally, the LAMP technique was used to assess the accuracy and validity of the results obtained by rGRA7 based ELISA. The consistency of the results of two tests was determined by using the Kappa coefficient of agreement. The rGRA7 showed higher and optimum immunoreactivity with 1:100 dilution of serum from Toxoplasma infected patients. The sensitivity and specificity of test were calculated as 92 and 94%, respectively. According to the Kappa coefficient of agreement, there was a significant conformance between the results obtained by ELISA based on the rGRA7 and the results of LAMP technique (≈96%, Ptoxoplasmosis in patients including patients with cancer. Copyright © 2015. Published by Elsevier GmbH.

  13. Modelling dense relational data

    DEFF Research Database (Denmark)

    Herlau, Tue; Mørup, Morten; Schmidt, Mikkel Nørgaard

    2012-01-01

    they are not naturally suited for kernel K-means. We propose a generative Bayesian model for dense matrices which generalize kernel K-means to consider off-diagonal interactions in matrices of interactions, and demonstrate its ability to detect structure on both artificial data and two real data sets....

  14. Is dense codeswitching complex?

    NARCIS (Netherlands)

    Dorleijn, M.

    In this paper the question is raised to what extent dense code switching can be considered complex. Psycholinguistic experiments indicate that code switching involves cognitive costs, both in production and comprehension, a conclusion that could indicate that code switching is indeed complex. In

  15. Simulation of dense colloids

    NARCIS (Netherlands)

    Herrmann, H.J.; Harting, J.D.R.; Hecht, M.; Ben-Naim, E.

    2008-01-01

    We present in this proceeding recent large scale simulations of dense colloids. On one hand we simulate model clay consisting of nanometric aluminum oxide spheres in water using realistic DLVO potentials and a combination of MD and SRD. We find pronounced cluster formation and retrieve the shear

  16. Dilute and dense axion stars

    Science.gov (United States)

    Visinelli, Luca; Baum, Sebastian; Redondo, Javier; Freese, Katherine; Wilczek, Frank

    2018-02-01

    Axion stars are hypothetical objects formed of axions, obtained as localized and coherently oscillating solutions to their classical equation of motion. Depending on the value of the field amplitude at the core |θ0 | ≡ | θ (r = 0) |, the equilibrium of the system arises from the balance of the kinetic pressure and either self-gravity or axion self-interactions. Starting from a general relativistic framework, we obtain the set of equations describing the configuration of the axion star, which we solve as a function of |θ0 |. For small |θ0 | ≲ 1, we reproduce results previously obtained in the literature, and we provide arguments for the stability of such configurations in terms of first principles. We compare qualitative analytical results with a numerical calculation. For large amplitudes |θ0 | ≳ 1, the axion field probes the full non-harmonic QCD chiral potential and the axion star enters the dense branch. Our numerical solutions show that in this latter regime the axions are relativistic, and that one should not use a single frequency approximation, as previously applied in the literature. We employ a multi-harmonic expansion to solve the relativistic equation for the axion field in the star, and demonstrate that higher modes cannot be neglected in the dense regime. We interpret the solutions in the dense regime as pseudo-breathers, and show that the life-time of such configurations is much smaller than any cosmological time scale.

  17. DNA-Enabled Integrated Molecular Systems for Computation and Sensing

    Science.gov (United States)

    2014-05-21

    Computational devices can be chemically conjugated to different strands of DNA that are then self-assembled according to strict Watson − Crick binding rules... DNA -Enabled Integrated Molecular Systems for Computation and Sensing Craig LaBoda,† Heather Duschl,† and Chris L. Dwyer*,†,‡ †Department of...guided folding of DNA , inspired by nature, allows designs to manipulate molecular-scale processes unlike any other material system. Thus, DNA can be

  18. Interpretation Time Using a Concurrent-Read Computer-Aided Detection System for Automated Breast Ultrasound in Breast Cancer Screening of Women With Dense Breast Tissue.

    Science.gov (United States)

    Jiang, Yulei; Inciardi, Marc F; Edwards, Alexandra V; Papaioannou, John

    2018-05-24

    The purpose of this study was to compare diagnostic accuracy and interpretation time of screening automated breast ultrasound (ABUS) for women with dense breast tissue without and with use of a recently U.S. Food and Drug Administration-approved computer-aided detection (CAD) system for concurrent read. In a retrospective observer performance study, 18 radiologists interpreted a cancer-enriched set (i.e., cancer prevalence higher than in the original screening cohort) of 185 screening ABUS studies (52 with and 133 without breast cancer). These studies were from a large cohort of ABUS screened patients interpreted as BI-RADS density C or D. Each reader interpreted each case twice in a counterbalanced study, once without the CAD system and once with it, separated by 4 weeks. For each case, each reader identified abnormal findings and reported BI-RADS assessment category and level of suspicion for breast cancer. Interpretation time was recorded. Level of suspicion data were compared to evaluate diagnostic accuracy by means of the Dorfman-Berbaum-Metz method of jackknife with ANOVA ROC analysis. Interpretation times were compared by ANOVA. The ROC AUC was 0.848 with the CAD system, compared with 0.828 without it, for a difference of 0.020 (95% CI, -0.011 to 0.051) and was statistically noninferior to the AUC without the CAD system with respect to a margin of -0.05 (p = 0.000086). The mean interpretation time was 3 minutes 33 seconds per case without the CAD system and 2 minutes 24 seconds with it, for a difference of 1 minute 9 seconds saved (95% CI, 44-93 seconds; p = 0.000014), or a reduction in interpretation time to 67% of the time without the CAD system. Use of the concurrent-read CAD system for interpretation of screening ABUS studies of women with dense breast tissue who do not have symptoms is expected to make interpretation significantly faster and produce noninferior diagnostic accuracy compared with interpretation without the CAD system.

  19. Interactive analysis of systems biology molecular expression data

    Directory of Open Access Journals (Sweden)

    Prabhakar Sunil

    2008-02-01

    Full Text Available Abstract Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations. Results Presented is a novel interactive visual data mining application, SysNet that provides an interactive environment for the analysis of high data volume molecular expression information of most any type from biological systems. It integrates interactive graphic visualization and statistical data mining into a single package. SysNet interactively presents intermolecular correlation information with circular and heatmap layouts. It is also applicable to comparative analysis of molecular expression data, such as time course data. Conclusion The SysNet program has been utilized to analyze elemental profile changes in response to an increasing concentration of iron (Fe in growth media (an ionomics dataset. This study case demonstrates that the SysNet software is an effective platform for interactive analysis of molecular expression information in systems biology.

  20. Atoms in dense plasmas

    International Nuclear Information System (INIS)

    More, R.M.

    1987-01-01

    This paper covers some aspects of the theory of atomic processes in dense plasmas. Because the topic is very broad, a few general rules which give useful guidance about the typical behavior of dense plasmas have been selected. These rules are illustrated by semiclassical estimates, scaling laws and appeals to more elaborate calculations. Included in the paper are several previously unpublished results including a new mechanism for electron-ion heat exchange (section II), and an approximate expression for oscillator-strengths of highly charged ions (section V). However the main emphasis is not upon practical formulas but rather on questions of fundamental theory, the structural ingredients which must be used in building a model for plasma events. What are the density effects and how does one represent them? Which are most important? How does one identify an incorrect theory? The general rules help to answer these questions. 106 references, 23 figures, 2 tables

  1. Probing Interactions in Complex Molecular Systems through Ordered Assembly

    International Nuclear Information System (INIS)

    De Yoreo, J.J.; Bartelt, M.C.; Orme, C.A.; Villacampa, A.; Weeks, B.L.; Miller, A.E.

    2002-01-01

    Emerging from the machinery of epitaxial science and chemical synthesis, is a growing emphasis on development of self-organized systems of complex molecular species. The nature of self-organization in these systems spans the continuum from simple crystallization of large molecules such as dendrimers and proteins, to assembly into large organized networks of nanometer-scale structures such as quantum dots or nanoparticles. In truth, self-organization in complex molecular systems has always been a central feature of many scientific disciplines including fields as diverse as structural biology, polymer science and geochemistry. But over the past decade, changes in those fields have often been marked by the degree to which researchers are using molecular-scale approaches to understand the hierarchy of structures and processes driven by this ordered assembly. At the same time, physical scientists have begun to use their knowledge of simple atomic and molecular systems to fabricate synthetic self-organized systems. This increasing activity in the field of self-organization is testament to the success of the physical and chemical sciences in building a detailed understanding of crystallization and epitaxy in simple atomic and molecular systems, one that is soundly rooted in thermodynamics and chemical kinetics. One of the fundamental challenges of chemistry and materials science in the coming decades is to develop a similarly well-founded physical understanding of assembly processes in complex molecular systems. Over the past five years, we have successfully used in situ atomic force microscopy (AFM) to investigate the physical controls on single crystal epitaxy from solutions for a wide range of molecular species. More recently, we have combined this method with grazing incidence X-ray diffraction and kinetic Monte Carlo modeling in order to relate morphology to surface atomic structure and processes. The purpose of this proposal was to extend this approach to assemblies

  2. Dense Plasma Focus Modeling

    Energy Technology Data Exchange (ETDEWEB)

    Li, Hui [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Li, Shengtai [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Jungman, Gerard [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Hayes-Sterbenz, Anna Catherine [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-08-31

    The mechanisms for pinch formation in Dense Plasma Focus (DPF) devices, with the generation of high-energy ions beams and subsequent neutron production over a relatively short distance, are not fully understood. Here we report on high-fidelity 2D and 3D numerical magnetohydrodynamic (MHD) simulations using the LA-COMPASS code to study the pinch formation dynamics and its associated instabilities and neutron production.

  3. Dynamical theory of dense groups of galaxies

    Science.gov (United States)

    Mamon, Gary A.

    1990-01-01

    It is well known that galaxies associate in groups and clusters. Perhaps 40% of all galaxies are found in groups of 4 to 20 galaxies (e.g., Tully 1987). Although most groups appear to be so loose that the galaxy interactions within them ought to be insignificant, the apparently densest groups, known as compact groups appear so dense when seen in projection onto the plane of the sky that their members often overlap. These groups thus appear as dense as the cores of rich clusters. The most popular catalog of compact groups, compiled by Hickson (1982), includes isolation among its selection critera. Therefore, in comparison with the cores of rich clusters, Hickson's compact groups (HCGs) appear to be the densest isolated regions in the Universe (in galaxies per unit volume), and thus provide in principle a clean laboratory for studying the competition of very strong gravitational interactions. The $64,000 question here is then: Are compact groups really bound systems as dense as they appear? If dense groups indeed exist, then one expects that each of the dynamical processes leading to the interaction of their member galaxies should be greatly enhanced. This leads us to the questions: How stable are dense groups? How do they form? And the related question, fascinating to any theorist: What dynamical processes predominate in dense groups of galaxies? If HCGs are not bound dense systems, but instead 1D change alignments (Mamon 1986, 1987; Walke & Mamon 1989) or 3D transient cores (Rose 1979) within larger looser systems of galaxies, then the relevant question is: How frequent are chance configurations within loose groups? Here, the author answers these last four questions after comparing in some detail the methods used and the results obtained in the different studies of dense groups.

  4. A Static and Dynamic Investigation of Quantum Nonlinear Transport in Highly Dense and Mobile 2D Electron Systems

    Science.gov (United States)

    Dietrich, Scott

    Heterostructures made of semiconductor materials may be one of most versatile environments for the study of the physics of electron transport in two dimensions. These systems are highly customizable and demonstrate a wide range of interesting physical phenomena. In response to both microwave radiation and DC excitations, strongly nonlinear transport that gives rise to non-equilibrium electron states has been reported and investigated. We have studied GaAs quantum wells with a high density of high mobility two-dimensional electrons placed in a quantizing magnetic field. This study presents the observation of several nonlinear transport mechanisms produced by the quantum nature of these materials. The quantum scattering rate, 1tau/q, is an important parameter in these systems, defining the width of the quantized energy levels. Traditional methods of extracting 1tau/q involve studying the amplitude of Shubnikov-de Haas oscillations. We analyze the quantum positive magnetoresistance due to the cyclotron motion of electrons in a magnetic field. This method gives 1tau/q and has the additional benefit of providing access to the strength of electron-electron interactions, which is not possible by conventional techniques. The temperature dependence of the quantum scattering rate is found to be proportional to the square of the temperature and is in very good agreement with theory that considers electron-electron interactions in 2D systems. In quantum wells with a small scattering rate - which corresponds to well-defined Landau levels - quantum oscillations of nonlinear resistance that are independent of magnetic field strength have been observed. These oscillations are periodic in applied bias current and are connected to quantum oscillations of resistance at zero bias: either Shubnikov-de Haas oscillations for single subband systems or magnetointersubband oscillations for two subband systems. The bias-induced oscillations can be explained by a spatial variation of electron

  5. Effect of particle-size dynamics on properties of dense spongy-particle systems: Approach towards equilibrium

    Science.gov (United States)

    Zakhari, Monica E. A.; Anderson, Patrick D.; Hütter, Markus

    2017-07-01

    Open-porous deformable particles, often envisaged as sponges, are ubiquitous in biological and industrial systems (e.g., casein micelles in dairy products and microgels in cosmetics). The rich behavior of these suspensions is owing to the elasticity of the supporting network of the particle, and the viscosity of permeating solvent. Therefore, the rate-dependent size change of these particles depends on their structure, i.e., the permeability. This work aims at investigating the effect of the particle-size dynamics and the underlying particle structure, i.e., the particle permeability, on the transient and long-time behavior of suspensions of spongy particles in the absence of applied deformation, using the dynamic two-scale model developed by Hütter et al. [Farad. Discuss. 158, 407 (2012), 10.1039/c2fd20025b]. In the high-density limit, the transient behavior is found to be accelerated by the particle-size dynamics, even at average size changes as small as 1 % . The accelerated dynamics is evidenced by (i) the higher short-time diffusion coefficient as compared to elastic-particle systems and (ii) the accelerated formation of the stable fcc crystal structure. Furthermore, after long times, the particle-size dynamics of spongy particles is shown to result in lower stationary values of the energy and normal stresses as compared to elastic-particle systems. This dependence of the long-time behavior of these systems on the permeability, that essentially is a transport coefficient and hence must not affect the equilibrium properties, confirms that full equilibration has not been reached.

  6. Energy conservation in molecular dynamics simulations of classical systems

    DEFF Research Database (Denmark)

    Toxværd, Søren; Heilmann, Ole; Dyre, J. C.

    2012-01-01

    Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete “Verlet” algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence...

  7. Conceptual design of the tomographic system for simultaneous studying of soft and hard X-ray emission from dense magnetized plasma

    Energy Technology Data Exchange (ETDEWEB)

    Bielecki, J., E-mail: jakub.bielecki@ifj.edu.edu; Wójcik-Gargula, A.; Scholz, M.

    2016-11-15

    The article presents a new approach for investigation of spatial distributions of soft and hard X-rays emitted from dense magnetized plasma. The approach is based on the application of tomographic methods to the X-ray emission reconstruction in a plasma focus (PF) device. Quantitative investigation of the anisotropy of the reconstructed X–ray plasma emissivity may help to explain the nature of fusion reaction mechanisms in a PF device. The aim of this work is to present a conceptual design of a novel dual-energy X-ray emission tomographic system dedicated to the PF-24 plasma focus device. The system, which enables the simultaneous registration of soft and hard X-rays, is composed of three X‐ray pinhole cameras. Each camera is equipped with a pair of 16-element Si photodiode arrays arranged in two layers separated by an aluminum attenuator. The Geant4 code was used to optimize the layout and parameters of the applied detectors. In addition, a method of tomographic reconstruction from a sparse data set provided by the experimental setup has been presented.

  8. WARM EXTENDED DENSE GAS AT THE HEART OF A COLD COLLAPSING DENSE CORE

    International Nuclear Information System (INIS)

    Shinnaga, Hiroko; Phillips, Thomas G.; Furuya, Ray S.; Kitamura, Yoshimi

    2009-01-01

    In order to investigate when and how the birth of a protostellar core occurs, we made survey observations of four well-studied dense cores in the Taurus molecular cloud using CO transitions in submillimeter bands. We report here the detection of unexpectedly warm (∼30-70 K), extended (radius of ∼2400 AU), dense (a few times 10 5 cm -3 ) gas at the heart of one of the dense cores, L1521F (MC27), within the cold dynamically collapsing components. We argue that the detected warm, extended, dense gas may originate from shock regions caused by collisions between the dynamically collapsing components and outflowing/rotating components within the dense core. We propose a new stage of star formation, 'warm-in-cold core stage (WICCS)', i.e., the cold collapsing envelope encases the warm extended dense gas at the center due to the formation of a protostellar core. WICCS would constitute a missing link in evolution between a cold quiescent starless core and a young protostar in class 0 stage that has a large-scale bipolar outflow.

  9. Dense ceramic articles

    International Nuclear Information System (INIS)

    Cockbain, A.G.

    1976-01-01

    A method is described for the manufacture of articles of substantially pure dense ceramic materials, for use in severe environments. Si N is very suitable for use in such environments, but suffers from the disadvantage that it is not amenable to sintering. Some disadvantages of the methods normally used for making articles of Si N are mentioned. The method described comprises mixing a powder of the substantially pure ceramic material with an additive that promotes densification, and which is capable of nuclear transmutation into a gas when exposed to radiation, and hot pressing the mixture to form a billet. The billet is then irradiated to convert the additive into a gas which is held captive in the billet, and it is then subjected to a hot forging operation, during which the captive gas escapes and an article of substantially pure dense ceramic material is forged. The method is intended primarily for use for Si N, but may be applied to other ceramic materials. The additive may be Li or Be or their compounds, to the extent of at least 5 ppm and not more than 5% by weight. Irradiation is effected by proton or neutron bombardment. (UK)

  10. Computing Low-Rank Approximation of a Dense Matrix on Multicore CPUs with a GPU and Its Application to Solving a Hierarchically Semiseparable Linear System of Equations

    Directory of Open Access Journals (Sweden)

    Ichitaro Yamazaki

    2015-01-01

    of their low-rank properties. To compute a low-rank approximation of a dense matrix, in this paper, we study the performance of QR factorization with column pivoting or with restricted pivoting on multicore CPUs with a GPU. We first propose several techniques to reduce the postprocessing time, which is required for restricted pivoting, on a modern CPU. We then examine the potential of using a GPU to accelerate the factorization process with both column and restricted pivoting. Our performance results on two eight-core Intel Sandy Bridge CPUs with one NVIDIA Kepler GPU demonstrate that using the GPU, the factorization time can be reduced by a factor of more than two. In addition, to study the performance of our implementations in practice, we integrate them into a recently developed software StruMF which algebraically exploits such low-rank structures for solving a general sparse linear system of equations. Our performance results for solving Poisson's equations demonstrate that the proposed techniques can significantly reduce the preconditioner construction time of StruMF on the CPUs, and the construction time can be further reduced by 10%–50% using the GPU.

  11. Superconductivity in dense electroweak system

    International Nuclear Information System (INIS)

    Ferrer, E.J.; De La Incera, V.; Shabad, A.E.

    1988-01-01

    The spectrum of fermions in the presence of the W-boson-condensed electro-weak liquid is obtained and nonvanishing spatial component of the fermionic polarization operator is calculated for zero 4-momentum. The manifestation of the Meissner effect is studied. The London penetration depthλ/sub L/ is calculated in the limit of small W-condensate amplitude. The possibility of a special phenomenon of partial magnetic screening due to the mixing angle dependence on the leptonic density is discussed in connection with the magnetic mass problem

  12. Atomic physics in dense plasmas. Recent advances

    International Nuclear Information System (INIS)

    Leboucher-Dalimier, E.; Angelo, P.; Ceccotti, T.; Derfoul, H.; Poquerusse, A.; Sauvan, P.; Oks, E.

    2000-01-01

    This paper presents observations and simulations of novel density-dependent spectroscopic features in hot and dense plasmas. Both time-integrated and time-resolved results using ultra-high resolutions spectrometers are presented; they are justified within the standard spectral line shape theory or the quasi-molecular alternative treatment. A particular attention is paid to the impact of the spatio-temporal evolution of the plasma on the experimental spectra. Satellite-like features and molecular lines in the cases of Flyβ, Heβ are discussed emphasizing their importance for the density diagnostics when ion-ion correlations are significant. (authors)

  13. Multi-Scale Molecular Deconstruction of the Serotonin Neuron System.

    Science.gov (United States)

    Okaty, Benjamin W; Freret, Morgan E; Rood, Benjamin D; Brust, Rachael D; Hennessy, Morgan L; deBairos, Danielle; Kim, Jun Chul; Cook, Melloni N; Dymecki, Susan M

    2015-11-18

    Serotonergic (5HT) neurons modulate diverse behaviors and physiology and are implicated in distinct clinical disorders. Corresponding diversity in 5HT neuronal phenotypes is becoming apparent and is likely rooted in molecular differences, yet a comprehensive approach characterizing molecular variation across the 5HT system is lacking, as is concomitant linkage to cellular phenotypes. Here we combine intersectional fate mapping, neuron sorting, and genome-wide RNA-seq to deconstruct the mouse 5HT system at multiple levels of granularity-from anatomy, to genetic sublineages, to single neurons. Our unbiased analyses reveal principles underlying system organization, 5HT neuron subtypes, constellations of differentially expressed genes distinguishing subtypes, and predictions of subtype-specific functions. Using electrophysiology, subtype-specific neuron silencing, and conditional gene knockout, we show that these molecularly defined 5HT neuron subtypes are functionally distinct. Collectively, this resource classifies molecular diversity across the 5HT system and discovers sertonergic subtypes, markers, organizing principles, and subtype-specific functions with potential disease relevance. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Hyperons in dense matter

    Energy Technology Data Exchange (ETDEWEB)

    Dapo, Haris

    2009-01-28

    The hyperon-nucleon YN low momentum effective interaction (V{sub low} {sub k}) allows for an extensive study of the behavior of hyperons in dense matter, together with an investigation of effects of the presence of hyperons on dense matter. The first step towards this goal is the construction of the matrix elements for the hyperon-nucleon low momentum potential. In order to assess the different properties of hyperons within these potentials we calculate the hyperon single-particle potentials in the Hartree-Fock approximation for all of the interactions. Their dependence on both momentum and density, is studied. The single-particle potentials are then used to determine the chemical potential of hyperons in neutron stars. For nucleonic properties, the nucleon-nucleon V{sub low} {sub k} can be used with the caveat that the calculation of the ground-state energy of symmetric nuclear matter does not correctly reproduce the properties of matter at saturation. With the nucleon-nucleon V{sub low} {sub k} one is unable to reach the densities needed for the calculation of neutron star masses. To circumvent this problem we use two approaches: in the first one, we parametrize the entire nucleonic sector. In the second one, we replace only the three-body force. The former will enable us to study neutron star masses, and the latter for studying the medium's response to the external probe. In this thesis we take the external probe to be the neutrino. By combining this parametrization with the YN V{sub low} {sub k} potential, we calculate the equation of state of equilibrated matter. Performing the calculation in the Hartree-Fock approximation at zero temperature, the concentrations of all particles are calculated. From these we can ascertain at which densities hyperons appear for a wide range of parameters. Finally, we calculate the masses of neutron stars with these concentrations. For the calculation of the medium's response to an external probe, we replace the three

  15. Hyperons in dense matter

    International Nuclear Information System (INIS)

    Dapo, Haris

    2009-01-01

    The hyperon-nucleon YN low momentum effective interaction (V low k ) allows for an extensive study of the behavior of hyperons in dense matter, together with an investigation of effects of the presence of hyperons on dense matter. The first step towards this goal is the construction of the matrix elements for the hyperon-nucleon low momentum potential. In order to assess the different properties of hyperons within these potentials we calculate the hyperon single-particle potentials in the Hartree-Fock approximation for all of the interactions. Their dependence on both momentum and density, is studied. The single-particle potentials are then used to determine the chemical potential of hyperons in neutron stars. For nucleonic properties, the nucleon-nucleon V low k can be used with the caveat that the calculation of the ground-state energy of symmetric nuclear matter does not correctly reproduce the properties of matter at saturation. With the nucleon-nucleon V low k one is unable to reach the densities needed for the calculation of neutron star masses. To circumvent this problem we use two approaches: in the first one, we parametrize the entire nucleonic sector. In the second one, we replace only the three-body force. The former will enable us to study neutron star masses, and the latter for studying the medium's response to the external probe. In this thesis we take the external probe to be the neutrino. By combining this parametrization with the YN V low k potential, we calculate the equation of state of equilibrated matter. Performing the calculation in the Hartree-Fock approximation at zero temperature, the concentrations of all particles are calculated. From these we can ascertain at which densities hyperons appear for a wide range of parameters. Finally, we calculate the masses of neutron stars with these concentrations. For the calculation of the medium's response to an external probe, we replace the three-body force with a density-dependent interaction. This

  16. Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.

    Science.gov (United States)

    Li, Jianwei; Nowak, Piotr; Otto, Sijbren

    2013-06-26

    Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many fascinating molecules, ranging from interlocked structures to self-replicators. Furthermore, dynamic combinatorial molecular networks can produce emergent properties at systems level, which provide exciting new opportunities in systems chemistry. In this perspective we will highlight some new methodologies in this field and analyze selected examples of DCLs that are under thermodynamic control, leading to synthetic receptors, catalytic systems, and complex self-assembled supramolecular architectures. Also reviewed are extensions of the principles of DCC to systems that are not at equilibrium and may therefore harbor richer functional behavior. Examples include self-replication and molecular machines.

  17. Geometrical optics of dense aerosols: forming dense plasma slabs.

    Science.gov (United States)

    Hay, Michael J; Valeo, Ernest J; Fisch, Nathaniel J

    2013-11-01

    Assembling a freestanding, sharp-edged slab of homogeneous material that is much denser than gas, but much more rarefied than a solid, is an outstanding technological challenge. The solution may lie in focusing a dense aerosol to assume this geometry. However, whereas the geometrical optics of dilute aerosols is a well-developed field, the dense aerosol limit is mostly unexplored. Yet controlling the geometrical optics of dense aerosols is necessary in preparing such a material slab. Focusing dense aerosols is shown here to be possible, but the finite particle density reduces the effective Stokes number of the flow, a critical result for controlled focusing.

  18. Influence of control group therapy on the benefit from dose-dense chemotherapy in early breast cancer: a systemic review and meta-analysis.

    Science.gov (United States)

    Goldvaser, Hadar; Majeed, Habeeb; Ribnikar, Domen; Šeruga, Boštjan; Ocaña, Alberto; Cescon, David W; Amir, Eitan

    2018-02-08

    Results from clinical trials of adjuvant dose-dense chemotherapy in patients with breast cancer are inconsistent. A systematic search of MEDLINE identified studies comparing the efficacy of dose-dense adjuvant chemotherapy to a standard treatment. The primary analysis included studies that used identical regimens in the experimental and control groups, but varied only dose density. A secondary analysis included studies that used either different drugs or doses in the experimental and the control groups. Hazard ratios (HRs) and 95% confidence intervals were computed for disease-free survival (DFS) and overall survival (OS) and pooled in a meta-analysis. Subgroup analyses and meta-regression explored drug schedules utilized in control groups and the influence of clinicopathologic variables on benefit from dose-dense therapy. The primary analysis included 5 studies comprising 9819 patients while the secondary analysis included 6 studies comprising 9679 patients. Dose-dense treatment significantly improved DFS (HR 0.85, p benefit was observed in pre-menopausal women and those with nodal involvement, but there was no influence of hormone receptor status on results. Adjuvant dose-dense regimens improve breast cancer outcomes. It remains uncertain whether the observed benefit reflects the impact of dose density or the inferiority of paclitaxel every 3 weeks as a control group.

  19. Molecular biophysics: detection and characterization of damage in molecular, cellular, and physiological systems

    International Nuclear Information System (INIS)

    Danyluk, S.S.

    1979-01-01

    This section contains summaries of research on the detection and characterization of damage in molecular, cellular, and physiological systems. Projects under investigation in this section include: chemical synthesis of nucleic acid derivatives; structural and conformational properties of biological molecules in solution; crystallographic and chemical studies of immunoglobulin structure; instrument design and development for x-ray and neutron scattering studies of biological molecules; and chromobiology and circadian regulation

  20. Lattice cluster theory for dense, thin polymer films.

    Science.gov (United States)

    Freed, Karl F

    2015-04-07

    While the application of the lattice cluster theory (LCT) to study the miscibility of polymer blends has greatly expanded our understanding of the monomer scale molecular details influencing miscibility, the corresponding theory for inhomogeneous systems has not yet emerged because of considerable technical difficulties and much greater complexity. Here, we present a general formulation enabling the extension of the LCT to describe the thermodynamic properties of dense, thin polymer films using a high dimension, high temperature expansion. Whereas the leading order of the LCT for bulk polymer systems is essentially simple Flory-Huggins theory, the highly non-trivial leading order inhomogeneous LCT (ILCT) for a film with L layers already involves the numerical solution of 3(L - 1) coupled, highly nonlinear equations for the various density profiles in the film. The new theory incorporates the essential "transport" constraints of Helfand and focuses on the strict imposition of excluded volume constraints, appropriate to dense polymer systems, rather than the maintenance of chain connectivity as appropriate for lower densities and as implemented in self-consistent theories of polymer adsorption at interfaces. The ILCT is illustrated by presenting examples of the computed profiles of the density, the parallel and perpendicular bonds, and the chain ends for free standing and supported films as a function of average film density, chain length, temperature, interaction with support, and chain stiffness. The results generally agree with expected general trends.

  1. Lattice cluster theory for dense, thin polymer films

    International Nuclear Information System (INIS)

    Freed, Karl F.

    2015-01-01

    While the application of the lattice cluster theory (LCT) to study the miscibility of polymer blends has greatly expanded our understanding of the monomer scale molecular details influencing miscibility, the corresponding theory for inhomogeneous systems has not yet emerged because of considerable technical difficulties and much greater complexity. Here, we present a general formulation enabling the extension of the LCT to describe the thermodynamic properties of dense, thin polymer films using a high dimension, high temperature expansion. Whereas the leading order of the LCT for bulk polymer systems is essentially simple Flory-Huggins theory, the highly non-trivial leading order inhomogeneous LCT (ILCT) for a film with L layers already involves the numerical solution of 3(L − 1) coupled, highly nonlinear equations for the various density profiles in the film. The new theory incorporates the essential “transport” constraints of Helfand and focuses on the strict imposition of excluded volume constraints, appropriate to dense polymer systems, rather than the maintenance of chain connectivity as appropriate for lower densities and as implemented in self-consistent theories of polymer adsorption at interfaces. The ILCT is illustrated by presenting examples of the computed profiles of the density, the parallel and perpendicular bonds, and the chain ends for free standing and supported films as a function of average film density, chain length, temperature, interaction with support, and chain stiffness. The results generally agree with expected general trends

  2. Atomic and Molecular Systems in Intense Ultrashort Laser Pulses

    Science.gov (United States)

    Saenz, A.

    2008-07-01

    The full quantum mechanical treatment of atomic and molecular systems exposed to intense laser pulses is a so far unsolved challenge, even for systems as small as molecular hydrogen. Therefore, a number of simplified qualitative and quantitative models have been introduced in order to provide at least some interpretational tools for experimental data. The assessment of these models describing the molecular response is complicated, since a comparison to experiment requires often a number of averages to be performed. This includes in many cases averaging of different orientations of the molecule with respect to the laser field, focal volume effects, etc. Furthermore, the pulse shape and even the peak intensity is experimentally not known with very high precision; considering, e.g., the exponential intensity dependence of the ionization signal. Finally, experiments usually provide only relative yields. As a consequence of all these averagings and uncertainties, it is possible that different models may successfully explain some experimental results or features, although these models disagree substantially, if their predictions are compared before averaging. Therefore, fully quantum-mechanical approaches at least for small atomic and molecular systems are highly desirable and have been developed in our group. This includes efficient codes for solving the time-dependent Schrodinger equation of atomic hydrogen, helium or other effective one- or two-electron atoms as well as for the electronic motion in linear (effective) one-and two-electron diatomic molecules like H_2.Very recently, a code for larger molecular systems that adopts the so-called single-active electron approximation was also successfully implemented and applied. In the first part of this talk popular models describing intense laser-field ionization of atoms and their extensions to molecules are described. Then their validity is discussed on the basis of quantum-mechanical calculations. Finally, some

  3. Hybrid Metaheuristic Approach for Nonlocal Optimization of Molecular Systems.

    Science.gov (United States)

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

    2013-04-09

    Accurate modeling of molecular systems requires a good knowledge of the structure; therefore, conformation searching/optimization is a routine necessity in computational chemistry. Here we present a hybrid metaheuristic optimization (HMO) algorithm, which combines ant colony optimization (ACO) and particle swarm optimization (PSO) for the optimization of molecular systems. The HMO implementation meta-optimizes the parameters of the ACO algorithm on-the-fly by the coupled PSO algorithm. The ACO parameters were optimized on a set of small difluorinated polyenes where the parameters exhibited small variance as the size of the molecule increased. The HMO algorithm was validated by searching for the closed form of around 100 molecular balances. Compared to the gradient-based optimized molecular balance structures, the HMO algorithm was able to find low-energy conformations with a 87% success rate. Finally, the computational effort for generating low-energy conformation(s) for the phenylalanyl-glycyl-glycine tripeptide was approximately 60 CPU hours with the ACO algorithm, in comparison to 4 CPU years required for an exhaustive brute-force calculation.

  4. Molecular mechanisms of aging and immune system regulation in Drosophila.

    Science.gov (United States)

    Eleftherianos, Ioannis; Castillo, Julio Cesar

    2012-01-01

    Aging is a complex process that involves the accumulation of deleterious changes resulting in overall decline in several vital functions, leading to the progressive deterioration in physiological condition of the organism and eventually causing disease and death. The immune system is the most important host-defense mechanism in humans and is also highly conserved in insects. Extensive research in vertebrates has concluded that aging of the immune function results in increased susceptibility to infectious disease and chronic inflammation. Over the years, interest has grown in studying the molecular interaction between aging and the immune response to pathogenic infections. The fruit fly Drosophila melanogaster is an excellent model system for dissecting the genetic and genomic basis of important biological processes, such as aging and the innate immune system, and deciphering parallel mechanisms in vertebrate animals. Here, we review the recent advances in the identification of key players modulating the relationship between molecular aging networks and immune signal transduction pathways in the fly. Understanding the details of the molecular events involved in aging and immune system regulation will potentially lead to the development of strategies for decreasing the impact of age-related diseases, thus improving human health and life span.

  5. Selective excitation, relaxation, and energy channeling in molecular systems

    International Nuclear Information System (INIS)

    Rhodes, W.C.

    1993-08-01

    Research involves theoretical studies of response, relaxation, and correlated motion in time-dependent behavior of large molecular systems ranging from polyatomic molecules to protein molecules in their natural environment. Underlying theme is subsystem modulation dynamics. Main idea is that quantum mechanical correlations between components of a system develop with time, playing a major role in determining the balance between coherent and dissipative forces. Central theme is interplay of coherence and dissipation in determining the nature of dynamic structuring and energy flow in molecular transformation mechanisms. Subsystem equations of motion are being developed to show how nonlinear, dissipative dynamics of a particular subsystem arise from correlated interactions with the rest of the system (substituent groups, solvent, lattice modes, etc.); one consequence is resonance structures and networks. Quantum dynamics and thermodynamics are being applied to understand control and energy transfer mechanisms in biological functions of protein molecules; these mechanisms are both global and local. Besides the above theory, the research deals with phenomenological aspects of molecular systems

  6. Mercury's Densely Cratered Surface

    Science.gov (United States)

    1974-01-01

    Mariner 10 took this picture (FDS 27465) of the densely cratered surface of Mercury when the spacecraft was 18,200 kilometers (8085 miles) from the planet on March 29. The dark line across top of picture is a 'dropout' of a few TV lines of data. At lower left, a portion of a 61 kilometer (38 mile) crater shows a flow front extending across the crater floor and filling more than half of the crater. The smaller, fresh crater at center is about 25 kilometers (15 miles) in diameter. Craters as small as one kilometer (about one-half mile) across are visible in the picture.The Mariner 10 mission, managed by the Jet Propulsion Laboratory for NASA's Office of Space Science, explored Venus in February 1974 on the way to three encounters with Mercury-in March and September 1974 and in March 1975. The spacecraft took more than 7,000 photos of Mercury, Venus, the Earth and the Moon.Image Credit: NASA/JPL/Northwestern University

  7. Photocatalytic and biocidal activities of novel coating systems of mesoporous and dense TiO{sub 2}-anatase containing silver nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Roldán, María V. [Laboratorio de Materiales Cerámicos, FCEIA-UNR, IFIR-CONICET, Pellegrini 250, Rosario S2000BTP (Argentina); Oña, Paula de [Laboratorio de Microbiología Molecular, FCByF-UNR-CONICET, Suipacha 531, Rosario S2002LRK (Argentina); Castro, Yolanda; Durán, Alicia [Instituto de Cerámica y Vidrio (CSIC), Campus de Cantoblanco, 28049, Madrid (Spain); Faccendini, Pablo; Lagier, Claudia [IQUIR-UNR-CONICET, Suipacha 531, Rosario S2002LRK (Argentina); Grau, Roberto, E-mail: robertograu@fulbrightmail.org [Laboratorio de Microbiología Molecular, FCByF-UNR-CONICET, Suipacha 531, Rosario S2002LRK (Argentina); Pellegri, Nora S., E-mail: pellegri@fceia.unr.edu.ar [Laboratorio de Materiales Cerámicos, FCEIA-UNR, IFIR-CONICET, Pellegrini 250, Rosario S2000BTP (Argentina)

    2014-10-01

    Here we describe the development of novel nanostructured coating systems with improved photocatalytic and antibacterial activities. These systems comprise a layer of SiO{sub 2} followed by a layer of mesoporous or dense TiO{sub 2}-anatase, and doping with silver nanoparticles (Ag NPs). The coatings were synthesized via a sol–gel technique by combining colloidal Ag NPs with TiO{sub 2} and SiO{sub 2} sols. The photocatalytic activity was studied through methyl orange decomposition under UV light. Results showed a great increase of photocatalytic activity by Ag NPs doping. The most active photocatalyst corresponded to the Ag–SiO{sub 2}/TiO{sub 2} mesoporous system, associated with the porosity of the coatings and with the decrease of e–h recombination for the presence of Ag NPs. All the TiO{sub 2} coatings showed a strong bactericidal activity against planktonic forms of Gram-negative (enterohemorrhagic Escherichia coli) and Gram-positive (Listeria monocytogenes) pathogens, as well as a strong germicidal effect against deadly spores of human gas gangrene- and anthrax-producing bacteria (Clostridium perfringens and Bacillus anthracis, respectively). The bactericidal and sporocidal activity was improved by doping the coatings with Ag NPs, even more when nanoparticles were in the outer layer of TiO{sub 2}, because they are more accessible to the environment. The mechanisms responsible for the increase of photocatalytic and bactericidal behaviors related to Ag NP doping were studied by spectroscopic ellipsometry, UV–vis spectroscopy, photoluminescence and anodic stripping voltammetry. It was found that the separation of the electron–hole pair contributed to the enhancement of photocatalysis, whereas the effect of the local electric field reinforcement was probably present. A possible involvement of a decrease of band-gap energy and dispersion by silver nanoparticles is ruled out. bactericidal efficacy was increased by Ag{sup +} ion release. Overall, the results

  8. Assembly, destruction and manipulation of atomic, molecular and complex systems

    International Nuclear Information System (INIS)

    Le Padellec, Arnaud Pierre Frederic

    2003-04-01

    In this report for Accreditation to Supervise Researches (HDR), the author first indicates his professional curriculum (diplomas, teaching activities, responsibilities in the field of education and research, publications), and then proposes a presentation of his scientific works and researches. He notably proposes an overview of the different experimental techniques he implemented: CRYRING storage ring, confluent beams, flow post-discharge with mass spectrometry and Langmuir probe, crossed beams, and so on. He reports works dealing with the manipulation and destruction of atomic, molecular and complex systems: detachment of atomic anions by electronic impact, detachment and dissociation of small carbon aggregates by electronic impact, dissociative recombination, dissociative ionisation and excitation, creation of pairs of ions, manipulation of sodium fluoride aggregates. He finally presents research projects regarding the assembly of molecular and complex systems

  9. Interactive display of molecular models using a microcomputer system

    Science.gov (United States)

    Egan, J. T.; Macelroy, R. D.

    1980-01-01

    A simple, microcomputer-based, interactive graphics display system has been developed for the presentation of perspective views of wire frame molecular models. The display system is based on a TERAK 8510a graphics computer system with a display unit consisting of microprocessor, television display and keyboard subsystems. The operating system includes a screen editor, file manager, PASCAL and BASIC compilers and command options for linking and executing programs. The graphics program, written in USCD PASCAL, involves the centering of the coordinate system, the transformation of centered model coordinates into homogeneous coordinates, the construction of a viewing transformation matrix to operate on the coordinates, clipping invisible points, perspective transformation and scaling to screen coordinates; commands available include ZOOM, ROTATE, RESET, and CHANGEVIEW. Data file structure was chosen to minimize the amount of disk storage space. Despite the inherent slowness of the system, its low cost and flexibility suggests general applicability.

  10. Hadrons in dense matter. Proceedings

    International Nuclear Information System (INIS)

    Buballa, M.; Noerenberg, W.; Schaefer, B.J.; Wambach, J.

    2000-03-01

    The following topics were dealt with: Elementary hadronic reactions, Delta dynamics in nuclei, in-medium s-wave ππ-correlations, strangeness in hot and dense matter, medium modifications of vector mesons and dilepton production, medium modifications of charmonium, thermal properties of hot and dense hadronic matter, nuclear matter, spectral functions and QCD sum rules

  11. Catecholaminergic systems in stress: structural and molecular genetic approaches.

    Science.gov (United States)

    Kvetnansky, Richard; Sabban, Esther L; Palkovits, Miklos

    2009-04-01

    Stressful stimuli evoke complex endocrine, autonomic, and behavioral responses that are extremely variable and specific depending on the type and nature of the stressors. We first provide a short overview of physiology, biochemistry, and molecular genetics of sympatho-adrenomedullary, sympatho-neural, and brain catecholaminergic systems. Important processes of catecholamine biosynthesis, storage, release, secretion, uptake, reuptake, degradation, and transporters in acutely or chronically stressed organisms are described. We emphasize the structural variability of catecholamine systems and the molecular genetics of enzymes involved in biosynthesis and degradation of catecholamines and transporters. Characterization of enzyme gene promoters, transcriptional and posttranscriptional mechanisms, transcription factors, gene expression and protein translation, as well as different phases of stress-activated transcription and quantitative determination of mRNA levels in stressed organisms are discussed. Data from catecholamine enzyme gene knockout mice are shown. Interaction of catecholaminergic systems with other neurotransmitter and hormonal systems are discussed. We describe the effects of homotypic and heterotypic stressors, adaptation and maladaptation of the organism, and the specificity of stressors (physical, emotional, metabolic, etc.) on activation of catecholaminergic systems at all levels from plasma catecholamines to gene expression of catecholamine enzymes. We also discuss cross-adaptation and the effect of novel heterotypic stressors on organisms adapted to long-term monotypic stressors. The extra-adrenal nonneuronal adrenergic system is described. Stress-related central neuronal regulatory circuits and central organization of responses to various stressors are presented with selected examples of regulatory molecular mechanisms. Data summarized here indicate that catecholaminergic systems are activated in different ways following exposure to distinct

  12. Impact assessment of biomass-based district heating systems in densely populated communities. Part II: Would the replacement of fossil fuels improve ambient air quality and human health?

    Science.gov (United States)

    Petrov, Olga; Bi, Xiaotao; Lau, Anthony

    2017-07-01

    To determine if replacing fossil fuel combustion with biomass gasification would impact air quality, we evaluated the impact of a small-scale biomass gasification plant (BRDF) at a university campus over 5 scenarios. The overall incremental contribution of fine particles (PM2.5) is found to be at least one order of magnitude lower than the provincial air quality objectives. The maximum PM2.5 emission from the natural gas fueled power house (PH) could adversely add to the already high background concentration levels. Nitrogen dioxide (NO2) emissions from the BRDF with no engineered pollution controls for NOx in place exceeded the provincial objective in all seasons except during summer. The impact score, IS, was the highest for NO2 (677 Disability Adjusted Life Years, DALY) when biomass entirely replaced fossil fuels, and the highest for PM2.5 (64 DALY) and CO (3 DALY) if all energy was produced by natural gas at PH. Complete replacement of fossil fuels by one biomass plant can result in almost 28% higher health impacts (708 DALY) compared to 513 DALY when both the current BRDF and the PH are operational mostly due to uncontrolled NO2 emissions. Observations from this study inform academic community, city planners, policy makers and technology developers on the impacts of community district heating systems and possible mitigation strategies: a) community energy demand could be met either by splitting emissions into more than one source at different locations and different fuel types or by a single source with the least-impact-based location selection criteria with biomass as a fuel; b) advanced high-efficiency pollution control devices are essential to lower emissions for emission sources located in a densely populated community; c) a spatial and temporal impact assessment should be performed in developing bioenergy-based district heating systems, in which the capital and operational costs should be balanced with not only the benefit to greenhouse gas emission

  13. Review and application of group theory to molecular systems biology.

    Science.gov (United States)

    Rietman, Edward A; Karp, Robert L; Tuszynski, Jack A

    2011-06-22

    In this paper we provide a review of selected mathematical ideas that can help us better understand the boundary between living and non-living systems. We focus on group theory and abstract algebra applied to molecular systems biology. Throughout this paper we briefly describe possible open problems. In connection with the genetic code we propose that it may be possible to use perturbation theory to explore the adjacent possibilities in the 64-dimensional space-time manifold of the evolving genome. With regards to algebraic graph theory, there are several minor open problems we discuss. In relation to network dynamics and groupoid formalism we suggest that the network graph might not be the main focus for understanding the phenotype but rather the phase space of the network dynamics. We show a simple case of a C6 network and its phase space network. We envision that the molecular network of a cell is actually a complex network of hypercycles and feedback circuits that could be better represented in a higher-dimensional space. We conjecture that targeting nodes in the molecular network that have key roles in the phase space, as revealed by analysis of the automorphism decomposition, might be a better way to drug discovery and treatment of cancer.

  14. Olfactory memory formation in Drosophila: from molecular to systems neuroscience.

    Science.gov (United States)

    Davis, Ronald L

    2005-01-01

    The olfactory nervous system of insects and mammals exhibits many similarities, which suggests that the mechanisms for olfactory learning may be shared. Molecular genetic investigations of Drosophila learning have uncovered numerous genes whose gene products are essential for olfactory memory formation. Recent studies of the products of these genes have continued to expand the range of molecular processes known to underlie memory formation. Recent research has also broadened the neuroanatomical areas thought to mediate olfactory learning to include the antennal lobes in addition to a previously accepted and central role for the mushroom bodies. The roles for neurons extrinsic to the mushroom body neurons are becoming better defined. Finally, the genes identified to participate in Drosophila olfactory learning have conserved roles in mammalian organisms, highlighting the value of Drosophila for gene discovery.

  15. Nucleocytoplasmic Transport: A Paradigm for Molecular Logistics in Artificial Systems.

    Science.gov (United States)

    Vujica, Suncica; Zelmer, Christina; Panatala, Radhakrishnan; Lim, Roderick Y H

    2016-01-01

    Artificial organelles, molecular factories and nanoreactors are membrane-bound systems envisaged to exhibit cell-like functionality. These constitute liposomes, polymersomes or hybrid lipo-polymersomes that display different membrane-spanning channels and/or enclose molecular modules. To achieve more complex functionality, an artificial organelle should ideally sustain a continuous influx of essential macromolecular modules (i.e. cargoes) and metabolites against an outflow of reaction products. This would benefit from the incorporation of selective nanopores as well as specific trafficking factors that facilitate cargo selectivity, translocation efficiency, and directionality. Towards this goal, we describe how proteinaceous cargoes are transported between the nucleus and cytoplasm by nuclear pore complexes and the biological trafficking machinery in living cells (i.e. nucleocytoplasmic transport). On this basis, we discuss how biomimetic control may be implemented to selectively import, compartmentalize and accumulate diverse macromolecular modules against concentration gradients in artificial organelles.

  16. Dense hydrogen plasma: Comparison between models

    International Nuclear Information System (INIS)

    Clerouin, J.G.; Bernard, S.

    1997-01-01

    Static and dynamical properties of the dense hydrogen plasma (ρ≥2.6gcm -3 , 0.1< T<5eV) in the strongly coupled regime are compared through different numerical approaches. It is shown that simplified density-functional molecular-dynamics simulations (DFMD), without orbitals, such as Thomas-Fermi Dirac or Thomas-Fermi-Dirac-Weiszaecker simulations give similar results to more sophisticated descriptions such as Car-Parrinello (CP), tight binding, or path-integral Monte Carlo, in a wide range of temperatures. At very low temperature, screening effects predicted by DFMD are still less pronounced than CP simulations. copyright 1997 The American Physical Society

  17. Electrical and thermal conductivities in dense plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Faussurier, G., E-mail: gerald.faussurier@cea.fr; Blancard, C.; Combis, P.; Videau, L. [CEA, DAM, DIF, F-91297 Arpajon (France)

    2014-09-15

    Expressions for the electrical and thermal conductivities in dense plasmas are derived combining the Chester-Thellung-Kubo-Greenwood approach and the Kramers approximation. The infrared divergence is removed assuming a Drude-like behaviour. An analytical expression is obtained for the Lorenz number that interpolates between the cold solid-state and the hot plasma phases. An expression for the electrical resistivity is proposed using the Ziman-Evans formula, from which the thermal conductivity can be deduced using the analytical expression for the Lorenz number. The present method can be used to estimate electrical and thermal conductivities of mixtures. Comparisons with experiment and quantum molecular dynamics simulations are done.

  18. Unified approach to dense matter

    International Nuclear Information System (INIS)

    Park, Byung-Yoon; Lee, Hee-Jung; Vento, Vicente; Kim, Joon-Il; Min, Dong-Pil; Rho, Mannque

    2005-01-01

    We apply the Skyrme model to dense hadronic matter, which provides a unified approach to high density, valid in the large N c limit. In our picture, dense hadronic matter is described by the classical soliton configuration with minimum energy for the given baryon number density. By incorporating the meson fluctuations on such ground state we obtain an effective Lagrangian for meson dynamics in a dense medium. Our starting point has been the Skyrme model defined in terms of pions, thereafter we have extended and improved the model by incorporating other degrees of freedom such as dilaton, kaons and vector mesons

  19. A new parallel molecular dynamics algorithm for organic systems

    International Nuclear Information System (INIS)

    Plimpton, S.; Hendrickson, B.; Heffelfinger, G.

    1993-01-01

    A new parallel algorithm for simulating bonded molecular systems such as polymers and proteins by molecular dynamics (MD) is presented. In contrast to methods that extract parallelism by breaking the spatial domain into sub-pieces, the new method does not require regular geometries or uniform particle densities to achieve high parallel efficiency. For very large, regular systems spatial methods are often the best choice, but in practice the new method is faster for systems with tens-of-thousands of atoms simulated on large numbers of processors. It is also several times faster than the techniques commonly used for parallelizing bonded MD that assign a subset of atoms to each processor and require all-to-all communication. Implementation of the algorithm in a CHARMm-like MD model with many body forces and constraint dynamics is discussed and timings on the Intel Delta and Paragon machines are given. Example calculations using the algorithm in simulations of polymers and liquid-crystal molecules will also be briefly discussed

  20. DNA barcode-based molecular identification system for fish species.

    Science.gov (United States)

    Kim, Sungmin; Eo, Hae-Seok; Koo, Hyeyoung; Choi, Jun-Kil; Kim, Won

    2010-12-01

    In this study, we applied DNA barcoding to identify species using short DNA sequence analysis. We examined the utility of DNA barcoding by identifying 53 Korean freshwater fish species, 233 other freshwater fish species, and 1339 saltwater fish species. We successfully developed a web-based molecular identification system for fish (MISF) using a profile hidden Markov model. MISF facilitates efficient and reliable species identification, overcoming the limitations of conventional taxonomic approaches. MISF is freely accessible at http://bioinfosys.snu.ac.kr:8080/MISF/misf.jsp .

  1. Transport properties of dense matter

    International Nuclear Information System (INIS)

    Itoh, Naoki; Mitake, Shinichi; Iyetomi, Hiroshi; Ichimaru, Setsuo

    1983-01-01

    Transport coefficients, electrical and thermal conductivities in particular, are essential physical quantities for the theories of stellar structure. Since the discoveries of pulsars and X-ray stars, an accurate evaluation of the transport coefficients in the dense matter has become indispensable to the quantitative understanding of the observed neutron stars. The authors present improved calculations of the electrical and thermal conductivities of the dense matter in the liquid metal phase, appropriate to white dwarfs and neutron stars. (Auth.)

  2. DCMS: A data analytics and management system for molecular simulation.

    Science.gov (United States)

    Kumar, Anand; Grupcev, Vladimir; Berrada, Meryem; Fogarty, Joseph C; Tu, Yi-Cheng; Zhu, Xingquan; Pandit, Sagar A; Xia, Yuni

    Molecular Simulation (MS) is a powerful tool for studying physical/chemical features of large systems and has seen applications in many scientific and engineering domains. During the simulation process, the experiments generate a very large number of atoms and intend to observe their spatial and temporal relationships for scientific analysis. The sheer data volumes and their intensive interactions impose significant challenges for data accessing, managing, and analysis. To date, existing MS software systems fall short on storage and handling of MS data, mainly because of the missing of a platform to support applications that involve intensive data access and analytical process. In this paper, we present the database-centric molecular simulation (DCMS) system our team developed in the past few years. The main idea behind DCMS is to store MS data in a relational database management system (DBMS) to take advantage of the declarative query interface ( i.e. , SQL), data access methods, query processing, and optimization mechanisms of modern DBMSs. A unique challenge is to handle the analytical queries that are often compute-intensive. For that, we developed novel indexing and query processing strategies (including algorithms running on modern co-processors) as integrated components of the DBMS. As a result, researchers can upload and analyze their data using efficient functions implemented inside the DBMS. Index structures are generated to store analysis results that may be interesting to other users, so that the results are readily available without duplicating the analysis. We have developed a prototype of DCMS based on the PostgreSQL system and experiments using real MS data and workload show that DCMS significantly outperforms existing MS software systems. We also used it as a platform to test other data management issues such as security and compression.

  3. The Green Bank Ammonia Survey: Dense Cores under Pressure in Orion A

    Energy Technology Data Exchange (ETDEWEB)

    Kirk, Helen; Di Francesco, James [NRC Herzberg Astronomy and Astrophysics, 5071 West Saanich Rd, Victoria, BC, V9E 2E7 (Canada); Friesen, Rachel K. [Dunlap Institute for Astronomy and Astrophysics, University of Toronto, 50 St. George St., Toronto, Ontario M5S 3H4 (Canada); Pineda, Jaime E.; Caselli, Paola; Alves, Felipe O.; Chacón-Tanarro, Ana; Punanova, Anna [Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse 1, D-85748, Garching (Germany); Rosolowsky, Erik [Department of Physics, University of Alberta, Edmonton, AB (Canada); Offner, Stella S. R. [Department of Astronomy, University of Massachusetts, Amherst, MA 01003 (United States); Matzner, Christopher D.; Singh, Ayushi [Department of Astronomy and Astrophysics, University of Toronto, 50 St. George St., Toronto, Ontario, M5S 3H4 (Canada); Myers, Philip C.; Chen, How-Huan [Harvard-Smithsonian Center for Astrophysics, 60 Garden St., Cambridge, MA 02138 (United States); Chen, Michael Chun-Yuan; Keown, Jared [Department of Physics and Astronomy, University of Victoria, 3800 Finnerty Rd., Victoria, BC, V8P 5C2 (Canada); Seo, Young Min [Jet Propulsion Laboratory, NASA, 4800 Oak Grove Dr., Pasadena, CA 91109 (United States); Shirley, Yancy [Steward Observatory, 933 North Cherry Ave., Tucson, AZ 85721 (United States); Ginsburg, Adam [National Radio Astronomy Observatory, Socorro, NM 87801 (United States); Hall, Christine [Department of Physics, Engineering Physics and Astronomy, Queen’s University, Kingston, Ontario, K7L 3N6 (Canada); and others

    2017-09-10

    We use data on gas temperature and velocity dispersion from the Green Bank Ammonia Survey and core masses and sizes from the James Clerk Maxwell Telescope Gould Belt Survey to estimate the virial states of dense cores within the Orion A molecular cloud. Surprisingly, we find that almost none of the dense cores are sufficiently massive to be bound when considering only the balance between self-gravity and the thermal and non-thermal motions present in the dense gas. Including the additional pressure binding imposed by the weight of the ambient molecular cloud material and additional smaller pressure terms, however, suggests that most of the dense cores are pressure-confined.

  4. The Green Bank Ammonia Survey: Dense Cores under Pressure in Orion A

    International Nuclear Information System (INIS)

    Kirk, Helen; Di Francesco, James; Friesen, Rachel K.; Pineda, Jaime E.; Caselli, Paola; Alves, Felipe O.; Chacón-Tanarro, Ana; Punanova, Anna; Rosolowsky, Erik; Offner, Stella S. R.; Matzner, Christopher D.; Singh, Ayushi; Myers, Philip C.; Chen, How-Huan; Chen, Michael Chun-Yuan; Keown, Jared; Seo, Young Min; Shirley, Yancy; Ginsburg, Adam; Hall, Christine

    2017-01-01

    We use data on gas temperature and velocity dispersion from the Green Bank Ammonia Survey and core masses and sizes from the James Clerk Maxwell Telescope Gould Belt Survey to estimate the virial states of dense cores within the Orion A molecular cloud. Surprisingly, we find that almost none of the dense cores are sufficiently massive to be bound when considering only the balance between self-gravity and the thermal and non-thermal motions present in the dense gas. Including the additional pressure binding imposed by the weight of the ambient molecular cloud material and additional smaller pressure terms, however, suggests that most of the dense cores are pressure-confined.

  5. International Conference on Intelligent Systems for Molecular Biology (ISMB)

    Energy Technology Data Exchange (ETDEWEB)

    Goldberg, Debra; Hibbs, Matthew; Kall, Lukas; Komandurglayavilli, Ravikumar; Mahony, Shaun; Marinescu, Voichita; Mayrose, Itay; Minin, Vladimir; Neeman, Yossef; Nimrod, Guy; Novotny, Marian; Opiyo, Stephen; Portugaly, Elon; Sadka, Tali; Sakabe, Noboru; Sarkar, Indra; Schaub, Marc; Shafer, Paul; Shmygelska, Olena; Singer, Gregory; Song, Yun; Soumyaroop, Bhattacharya; Stadler, Michael; Strope, Pooja; Su, Rong; Tabach, Yuval; Tae, Hongseok; Taylor, Todd; Terribilini, Michael; Thomas, Asha; Tran, Nam; Tseng, Tsai-Tien; Vashist, Akshay; Vijaya, Parthiban; Wang, Kai; Wang, Ting; Wei, Lai; Woo, Yong; Wu, Chunlei; Yamanishi, Yoshihiro; Yan, Changhui; Yang, Jack; Yang, Mary; Ye, Ping; Zhang, Miao

    2009-12-29

    The Intelligent Systems for Molecular Biology (ISMB) conference has provided a general forum for disseminating the latest developments in bioinformatics on an annual basis for the past 13 years. ISMB is a multidisciplinary conference that brings together scientists from computer science, molecular biology, mathematics and statistics. The goal of the ISMB meeting is to bring together biologists and computational scientists in a focus on actual biological problems, i.e., not simply theoretical calculations. The combined focus on "intelligent systems" and actual biological data makes ISMB a unique and highly important meeting, and 13 years of experience in holding the conference has resulted in a consistently well organized, well attended, and highly respected annual conference. The ISMB 2005 meeting was held June 25-29, 2005 at the Renaissance Center in Detroit, Michigan. The meeting attracted over 1,730 attendees. The science presented was exceptional, and in the course of the five-day meeting, 56 scientific papers, 710 posters, 47 Oral Abstracts, 76 Software demonstrations, and 14 tutorials were presented. The attendees represented a broad spectrum of backgrounds with 7% from commercial companies, over 28% qualifying for student registration, and 41 countries were represented at the conference, emphasizing its important international aspect. The ISMB conference is especially important because the cultures of computer science and biology are so disparate. ISMB, as a full-scale technical conference with refereed proceedings that have been indexed by both MEDLINE and Current Contents since 1996, bridges this cultural gap.

  6. Diffusion-controlled interface kinetics-inclusive system-theoretic propagation models for molecular communication systems

    Science.gov (United States)

    Chude-Okonkwo, Uche A. K.; Malekian, Reza; Maharaj, B. T.

    2015-12-01

    Inspired by biological systems, molecular communication has been proposed as a new communication paradigm that uses biochemical signals to transfer information from one nano device to another over a short distance. The biochemical nature of the information transfer process implies that for molecular communication purposes, the development of molecular channel models should take into consideration diffusion phenomenon as well as the physical/biochemical kinetic possibilities of the process. The physical and biochemical kinetics arise at the interfaces between the diffusion channel and the transmitter/receiver units. These interfaces are herein termed molecular antennas. In this paper, we present the deterministic propagation model of the molecular communication between an immobilized nanotransmitter and nanoreceiver, where the emission and reception kinetics are taken into consideration. Specifically, we derived closed-form system-theoretic models and expressions for configurations that represent different communication systems based on the type of molecular antennas used. The antennas considered are the nanopores at the transmitter and the surface receptor proteins/enzymes at the receiver. The developed models are simulated to show the influence of parameters such as the receiver radius, surface receptor protein/enzyme concentration, and various reaction rate constants. Results show that the effective receiver surface area and the rate constants are important to the system's output performance. Assuming high rate of catalysis, the analysis of the frequency behavior of the developed propagation channels in the form of transfer functions shows significant difference introduce by the inclusion of the molecular antennas into the diffusion-only model. It is also shown that for t > > 0 and with the information molecules' concentration greater than the Michaelis-Menten kinetic constant of the systems, the inclusion of surface receptors proteins and enzymes in the models

  7. Chaotic dynamics in dense fluids

    International Nuclear Information System (INIS)

    Posch, H.A.; Hoover, W.G.

    1987-09-01

    We present calculations of the full spectra of Lyapunov exponents for 8- and 32-particle systems with periodic boundary conditions and interacting with the repulsive part of a Lennard-Jones potential both in equilibrium and nonequilibrium steady states. Lyapunov characteristic exponents λ/sub n/ describe the mean exponential rates of divergence and convergence of neighbouring trajectories in phase-space. They are useful in characterizing the stochastic properties of a dynamical system. A new algorithm for their calculation is presented which incorporates ideas from control theory and constraint nonequilibrium molecular dynamics. 4 refs., 1 fig

  8. Electronic structure, transport, and collective effects in molecular layered systems

    Directory of Open Access Journals (Sweden)

    Torsten Hahn

    2017-10-01

    Full Text Available The great potential of organic heterostructures for organic device applications is exemplified by the targeted engineering of the electronic properties of phthalocyanine-based systems. The transport properties of two different phthalocyanine systems, a pure copper phthalocyanine (CoPc and a flourinated copper phthalocyanine–manganese phthalocyanine (F16CoPc/MnPc heterostructure, are investigated by means of density functional theory (DFT and the non-equilibrium Green’s function (NEGF approach. Furthermore, a master-equation-based approach is used to include electronic correlations beyond the mean-field-type approximation of DFT. We describe the essential theoretical tools to obtain the parameters needed for the master equation from DFT results. Finally, an interacting molecular monolayer is considered within a master-equation approach.

  9. Stability of molecular dynamics simulations of classical systems

    DEFF Research Database (Denmark)

    Toxværd, Søren

    2012-01-01

    The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The investigation is based on the stability of the shadow energy, obtained by including the first term in the asymptotic expansion, and on the exact solution of discrete dynamics for a single harmonic mode. The exact solution of discrete dynamics for a harmonic potential with frequency ω gives a criterion...... for the limit of stability h ⩽ 2/ω. Simulations of the Lennard-Jones system and the viscous Kob-Andersen system show that one can use the limit of stability of the shadow energy or the stability criterion for a harmonic mode on the spectrum of instantaneous frequencies to determine the limit of stability of MD...

  10. Intermolecular thermoelectric-like effects in molecular nano electronic systems

    International Nuclear Information System (INIS)

    Sabzyan, H.; Safari, R.

    2012-01-01

    Intramolecular thermoelectric-like coefficients are introduced and computed of a single molecule nano electronic system. Values of the electronic Intramolecular thermoelectric-like coefficients are calculated based on the density and energy transfers between different parts of the molecule using quantum theory of atoms in molecule. Since, Joule and Peltier heating are even (symmetrical) and odd (antisymmetric) functions of the external bias, it is possible to divide Intramolecular thermoelectric-like coefficients into two components, symmetrical and antisymmetrical Intramolecular thermoelectric-like coefficients, which describe the intramolecular Joule-like and Peltier-like effects, respectively. In addition, a semiclassical temperature model is presented to describe intramolecular temperature mapping (intramolecular energy distributions) in molecular nano electronic systems.

  11. Encounters of The Solar System With Molecular Clouds

    International Nuclear Information System (INIS)

    Wickramasinghe, J. T.

    2008-01-01

    The solar system has penetrated about 5 -- 10 giant molecular clouds over its history, and passes within 5 parsecs of a star-forming nebula every 100 million years or so. Numerical simulations of the effect of such encounters in perturbing the Oort cloud of comets are carried out using standard n-body computational techniques. It is found that the ingress of comets into the inner planetary system during such encounters amounts to factors of ∼100 over the average. During an encounter the impact rate of comets onto Earth increases by a comparable factor. The of ages of impact craters on the Earth is shown to be consistent with predictions from the model

  12. Electronic transport coefficients from ab initio simulations and application to dense liquid hydrogen

    International Nuclear Information System (INIS)

    Holst, Bastian; French, Martin; Redmer, Ronald

    2011-01-01

    Using Kubo's linear response theory, we derive expressions for the frequency-dependent electrical conductivity (Kubo-Greenwood formula), thermopower, and thermal conductivity in a strongly correlated electron system. These are evaluated within ab initio molecular dynamics simulations in order to study the thermoelectric transport coefficients in dense liquid hydrogen, especially near the nonmetal-to-metal transition region. We also observe significant deviations from the widely used Wiedemann-Franz law, which is strictly valid only for degenerate systems, and give an estimate for its valid scope of application toward lower densities.

  13. Phase equilibria and molecular interaction studies on (naphthols + vanillin) systems

    International Nuclear Information System (INIS)

    Gupta, Preeti; Agrawal, Tanvi; Das, Shiva Saran; Singh, Nakshatra Bahadur

    2012-01-01

    Highlights: ► Phase equilibria of (naphthol + vanillin) systems have been studied for the first time. ► Eutectic type phase diagrams are obtained. ► Eutectic mixtures show nonideal behaviour. ► There is a weak molecular interaction between the components in the eutectic mixtures. ► α-Naphthol–vanillin eutectic is more stable as compared to β-naphthol–vanillin. - Abstract: Phase equilibria between (α-naphthol + vanillin) and (β-naphthol + vanillin) systems have been studied by thaw-melt method and the results show the formation of simple eutectic mixtures. Crystallization velocities of components and eutectic mixtures were determined at different stages under cooling. With the help of differential scanning calorimeter (DSC), the enthalpy of fusion of components and eutectic mixtures was determined and from the values excess thermodynamic functions viz., excess Gibbs free energy (G E ), excess entropy (S E ), excess enthalpy (H E ) of hypo-, hyper- and eutectic mixtures were calculated. Flexural strength measurements were made in order to understand the non-ideal nature of eutectics. FT-IR spectral studies indicate the formation of hydrogen bond in the eutectic mixture. Anisotropic and isotropic microstructural studies of components, hypo-, hyper- and eutectic mixtures were made. Jackson’s roughness parameter was calculated and found to be greater than 2 suggesting the faceted morphology with irregular structures. The overall results have shown that there is a weak molecular interaction between the components in the eutectic mixtures and the (α-naphthol + vanillin) eutectic is more stable as compared to the (β-naphthol + vanillin) eutectic system.

  14. Gas-particle interactions in dense gas-fluidised beds

    NARCIS (Netherlands)

    Li, J.; Kuipers, J.A.M.

    2003-01-01

    The occurrence of heterogeneous flow structures in gas-particle flows seriously affects gas¿solid contacting and transport processes in dense gas-fluidized beds. A computational study, using a discrete particle method based on Molecular Dynamics techniques, has been carried out to explore the

  15. Charge migration and charge transfer in molecular systems

    Directory of Open Access Journals (Sweden)

    Hans Jakob Wörner

    2017-11-01

    Full Text Available The transfer of charge at the molecular level plays a fundamental role in many areas of chemistry, physics, biology and materials science. Today, more than 60 years after the seminal work of R. A. Marcus, charge transfer is still a very active field of research. An important recent impetus comes from the ability to resolve ever faster temporal events, down to the attosecond time scale. Such a high temporal resolution now offers the possibility to unravel the most elementary quantum dynamics of both electrons and nuclei that participate in the complex process of charge transfer. This review covers recent research that addresses the following questions. Can we reconstruct the migration of charge across a molecule on the atomic length and electronic time scales? Can we use strong laser fields to control charge migration? Can we temporally resolve and understand intramolecular charge transfer in dissociative ionization of small molecules, in transition-metal complexes and in conjugated polymers? Can we tailor molecular systems towards specific charge-transfer processes? What are the time scales of the elementary steps of charge transfer in liquids and nanoparticles? Important new insights into each of these topics, obtained from state-of-the-art ultrafast spectroscopy and/or theoretical methods, are summarized in this review.

  16. Evidence for systems-level molecular mechanisms of tumorigenesis

    Directory of Open Access Journals (Sweden)

    Capellá Gabriel

    2007-06-01

    Full Text Available Abstract Background Cancer arises from the consecutive acquisition of genetic alterations. Increasing evidence suggests that as a consequence of these alterations, molecular interactions are reprogrammed in the context of highly connected and regulated cellular networks. Coordinated reprogramming would allow the cell to acquire the capabilities for malignant growth. Results Here, we determine the coordinated function of cancer gene products (i.e., proteins encoded by differentially expressed genes in tumors relative to healthy tissue counterparts, hereafter referred to as "CGPs" defined as their topological properties and organization in the interactome network. We show that CGPs are central to information exchange and propagation and that they are specifically organized to promote tumorigenesis. Centrality is identified by both local (degree and global (betweenness and closeness measures, and systematically appears in down-regulated CGPs. Up-regulated CGPs do not consistently exhibit centrality, but both types of cancer products determine the overall integrity of the network structure. In addition to centrality, down-regulated CGPs show topological association that correlates with common biological processes and pathways involved in tumorigenesis. Conclusion Given the current limited coverage of the human interactome, this study proposes that tumorigenesis takes place in a specific and organized way at the molecular systems-level and suggests a model that comprises the precise down-regulation of groups of topologically-associated proteins involved in particular functions, orchestrated with the up-regulation of specific proteins.

  17. Multiscale Molecular Dynamics Model for Heterogeneous Charged Systems

    Science.gov (United States)

    Stanton, L. G.; Glosli, J. N.; Murillo, M. S.

    2018-04-01

    Modeling matter across large length scales and timescales using molecular dynamics simulations poses significant challenges. These challenges are typically addressed through the use of precomputed pair potentials that depend on thermodynamic properties like temperature and density; however, many scenarios of interest involve spatiotemporal variations in these properties, and such variations can violate assumptions made in constructing these potentials, thus precluding their use. In particular, when a system is strongly heterogeneous, most of the usual simplifying assumptions (e.g., spherical potentials) do not apply. Here, we present a multiscale approach to orbital-free density functional theory molecular dynamics (OFDFT-MD) simulations that bridges atomic, interionic, and continuum length scales to allow for variations in hydrodynamic quantities in a consistent way. Our multiscale approach enables simulations on the order of micron length scales and 10's of picosecond timescales, which exceeds current OFDFT-MD simulations by many orders of magnitude. This new capability is then used to study the heterogeneous, nonequilibrium dynamics of a heated interface characteristic of an inertial-confinement-fusion capsule containing a plastic ablator near a fuel layer composed of deuterium-tritium ice. At these scales, fundamental assumptions of continuum models are explored; features such as the separation of the momentum fields among the species and strong hydrogen jetting from the plastic into the fuel region are observed, which had previously not been seen in hydrodynamic simulations.

  18. FttC-Based Fronthaul for 5G Dense/Ultra-Dense Access Network: Performance and Costs in Realistic Scenarios

    Directory of Open Access Journals (Sweden)

    Franco Mazzenga

    2017-10-01

    Full Text Available One distinctive feature of the next 5G systems is the presence of a dense/ultra-dense wireless access network with a large number of access points (or nodes at short distances from each other. Dense/ultra-dense access networks allow for providing very high transmission capacity to terminals. However, the deployment of dense/ultra-dense networks is slowed down by the cost of the fiber-based infrastructure required to connect radio nodes to the central processing units and then to the core network. In this paper, we investigate the possibility for existing FttC access networks to provide fronthaul capabilities for dense/ultra-dense 5G wireless networks. The analysis is realistic in that it is carried out considering an actual access network scenario, i.e., the Italian FttC deployment. It is assumed that access nodes are connected to the Cabinets and to the corresponding distributors by a number of copper pairs. Different types of cities grouped in terms of population have been considered. Results focus on fronthaul transport capacity provided by the FttC network and have been expressed in terms of the available fronthaul bit rate per node and of the achievable coverage.

  19. Molecular dynamic simulations of the sputtering of multilayer organic systems

    CERN Document Server

    Postawa, Z; Piaskowy, J; Krantzman, K; Winograd, N; Garrison, B J

    2003-01-01

    Sputtering of organic overlayers has been modeled using molecular dynamics computer simulations. The investigated systems are composed of benzene molecules condensed into one, two and three layers on an Ag left brace 1 1 1 right brace surface. The formed organic overlayers were bombarded with 4 keV Ar projectiles at normal incidence. The development of the collision cascade in the organic overlayer was investigated. The sputtering yield, mass, internal and kinetic energy distributions of ejected particles have been analyzed as a function of the thickness of the organic layer. The results show that all emission characteristics are sensitive to the variation of layer thickness. Although most of the ejected intact benzene molecules originate from the topmost layer, the emission of particles located initially in second and third layers is significant. The analysis indicates that the metallic substrate plays a dominant role in the ejection of intact organic molecules.

  20. Pancreatic Cancer Gene Therapy: From Molecular Targets to Delivery Systems

    Energy Technology Data Exchange (ETDEWEB)

    Fillat, Cristina, E-mail: cristina.fillat@crg.es; Jose, Anabel; Ros, Xavier Bofill-De; Mato-Berciano, Ana; Maliandi, Maria Victoria; Sobrevals, Luciano [Programa Gens i Malaltia, Centre de Regulació Genòmica-CRG, UPF, Parc de Recerca Biomedica de Barcelona-PRBB and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona (Spain)

    2011-01-18

    The continuous identification of molecular changes deregulating critical pathways in pancreatic tumor cells provides us with a large number of novel candidates to engineer gene-targeted approaches for pancreatic cancer treatment. Targets—both protein coding and non-coding—are being exploited in gene therapy to influence the deregulated pathways to facilitate cytotoxicity, enhance the immune response or sensitize to current treatments. Delivery vehicles based on viral or non-viral systems as well as cellular vectors with tumor homing characteristics are a critical part of the design of gene therapy strategies. The different behavior of tumoral versus non-tumoral cells inspires vector engineering with the generation of tumor selective products that can prevent potential toxic-associated effects. In the current review, a detailed analysis of the different targets, the delivery vectors, the preclinical approaches and a descriptive update on the conducted clinical trials are presented. Moreover, future possibilities in pancreatic cancer treatment by gene therapy strategies are discussed.

  1. Isolating strong-field dynamics in molecular systems

    Science.gov (United States)

    Orenstein, Gal; Pedatzur, Oren; Uzan, Ayelet J.; Bruner, Barry D.; Mairesse, Yann; Dudovich, Nirit

    2017-05-01

    Strong-field ionization followed by recollision provides a unique pump-probe measurement which reveals a range of electronic processes, combining sub-Angstrom spatial and attosecond temporal resolution. A major limitation of this approach is imposed by the coupling between the spatial and temporal degrees of freedom. In this paper we focus on the study of high harmonic generation and demonstrate the ability to isolate the internal dynamics—decoupling the temporal information from the spatial one. By applying an in situ approach we reveal the universality of the intrinsic pump-probe measurement and establish its validity in molecular systems. When several orbitals are involved we identify the fingerprint of the transition from the single-channel case into the multiple-channel dynamics, where complex multielectron phenomena are expected to be observed.

  2. PathSys: integrating molecular interaction graphs for systems biology

    Directory of Open Access Journals (Sweden)

    Raval Alpan

    2006-02-01

    Full Text Available Abstract Background The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately. Results Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping. Conclusion Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at http://brak.sdsc.edu/pub/BiologicalNetworks.

  3. Bicanonical ab Initio Molecular Dynamics for Open Systems.

    Science.gov (United States)

    Frenzel, Johannes; Meyer, Bernd; Marx, Dominik

    2017-08-08

    Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.

  4. Parametrizing coarse grained models for molecular systems at equilibrium

    KAUST Repository

    Kalligiannaki, Evangelia; Chazirakis, A.; Tsourtis, A.; Katsoulakis, M. A.; Plechá č, P.; Harmandaris, V.

    2016-01-01

    Hierarchical coarse graining of atomistic molecular systems at equilibrium has been an intensive research topic over the last few decades. In this work we (a) review theoretical and numerical aspects of different parametrization methods (structural-based, force matching and relative entropy) to derive the effective interaction potential between coarse-grained particles. All methods approximate the many body potential of mean force; resulting, however, in different optimization problems. (b) We also use a reformulation of the force matching method by introducing a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (E. Kalligiannaki, et al., J. Chem. Phys. 2015). We apply and compare these methods to: (a) a benchmark system of two isolated methane molecules; (b) methane liquid; (c) water; and (d) an alkane fluid. Differences between the effective interactions, derived from the various methods, are found that depend on the actual system under study. The results further reveal the relation of the various methods and the sensitivities that may arise in the implementation of numerical methods used in each case.

  5. Parametrizing coarse grained models for molecular systems at equilibrium

    KAUST Repository

    Kalligiannaki, Evangelia

    2016-10-18

    Hierarchical coarse graining of atomistic molecular systems at equilibrium has been an intensive research topic over the last few decades. In this work we (a) review theoretical and numerical aspects of different parametrization methods (structural-based, force matching and relative entropy) to derive the effective interaction potential between coarse-grained particles. All methods approximate the many body potential of mean force; resulting, however, in different optimization problems. (b) We also use a reformulation of the force matching method by introducing a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (E. Kalligiannaki, et al., J. Chem. Phys. 2015). We apply and compare these methods to: (a) a benchmark system of two isolated methane molecules; (b) methane liquid; (c) water; and (d) an alkane fluid. Differences between the effective interactions, derived from the various methods, are found that depend on the actual system under study. The results further reveal the relation of the various methods and the sensitivities that may arise in the implementation of numerical methods used in each case.

  6. Molecular tailoring of interfaces for thin film on substrate systems

    Science.gov (United States)

    Grady, Martha Elizabeth

    Thin film on substrate systems appear most prevalently within the microelectronics industry, which demands that devices operate in smaller and smaller packages with greater reliability. The reliability of these multilayer film systems is strongly influenced by the adhesion of each of the bimaterial interfaces. During use, microelectronic components undergo thermo-mechanical cycling, which induces interfacial delaminations leading to failure of the overall device. The ability to tailor interfacial properties at the molecular level provides a mechanism to improve thin film adhesion, reliability and performance. This dissertation presents the investigation of molecular level control of interface properties in three thin film-substrate systems: photodefinable polyimide films on passivated silicon substrates, self-assembled monolayers at the interface of Au films and dielectric substrates, and mechanochemically active materials on rigid substrates. For all three materials systems, the effect of interfacial modifications on adhesion is assessed using a laser-spallation technique. Laser-induced stress waves are chosen because they dynamically load the thin film interface in a precise, noncontacting manner at high strain rates and are suitable for both weak and strong interfaces. Photodefinable polyimide films are used as dielectrics in flip chip integrated circuit packages to reduce the stress between silicon passivation layers and mold compound. The influence of processing parameters on adhesion is examined for photodefinable polyimide films on silicon (Si) substrates with three different passivation layers: silicon nitride (SiNx), silicon oxynitride (SiOxNy), and the native silicon oxide (SiO2). Interfacial strength increases when films are processed with an exposure step as well as a longer cure cycle. Additionally, the interfacial fracture energy is assessed using a dynamic delamination protocol. The high toughness of this interface (ca. 100 J/m2) makes it difficult

  7. Dense Crowds of Virtual Humans

    NARCIS (Netherlands)

    Stüvel, S.A.

    2016-01-01

    This thesis presents a novel crowd simulation method `Torso Crowds', aimed at the simulation of dense crowds. The method is based on the results of user studies and a motion capture experiment, which are also described in this thesis. Torso Crowds introduces a capsule shape to represent people in

  8. Molecular Physiology of Root System Architecture in Model Grasses

    Science.gov (United States)

    Hixson, K.; Ahkami, A. H.; Anderton, C.; Veličković, D.; Myers, G. L.; Chrisler, W.; Lindenmaier, R.; Fang, Y.; Yabusaki, S.; Rosnow, J. J.; Farris, Y.; Khan, N. E.; Bernstein, H. C.; Jansson, C.

    2017-12-01

    Unraveling the molecular and physiological mechanisms involved in responses of Root System Architecture (RSA) to abiotic stresses and shifts in microbiome structure is critical to understand and engineer plant-microbe-soil interactions in the rhizosphere. In this study, accessions of Brachypodium distachyon Bd21 (C3 model grass) and Setaria viridis A10.1 (C4 model grass) were grown in phytotron chambers under current and elevated CO2 levels. Detailed growth stage-based phenotypic analysis revealed different above- and below-ground morphological and physiological responses in C3 and C4 grasses to enhanced CO2 levels. Based on our preliminary results and by screening values of total biomass, water use efficiency, root to shoot ratio, RSA parameters and net assimilation rates, we postulated a three-phase physiological mechanism, i.e. RootPlus, BiomassPlus and YieldPlus phases, for grass growth under elevated CO2 conditions. Moreover, this comprehensive set of morphological and process-based observations are currently in use to develop, test, and calibrate biophysical whole-plant models and in particular to simulate leaf-level photosynthesis at various developmental stages of C3 and C4 using the model BioCro. To further link the observed phenotypic traits at the organismal level to tissue and molecular levels, and to spatially resolve the origin and fate of key metabolites involved in primary carbohydrate metabolism in different root sections, we complement root phenotypic observations with spatial metabolomics data using mass spectrometry imaging (MSI) methods. Focusing on plant-microbe interactions in the rhizosphere, six bacterial strains with plant growth promoting features are currently in use in both gel-based and soil systems to screen root growth and development in Brachypodium. Using confocal microscopy, GFP-tagged bacterial systems are utilized to study the initiation of different root types of RSA, including primary root (PR), coleoptile node axile root (CNR

  9. Kinetic theory of the interdiffusion coefficient in dense plasmas

    International Nuclear Information System (INIS)

    Boercker, D.B.

    1986-08-01

    Naive applications of Spitzer's theory to very dense plasmas can lead to negative diffusion coefficients. The interdiffusion coefficients in Binary Ionic Mixtures (two species of point ions in a uniform neutralizing background) have been calculated recently using molecular dynamics techniques. These calculations can provide useful benchmarks for theoretical evaluations of the diffusion coefficient in dense plasma mixtures. This paper gives a brief description of a kinetic theoretic approximation to the diffusion coefficient which generalizes Spitzer to high density and is in excellent agreement with the computer simulations. 15 refs., 1 fig., 2 tabs

  10. Free-Free Transitions of e-H System Inside a Dense Plasma Irradiated by a Laser Field at Very Low Incident Electron Energies

    Science.gov (United States)

    Bhatia, A. K.; Sinha, C.

    2012-01-01

    The free-free transition is studied for an electron-hydrogen in the ground state at low incident energies in the presence of an external homogenous, monochromatic, and linearly polarized laser-field inside a hot dense plasma.The effect of plasma screening is considered in the Debye-Huckel approximation. The calculations are performed in the soft photon limit, assuming that the plasma frequency is much higher than the laser frequency. The incident electron is considered to be dressed by the laser field in a nonperturbative manner by choosing the Volkov solutions in both the initial and final channels. The space part of the scattering wave function for the electron is solved numerically by taking into account the electron exchange. The laser-assisted differential and total cross sections are calculated for single-photon absorption /emission and no photon exchange in the soft photon limit, the laser intensity being much less than the atomic field intensity. The calculations have been carried out for various values of Debye parameter, ranging from 0.005 to 0.12. A strong suppression is noted in the laser-assisted cross sections as compared to the field-free situation. A significant difference is noted for the singlet and triplet cross sections. The suppression is much more in the triplet states.

  11. Spectroscopic Studies of Molecular Systems relevant in Astrobiology

    Science.gov (United States)

    Fornaro, Teresa

    2016-01-01

    In the Astrobiology context, the study of the physico-chemical interactions involving "building blocks of life" in plausible prebiotic and space-like conditions is fundamental to shed light on the processes that led to emergence of life on Earth as well as to molecular chemical evolution in space. In this PhD Thesis, such issues have been addressed both experimentally and computationally by employing vibrational spectroscopy, which has shown to be an effective tool to investigate the variety of intermolecular interactions that play a key role in self-assembling mechanisms of nucleic acid components and their binding to mineral surfaces. In particular, in order to dissect the contributions of the different interactions to the overall spectroscopic signals and shed light on the intricate experimental data, feasible computational protocols have been developed for the characterization of the spectroscopic properties of such complex systems. This study has been carried out through a multi-step strategy, starting the investigation from the spectroscopic properties of the isolated nucleobases, then studying the perturbation induced by the interaction with another molecule (molecular dimers), towards condensed phases like the molecular solid, up to the case of nucleic acid components adsorbed on minerals. A proper modeling of these weakly bound molecular systems has required, firstly, a validation of dispersion-corrected Density Functional Theory methods for simulating anharmonic vibrational properties. The isolated nucleobases and some of their dimers have been used as benchmark set for identifying a general, reliable and effective computational procedure based on fully anharmonic quantum mechanical computations of the vibrational wavenumbers and infrared intensities within the generalized second order vibrational perturbation theory (GVPT2) approach, combined with the cost-effective dispersion-corrected density functional B3LYP-D3, in conjunction with basis sets of

  12. Fast electronic structure methods for strongly correlated molecular systems

    International Nuclear Information System (INIS)

    Head-Gordon, Martin; Beran, Gregory J O; Sodt, Alex; Jung, Yousung

    2005-01-01

    A short review is given of newly developed fast electronic structure methods that are designed to treat molecular systems with strong electron correlations, such as diradicaloid molecules, for which standard electronic structure methods such as density functional theory are inadequate. These new local correlation methods are based on coupled cluster theory within a perfect pairing active space, containing either a linear or quadratic number of pair correlation amplitudes, to yield the perfect pairing (PP) and imperfect pairing (IP) models. This reduces the scaling of the coupled cluster iterations to no worse than cubic, relative to the sixth power dependence of the usual (untruncated) coupled cluster doubles model. A second order perturbation correction, PP(2), to treat the neglected (weaker) correlations is formulated for the PP model. To ensure minimal prefactors, in addition to favorable size-scaling, highly efficient implementations of PP, IP and PP(2) have been completed, using auxiliary basis expansions. This yields speedups of almost an order of magnitude over the best alternatives using 4-center 2-electron integrals. A short discussion of the scope of accessible chemical applications is given

  13. Holographic Renormalization in Dense Medium

    International Nuclear Information System (INIS)

    Park, Chanyong

    2014-01-01

    The holographic renormalization of a charged black brane with or without a dilaton field, whose dual field theory describes a dense medium at finite temperature, is investigated in this paper. In a dense medium, two different thermodynamic descriptions are possible due to an additional conserved charge. These two different thermodynamic ensembles are classified by the asymptotic boundary condition of the bulk gauge field. It is also shown that in the holographic renormalization regularity of all bulk fields can reproduce consistent thermodynamic quantities and that the Bekenstein-Hawking entropy is nothing but the renormalized thermal entropy of the dual field theory. Furthermore, we find that the Reissner-Nordström AdS black brane is dual to a theory with conformal matter as expected, whereas a charged black brane with a nontrivial dilaton profile is mapped to a theory with nonconformal matter although its leading asymptotic geometry still remains as AdS space

  14. Suprathermal viscosity of dense matter

    International Nuclear Information System (INIS)

    Alford, Mark; Mahmoodifar, Simin; Schwenzer, Kai

    2010-01-01

    Motivated by the existence of unstable modes of compact stars that eventually grow large, we study the bulk viscosity of dense matter, taking into account non-linear effects arising in the large amplitude regime, where the deviation μ Δ of the chemical potentials from chemical equilibrium fulfills μ Δ > or approx. T. We find that this supra-thermal bulk viscosity can provide a potential mechanism for saturating unstable modes in compact stars since the viscosity is strongly enhanced. Our study confirms previous results on strange quark matter and shows that the suprathermal enhancement is even stronger in the case of hadronic matter. We also comment on the competition of different weak channels and the presence of suprathermal effects in various color superconducting phases of dense quark matter.

  15. Large-scale theoretical calculations in molecular science - design of a large computer system for molecular science and necessary conditions for future computers

    Energy Technology Data Exchange (ETDEWEB)

    Kashiwagi, H [Institute for Molecular Science, Okazaki, Aichi (Japan)

    1982-06-01

    A large computer system was designed and established for molecular science under the leadership of molecular scientists. Features of the computer system are an automated operation system and an open self-service system. Large-scale theoretical calculations have been performed to solve many problems in molecular science, using the computer system. Necessary conditions for future computers are discussed on the basis of this experience.

  16. Large-scale theoretical calculations in molecular science - design of a large computer system for molecular science and necessary conditions for future computers

    International Nuclear Information System (INIS)

    Kashiwagi, H.

    1982-01-01

    A large computer system was designed and established for molecular science under the leadership of molecular scientists. Features of the computer system are an automated operation system and an open self-service system. Large-scale theoretical calculations have been performed to solve many problems in molecular science, using the computer system. Necessary conditions for future computers are discussed on the basis of this experience. (orig.)

  17. Gas-surface interactions using accommodation coefficients for a dilute and a dense gas in a micro/nano-channel : heat flux predictions using combined molecular dynamics and Monte Carlo techniques

    NARCIS (Netherlands)

    Gaastra - Nedea, S.V.; Steenhoven, van A.A.; Markvoort, A.J.; Spijker, P.; Giordano, D.

    2014-01-01

    The influence of gas-surface interactions of a dilute gas confined between two parallel walls on the heat flux predictions is investigated using a combined Monte Carlo (MC) and molecular dynamics (MD) approach. The accommodation coefficients are computed from the temperature of incident and

  18. Strange mesons in dense nuclear matter

    International Nuclear Information System (INIS)

    Senger, P.

    2000-10-01

    Experimental data on the production of kaons and antikaons in heavy ion collisions at relativistic energies are reviewed with respect to in-medium effects. The K - /K + ratios measured in nucleus-nucleus collisions are 1-2 orders of magnitude larger than in proton-proton collisions. The azimuthal angle distributions of K + mesons indicate a repulsive kaon-nucleon potential. Microscopic transport calculations consistently explain both the yields and the emission patterns of kaons and antikaons when assuming that their properties are modified in dense nuclear matter. The K + production excitation functions measured in light and heavy collision systems provide evidence for a soft nuclear equation-of-state. (orig.)

  19. Molecular photoionization studies of nucleobases and correlated systems

    Energy Technology Data Exchange (ETDEWEB)

    Poliakoff, Erwin D. [Louisiana State Univ., Baton Rouge, LA (United States)

    2015-03-11

    We proposed molecular photoionization studies in order to probe correlated events in fundamental scattering phenomena. In particular, we suggested that joint theoretical-experimental studies would provide a window into the microscopic aspects that are of central importance in AMO and chemical physics generally, and would generate useful data for wide array of important DOE topics, such as ultrafast dynamics, high harmonic generation, and probes of nonadiabatic processes. The unifying theme is that correlations between electron scattering dynamics and molecular geometry highlight inherently molecular aspects of the photoelectron behavior.

  20. Diffracted X-ray tracking: new system for single molecular detection with X-rays

    CERN Document Server

    Sasaki, Y C; Adachi, S; Suzuki, Y; Yagi, N

    2001-01-01

    We propose a new X-ray methodology for direct observations of the behaviors of single molecular units in real time and real space. This new system, which we call Diffracted X-ray Tracking (DXT), monitors the Brownian motions of a single molecular unit by observations of X-ray diffracted spots from a nanocrystal, tightly bound to the individual single molecular unit in bio-systems. DXT does not determine any translational movements, but only orientational movements.

  1. Diffracted X-ray tracking: new system for single molecular detection with X-rays

    International Nuclear Information System (INIS)

    Sasaki, Y.C.; Okumura, Y.; Adachi, S.; Suzuki, Y.; Yagi, N.

    2001-01-01

    We propose a new X-ray methodology for direct observations of the behaviors of single molecular units in real time and real space. This new system, which we call Diffracted X-ray Tracking (DXT), monitors the Brownian motions of a single molecular unit by observations of X-ray diffracted spots from a nanocrystal, tightly bound to the individual single molecular unit in bio-systems. DXT does not determine any translational movements, but only orientational movements

  2. Molecular Genetic and Gene Therapy Studies of the Musculoskeletal System

    National Research Council Canada - National Science Library

    Baylink, David

    2004-01-01

    The primary goal of the proposed work is to apply several state of the art molecular genetic and gene therapy technologies to address fundamental questions in bone biology with a particular emphasis on attempting: l...

  3. Dense Breasts: Answers to Commonly Asked Questions

    Science.gov (United States)

    ... Cancer Prevention Genetics of Breast & Gynecologic Cancers Breast Cancer Screening Research Dense Breasts: Answers to Commonly Asked Questions What are dense breasts? Breasts contain glandular, connective, and fat tissue. Breast density is a term that describes the ...

  4. Dense breasts: a review of reporting legislation and available supplemental screening options.

    Science.gov (United States)

    Ho, Jessica M; Jafferjee, Nasima; Covarrubias, Gabriel M; Ghesani, Munir; Handler, Bradley

    2014-08-01

    The objectives of this article are to discuss the Mammography Quality Standards Act (MQSA) and what it means for patients, define breast density and explain how it is measured, review the new state-based legislation regarding the reporting of dense breast tissue directly to patients and the possibility of an adjunct screening examination, describe possible supplemental screening options and the advantages and disadvantages of each, and outline the current shortcomings and unanswered questions regarding new legislation. Breast density is now established as an independent risk factor for developing breast cancer irrespective of other known risk factors. Women with breast density in the upper quartile have an associated four to five times greater risk of developing breast cancer relative to women with breast density in the lower quartile. Many states have enacted or proposed legislation requiring mammographers to report to patients directly if they have dense breast tissue and recommend discussing the possibility of a supplemental screening examination with their physicians. However, there is currently no consensus as to whether a supplemental screening examination should be pursued or which modality to use. Possible supplemental screening modalities include ultrasound, MRI, digital breast tomosynthesis, and molecular breast imaging. The U.S. Food and Drug Administration recently approved an automated breast ultrasound system for screening whole-breast ultrasound in patients with dense breasts. However, many questions are still unanswered including the impact on morbidity and mortality, cost-effectiveness, and insurance coverage.

  5. Quantum Simulations for Dense Matter

    International Nuclear Information System (INIS)

    Ceperley, David M.

    2010-01-01

    High pressure systems are important, for example, to understand the interiors of giant planets (Jupiter and Saturn), for experiments at NIF (the National Ignition Facility at Livermore) related to inertially confined fusion and for other interests of DOE. In this project, we are developing innovative simulation methods (Quantum Monte Carlo methods) to allow more accurate calculation of properties of systems under extreme conditions of pressure and temperature. These methods can use the power of current day supercomputers made of very many processors, starting from the basic equations of physics to model quantum phenomena important at the microscopic scale. During the grant period, we have settled two important questions of the physics of hydrogen and helium under extreme conditions. We have found the pressures and temperatures when hydrogen and helium mix together; this is important to understand the difference of the interiors of the planets Jupiter and Saturn. Secondly, we have shown that there exists a sharp transition as a function of pressure between molecular and atomic liquid hydrogen at temperatures below 2000K. This prediction can be confirmed with high pressure experiments.

  6. Constructing Dense Graphs with Unique Hamiltonian Cycles

    Science.gov (United States)

    Lynch, Mark A. M.

    2012-01-01

    It is not difficult to construct dense graphs containing Hamiltonian cycles, but it is difficult to generate dense graphs that are guaranteed to contain a unique Hamiltonian cycle. This article presents an algorithm for generating arbitrarily large simple graphs containing "unique" Hamiltonian cycles. These graphs can be turned into dense graphs…

  7. Ion-molecular equilibria and activity determination in the RbF-ZrF4 system

    International Nuclear Information System (INIS)

    Skokan, E.V.; Nikitin, M.I.; Sorokin, I.D.; Korenev, Yu.M.; Sidorov, L.N.

    1983-01-01

    Activity of zirconium tetrofluoride in 100-33.3 mol % ZrF 4 concentration range was determined during isothermal evaporation of samples of different initial composition of RbF-ZrF 4 system, using ion-molecular equilibrium method. It became possible, using the exchange ion-molecular reactions to determine ZrF 4 activity approximately 10 -10 in the region of state diagram of RbF-ZrF 4 system, adjoining to rubidium fluoride. The comparative analysis of results, obtained by the methods of isothermal evaporation, ion-molecular equilibria is given; the advantages and restrictions of ion-molecular equilibrium method are presented

  8. Screening in dense ionic fluids

    International Nuclear Information System (INIS)

    Tosi, M.P.

    1991-01-01

    There has been great progress in recent years in determining and understanding the structure of molten salts. I focus on molten alkali halides and discuss two main points concerning their liquid structure and its relationship with static electrical response in these dense ionic conductors. These are (i) the nature of screening and the related definitions and properties of the screening length and of the dielectric function, and (ii) developments in integral equations techniques for the evaluation of molten salt structure and static screening from given pair potentials. (author). 26 refs, 3 figs, 2 tabs

  9. Spatially and Temporally Resolved Diagnostics of Dense Sprays Using Gated, Femtosecond, Digital Holography, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — This is a proposal to develop a unique, gated, picosecond, digital holography system for characterizing dense particle fields in high pressure combustion...

  10. OH megamasers: dense gas & the infrared radiation field

    Science.gov (United States)

    Huang, Yong; Zhang, JiangShui; Liu, Wei; Xu, Jie

    2018-06-01

    To investigate possible factors related to OH megamaser formation (OH MM, L_{H2O}>10L_{⊙}), we compiled a large HCN sample from all well-sampled HCN measurements so far in local galaxies and identified with the OH MM, OH kilomasers (L_{H2O}gas and the dense gas, respectively), we found that OH MM galaxies tend to have stronger HCN emission and no obvious difference on CO luminosity exists between OH MM and non-OH MM. This implies that OH MM formation should be related to the dense molecular gas, instead of the low-density molecular gas. It can be also supported by other facts: (1) OH MMs are confirmed to have higher mean molecular gas density and higher dense gas fraction (L_{HCN}/L_{CO}) than non-OH MMs. (2) After taking the distance effect into account, the apparent maser luminosity is still correlated with the HCN luminosity, while no significant correlation can be found at all between the maser luminosity and the CO luminosity. (3) The OH kMs tend to have lower values than those of OH MMs, including the dense gas luminosity and the dense gas fraction. (4) From analysis of known data of another dense gas tracer HCO^+, similar results can also be obtained. However, from our analysis, the infrared radiation field can not be ruled out for the OH MM trigger, which was proposed by previous works on one small sample (Darling in ApJ 669:L9, 2007). On the contrary, the infrared radiation field should play one more important role. The dense gas (good tracers of the star formation) and its surrounding dust are heated by the ultra-violet (UV) radiation generated by the star formation and the heating of the high-density gas raises the emission of the molecules. The infrared radiation field produced by the re-radiation of the heated dust in turn serves for the pumping of the OH MM.

  11. Optimization of fuel ethanol recovery systems using molecular sieves

    International Nuclear Information System (INIS)

    Scheller, W.A.

    1989-01-01

    The use of molecular sieves for the dehydration of rectified fuel ethanol requires only about 58% of the energy required by azeotropic distillation, the usual commercial process. Recently molecular sieve prices have become low enough that their use can be economically competitive with azeotropic distillation. This paper contains results of mass and energy balances to determine the water content of the rectified ethanol (6.15 weight percent) that will result in the minimum energy requirement for producing anhydrous ethanol with the molecular sieve process and byproduct distillers soluble syrup from fermented corn mash containing 7.23 weight percent ethanol. In this paper results of economic evaluations to determine the water content of the rectified ethanol (7.58 weight percent) which results in a minimum investment and operating cost are presented

  12. Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut?

    Science.gov (United States)

    De Backer, Philippe; De Waele, Danny; Van Speybroeck, Linda

    2010-03-01

    The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology 'revolutionizes' molecular biology and 'transcends' its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology's use of modelling and bioinformatics, and by its scale enlargement.

  13. Molecular profiles to biology and pathways: a systems biology approach.

    Science.gov (United States)

    Van Laere, Steven; Dirix, Luc; Vermeulen, Peter

    2016-06-16

    Interpreting molecular profiles in a biological context requires specialized analysis strategies. Initially, lists of relevant genes were screened to identify enriched concepts associated with pathways or specific molecular processes. However, the shortcoming of interpreting gene lists by using predefined sets of genes has resulted in the development of novel methods that heavily rely on network-based concepts. These algorithms have the advantage that they allow a more holistic view of the signaling properties of the condition under study as well as that they are suitable for integrating different data types like gene expression, gene mutation, and even histological parameters.

  14. FROM ATOMISTIC TO SYSTEMATIC COARSE-GRAINED MODELS FOR MOLECULAR SYSTEMS

    KAUST Repository

    Harmandaris, Vagelis

    2017-10-03

    The development of systematic (rigorous) coarse-grained mesoscopic models for complex molecular systems is an intense research area. Here we first give an overview of methods for obtaining optimal parametrized coarse-grained models, starting from detailed atomistic representation for high dimensional molecular systems. Different methods are described based on (a) structural properties (inverse Boltzmann approaches), (b) forces (force matching), and (c) path-space information (relative entropy). Next, we present a detailed investigation concerning the application of these methods in systems under equilibrium and non-equilibrium conditions. Finally, we present results from the application of these methods to model molecular systems.

  15. Environmental Molecular Sciences Laboratory Operations System: Version 4.0 - system requirements specification

    Energy Technology Data Exchange (ETDEWEB)

    Kashporenko, D.

    1996-07-01

    This document is intended to provide an operations standard for the Environmental Molecular Sciences Laboratory OPerations System (EMSL OPS). It is directed toward three primary audiences: (1) Environmental Molecular Sciences Laboratory (EMSL) facility and operations personnel; (2) laboratory line managers and staff; and (3) researchers, equipment operators, and laboratory users. It is also a statement of system requirements for software developers of EMSL OPS. The need for a finely tuned, superior research environment as provided by the US Department of Energy`s (DOE) Environmental Molecular Sciences Laboratory has never been greater. The abrupt end of the Cold War and the realignment of national priorities caused major US and competing overseas laboratories to reposition themselves in a highly competitive research marketplace. For a new laboratory such as the EMSL, this means coming into existence in a rapidly changing external environment. For any major laboratory, these changes create funding uncertainties and increasing global competition along with concomitant demands for higher standards of research product quality and innovation. While more laboratories are chasing fewer funding dollars, research ideas and proposals, especially for molecular-level research in the materials and biological sciences, are burgeoning. In such an economically constrained atmosphere, reduced costs, improved productivity, and strategic research project portfolio building become essential to establish and maintain any distinct competitive advantage. For EMSL, this environment and these demands require clear operational objectives, specific goals, and a well-crafted strategy. Specific goals will evolve and change with the evolution of the nature and definition of DOE`s environmental research needs. Hence, EMSL OPS is designed to facilitate migration of these changes with ease into every pertinent job function, creating a facile {open_quotes}learning organization.{close_quotes}

  16. Molecular materials and devices: developing new functional systems based on the coordination chemistry approach

    Directory of Open Access Journals (Sweden)

    Toma Henrique E.

    2003-01-01

    Full Text Available At the onset of the nanotechnology age, molecular designing of materials and single molecule studies are opening wide possibilities of using molecular systems in electronic and photonic devices, as well as in technological applications based on molecular switching or molecular recognition. In this sense, inorganic chemists are privileged by the possibility of using the basic strategies of coordination chemistry to build up functional supramolecular materials, conveying the remarkable chemical properties of the metal centers and the characteristics of the ancillary ligands. Coordination chemistry also provides effective self-assembly strategies based on specific metal-ligand affinity and stereochemistry. Several molecular based materials, derived from inorganic and metal-organic compounds are focused on this article, with emphasis on new supramolecular porphyrins and porphyrazines, metal-clusters and metal-polyimine complexes. Such systems are also discussed in terms of their applications in catalysis, sensors and molecular devices.

  17. Electrochemistry of single molecules and biomolecules, molecular scale nanostructures, and low-dimensional systems

    DEFF Research Database (Denmark)

    Nazmutdinov, Renat R.; Zinkicheva, Tamara T.; Zinkicheva, Tamara T.

    2018-01-01

    Electrochemistry at ultra-small scales, where even the single molecule or biomolecule can be characterized and manipulated, is on the way to a consolidated status. At the same time molecular electrochemistry is expanding into other areas of sophisticated nano- and molecular scale systems includin...... molecular scale metal and semiconductor nanoparticles (NPs) and other nanostructures, e.g. nanotubes, “nanoflowers” etc.. The new structures offer both new electronic properties and highly confined novel charge transfer environments....

  18. The Physics of Coupled Atomic-Molecular Condensate System

    Science.gov (United States)

    2010-10-09

    electric dipoles represents a novel state of matter with long-range and anisotropic dipole-dipole interactions, that are highly amenable to the...free-bound FC factor. Simultaneously, a series of laser �elds of (molecular) Rabi frequency i (i 2) are applied to move the molecules from the

  19. Integrative pathway knowledge bases as a tool for systems molecular medicine.

    Science.gov (United States)

    Liang, Mingyu

    2007-08-20

    There exists a sense of urgency to begin to generate a cohesive assembly of biomedical knowledge as the pace of knowledge accumulation accelerates. The urgency is in part driven by the emergence of systems molecular medicine that emphasizes the combination of systems analysis and molecular dissection in the future of medical practice and research. A potentially powerful approach is to build integrative pathway knowledge bases that link organ systems function with molecules.

  20. A Comparative Study of Successful Central Nervous System Drugs Using Molecular Modeling

    Science.gov (United States)

    Kim, Hyosub; Sulaimon, Segun; Menezes, Sandra; Son, Anne; Menezes, Warren J. C.

    2011-01-01

    Molecular modeling is a powerful tool used for three-dimensional visualization and for exploring electrostatic forces involved in drug transport. This tool enhances student understanding of structure-property relationships, as well as actively engaging them in class. Molecular modeling of several central nervous system (CNS) drugs is used to…

  1. Exploring coherent transport through π-stacked systems for molecular electronic devices

    DEFF Research Database (Denmark)

    Li, Qian; Solomon, Gemma

    2014-01-01

    Understanding electron transport across π-stacked systems can help to elucidate the role of intermolecular tunneling in molecular junctions and potentially with the design of high-efficiency molecular devices. Here we show how conjugation length and substituent groups influence the electron trans...

  2. First-principles calculations of K-shell X-ray absorption spectra for warm dense nitrogen

    International Nuclear Information System (INIS)

    Li, Zi; Zhang, Shen; Kang, Wei; Wang, Cong; Zhang, Ping

    2016-01-01

    X-ray absorption spectrum is a powerful tool for atomic structure detection on warm dense matter. Here, we perform first-principles molecular dynamics and X-ray absorption spectrum calculations on warm dense nitrogen along a Hugoniot curve. From the molecular dynamics trajectory, the detailed atomic structures are examined for each thermodynamical condition. The K-shell X-ray absorption spectrum is calculated, and its changes with temperature and pressure along the Hugoniot curve are discussed. The warm dense nitrogen systems may contain isolated nitrogen atoms, N 2 molecules, and nitrogen clusters, which show quite different contributions to the total X-ray spectrum due to their different electron density of states. The changes of X-ray spectrum along the Hugoniot curve are caused by the different nitrogen structures induced by the temperature and the pressure. Some clear signatures on X-ray spectrum for different thermodynamical conditions are pointed out, which may provide useful data for future X-ray experiments.

  3. Molecular Dynamics Simulations of displacement cascades in metallic systems

    International Nuclear Information System (INIS)

    Doan, N.V.; Tietze, H.

    1995-01-01

    We use Molecular Dynamics Computer Simulations to investigate defect production induced by energetic displacement cascades up to 10 keV in pure metals (Cu, Ni) and in ordered intermetallic alloys NiAl, Ni 3 Al. Various model potentials were employed to describe the many-body nature of the interactions: the RGL (Rosato-Guillope-Legrand) model was used in pure Cu and Ni simulations; the modified version of the Vitek, Ackland and Cserti potentials (due to Gao, Bacon and Ackland) in Ni 3 Al and the EAM potentials of Foiles and Daw modified by Rubini and Ballone in NiAl, Ni 3 Al were used in alloy simulations. Atomic mixing and disordering were studied into details owing to imaging techniques and determined at different phases of the cascades. Some mixing mechanisms were identified. Our results were compared with existing data and those obtained by similar Molecular Dynamics Simulations available in the literature. (orig.)

  4. Molecular and supramolecular speciation of monoamide extractant systems

    International Nuclear Information System (INIS)

    Ferru, G.

    2012-01-01

    DEHiBA (N,N-di-(ethyl-2-hexyl)isobutyramide, a monoamide, was chosen as selective extractant for the recovery of uranium in the first cycle of the GANEX process, which aims to realize the grouped extraction of actinides in the second step of the process. The aim of this work is an improved description of monoamide organic solutions in alkane diluent after solutes extraction: water, nitric acid and uranyl nitrate. A parametric study was undertaken to characterize species at molecular scale (by IR spectroscopy, UV-visible spectroscopy, time-resolved laser-induced fluorescence spectroscopy, and electro-spray ionisation mass spectrometry) and at supramolecular scale (by vapor pressure osmometry and small angle X-ray scattering coupled to molecular dynamic simulations). Extraction isotherms were modelled taking into account the molecular and supramolecular speciation. These works showed that the organization of the organic solution depends on the amide concentration, the nature and the concentration of the extracted solute. Three regimes can be distinguished. 1/For extractant concentration less than 0.5 mol/L, monomers are predominate species. 2/ For extractant concentrations between 0.5 and 1 mol/L, small aggregates are formed containing 2 to 4 molecules of monoamide. 3/ For more concentrated solutions (greater than 1 mol/L), slightly larger species can be formed after water or nitric acid extraction. Concerning uranyl nitrate extraction, an important and strong organization of the organic phase is observed, which no longer allows the formation of well spherical defined aggregates. At molecular scale, complexes are not sensitive to the organization of the solution: the same species are observed, regardless of the solute and extractant concentrations in organic phase. (author) [fr

  5. Deterministic and unambiguous dense coding

    International Nuclear Information System (INIS)

    Wu Shengjun; Cohen, Scott M.; Sun Yuqing; Griffiths, Robert B.

    2006-01-01

    Optimal dense coding using a partially-entangled pure state of Schmidt rank D and a noiseless quantum channel of dimension D is studied both in the deterministic case where at most L d messages can be transmitted with perfect fidelity, and in the unambiguous case where when the protocol succeeds (probability τ x ) Bob knows for sure that Alice sent message x, and when it fails (probability 1-τ x ) he knows it has failed. Alice is allowed any single-shot (one use) encoding procedure, and Bob any single-shot measurement. For D≤D a bound is obtained for L d in terms of the largest Schmidt coefficient of the entangled state, and is compared with published results by Mozes et al. [Phys. Rev. A71, 012311 (2005)]. For D>D it is shown that L d is strictly less than D 2 unless D is an integer multiple of D, in which case uniform (maximal) entanglement is not needed to achieve the optimal protocol. The unambiguous case is studied for D≤D, assuming τ x >0 for a set of DD messages, and a bound is obtained for the average . A bound on the average requires an additional assumption of encoding by isometries (unitaries when D=D) that are orthogonal for different messages. Both bounds are saturated when τ x is a constant independent of x, by a protocol based on one-shot entanglement concentration. For D>D it is shown that (at least) D 2 messages can be sent unambiguously. Whether unitary (isometric) encoding suffices for optimal protocols remains a major unanswered question, both for our work and for previous studies of dense coding using partially-entangled states, including noisy (mixed) states

  6. Hydrothermal growth and characterization of vertically well-aligned and dense ZnO nanorods on glass and silicon using a simple optimizer system

    Energy Technology Data Exchange (ETDEWEB)

    Mohammad, Sabah M., E-mail: Sabahaskari14@gmail.com; Ahmed, Naser M.; Abd-Alghafour, Nabeel M. [Institute of Nano-Optoelectronics Research and Technology Laboratory (INOR), School of Physics, Universiti Sains Malaysia, Penang 11800 (Malaysia); Hassan, Z., E-mail: zai@usm.my [Institute of Nano-Optoelectronics Research and Technology Laboratory (INOR), School of Physics, Universiti Sains Malaysia, Penang 11800 (Malaysia); CRI Natural Sciences, Universiti Sains Malaysia, Penang 11800 (Malaysia); Talib, Rawnaq A. [Institute of Nano-Optoelectronics Research and Technology Laboratory (INOR), School of Physics, Universiti Sains Malaysia, Penang 11800 (Malaysia); Polymer Research Center, University of Basra (Iraq); Omar, A. F. [School of Physics, Universiti Sains Malaysia, Penang 11800 (Malaysia)

    2016-07-06

    Vertically, well-aligned and high density ZnO nanorods were successfully hydrothermally grown on glass and silicon substrates using a simple and low cost system. The mechanism of synthesis of ZnO nanorods, generated with our system under hydrothermal conditions, is investigated in this report. Field-emission scanning electron microscopy indicated that the fabricated ZnO nanorods on both substrates have hexagonal shape with diameters ranging from 20 nm to 70 nm which grew vertically from the substrate. XRD analysis confirms the formation of wurtzite ZnO phase with a preferred orientation along (002) direction perpendicular on the substrate and enhanced crystallinity. The low value of the tensile strain (0.126 %) revealed that ZnO nanorods preferred to grow along the c-axis for both substrates. Photoluminescence spectra exhibited a strong, sharp UV near band edge emission peak with narrow FWHM values for both samples.

  7. Hydrothermal growth and characterization of vertically well-aligned and dense ZnO nanorods on glass and silicon using a simple optimizer system

    International Nuclear Information System (INIS)

    Mohammad, Sabah M.; Ahmed, Naser M.; Abd-Alghafour, Nabeel M.; Hassan, Z.; Talib, Rawnaq A.; Omar, A. F.

    2016-01-01

    Vertically, well-aligned and high density ZnO nanorods were successfully hydrothermally grown on glass and silicon substrates using a simple and low cost system. The mechanism of synthesis of ZnO nanorods, generated with our system under hydrothermal conditions, is investigated in this report. Field-emission scanning electron microscopy indicated that the fabricated ZnO nanorods on both substrates have hexagonal shape with diameters ranging from 20 nm to 70 nm which grew vertically from the substrate. XRD analysis confirms the formation of wurtzite ZnO phase with a preferred orientation along (002) direction perpendicular on the substrate and enhanced crystallinity. The low value of the tensile strain (0.126 %) revealed that ZnO nanorods preferred to grow along the c-axis for both substrates. Photoluminescence spectra exhibited a strong, sharp UV near band edge emission peak with narrow FWHM values for both samples.

  8. Molecular-beam epitaxial growth and ion-beam analysis systems for functional materials research

    International Nuclear Information System (INIS)

    Takeshita, H.; Aoki, Y.; Yamamoto, S.; Naramoto, H.

    1992-01-01

    Experimental systems for molecular beam epitaxial growth and ion beam analysis have been designed and constructed for the research of inorganic functional materials such as thin films and superlattices. (author)

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

    Science.gov (United States)

    Merindol, Rémi; Walther, Andreas

    2017-09-18

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

  10. Pulse radiolysis studies of fast reactions in molecular systems. Progress report, November 1976--October 1977

    International Nuclear Information System (INIS)

    Dorfman, L.M.

    1977-01-01

    Results from research in the following two areas are given: formation, properties, and reactivity of molecular ionic species in irradiated liquid systems; and pulse radiolysis of elementary reactions in protein function

  11. Next Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology (Final Report)

    Science.gov (United States)

    EPA announced the release of the final report, Next Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology. This report describes new approaches that are faster, less resource intensive, and more robust that can help ...

  12. FROM ATOMISTIC TO SYSTEMATIC COARSE-GRAINED MODELS FOR MOLECULAR SYSTEMS

    KAUST Repository

    Harmandaris, Vagelis; Kalligiannaki, Evangelia; Katsoulakis, Markos; Plechac, Petr

    2017-01-01

    The development of systematic (rigorous) coarse-grained mesoscopic models for complex molecular systems is an intense research area. Here we first give an overview of methods for obtaining optimal parametrized coarse-grained models, starting from

  13. Social stars: Modeling the interactive lives of stars in dense clusters and binary systems in the era of time domain astronomy

    Science.gov (United States)

    MacLeod, Morgan Elowe

    This thesis uses computational modeling to study of phases of dramatic interaction that intersperse stellar lifetimes. In galactic centers stars trace dangerously wandering orbits dictated by the combined gravitational force of a central, supermassive black hole and all of the surrounding stars. In binary systems, stars' evolution -- which causes their radii to increase substantially -- can bring initially non-interacting systems into contact. Moments of strong stellar interaction transform stars, their subsequent evolution, and the stellar environments they inhabit. In tidal disruption events, a star is partially or completely destroyed as tidal forces from a supermassive black hole overwhelm the star's self gravity. A portion of the stellar debris falls back to the black hole powering a luminous flare as it accretes. This thesis studies the relative event rates and properties of tidal disruption events for stars across the stellar evolutionary spectrum. Tidal disruptions of giant stars occur with high specific frequency; these objects' extended envelopes make them vulnerable to disruption. More-compact white dwarf stars are tidally disrupted relatively rarely. Their transients are also of very different duration and luminosity. Giant star disruptions power accretion flares with timescales of tens to hundreds of years; white dwarf disruption flares take hours to days. White dwarf tidal interactions can additionally trigger thermonuclear burning and lead to transients with signatures similar to type I supernovae. In binary star systems, a phase of hydrodynamic interaction called a common envelope episode occurs when one star evolves to swallow its companion. Dragged by the surrounding gas, the companion star spirals through the envelope to tighter orbits. This thesis studies accretion and flow morphologies during this phase. Density gradients across the gravitationally-focussed material lead to a strong angular momentum barrier to accretion during common envelope

  14. Molecular quenching and relaxation in a plasmonic tunable system

    Science.gov (United States)

    Baffou, Guillaume; Girard, Christian; Dujardin, Erik; Colas Des Francs, Gérard; Martin, Olivier J. F.

    2008-03-01

    Molecular fluorescence decay is significantly modified when the emitting molecule is located near a plasmonic structure. When the lateral sizes of such structures are reduced to nanometer-scale cross sections, they can be used to accurately control and amplify the emission rate. In this Rapid Communication, we extend Green’s dyadic method to quantitatively investigate both radiative and nonradiative decay channels experienced by a single fluorescent molecule confined in an adjustable dielectric-metal nanogap. The technique produces data in excellent agreement with current experimental work.

  15. Mixed 2D molecular systems: Mechanic, thermodynamic and dielectric properties

    Energy Technology Data Exchange (ETDEWEB)

    Beno, Juraj [Department of Physics, Faculty of Electrical Engineering and Information Technology, Slovak University of Technology, Ilkovicova 3, 812 19-SK Bratislava (Slovakia); Weis, Martin [Department of Physics, Faculty of Electrical Engineering and Information Technology, Slovak University of Technology, Ilkovicova 3, 812 19-SK Bratislava (Slovakia)], E-mail: Martin.Weis@stuba.sk; Dobrocka, Edmund [Department of Physics, Faculty of Electrical Engineering and Information Technology, Slovak University of Technology, Ilkovicova 3, 812 19-SK Bratislava (Slovakia); Institute of Electrical Engineering, Slovak Academy of Sciences, Dubravska cesta 9, 841 04-SK Bratislava (Slovakia); Hasko, Daniel [International Laser Centre, Ilkovicova 3, 812 19-SK Bratislava (Slovakia)

    2008-08-15

    Study of Langmuir monolayers consisting of stearic acid (SA) and dipalmitoylphosphatidylcholine (DPPC) molecules was done by surface pressure-area isotherms ({pi}-A), the Maxwell displacement current (MDC) measurement, X-ray reflectivity (XRR) and atomic force microscopy (AFM) to investigate the selected mechanic, thermodynamic and dielectric properties based on orientational structure of monolayers. On the base of {pi}-A isotherms analysis we explain the creation of stable structures and found optimal monolayer composition. The dielectric properties represented by MDC generated monolayers were analyzed in terms of excess dipole moment, proposing the effect of dipole-dipole interaction. XRR and AFM results illustrate deposited film structure and molecular ordering.

  16. Optimal super dense coding over memory channels

    OpenAIRE

    Shadman, Zahra; Kampermann, Hermann; Macchiavello, Chiara; Bruß, Dagmar

    2011-01-01

    We study the super dense coding capacity in the presence of quantum channels with correlated noise. We investigate both the cases of unitary and non-unitary encoding. Pauli channels for arbitrary dimensions are treated explicitly. The super dense coding capacity for some special channels and resource states is derived for unitary encoding. We also provide an example of a memory channel where non-unitary encoding leads to an improvement in the super dense coding capacity.

  17. Deuterium fractionation in dense interstellar clouds

    International Nuclear Information System (INIS)

    Millar, T.J.; Bennett, A.; Herbst, E.

    1989-01-01

    The time-dependent gas-phase chemistry of deuterium fractionation in dense interstellar clouds ranging in temperature between 10 and 70 K was investigated using a pseudo-time-dependent model similar to that of Brown and Rice (1986). The present approach, however, considers much more complex species, uses more deuterium fractionation reactions, and includes the use of new branching ratios for dissociative recombinations reactions. Results indicate that, in cold clouds, the major and most global source of deuterium fractionation is H2D(+) and ions derived from it, such as DCO(+) and H2DO(+). In warmer clouds, reactions of CH2D(+), C2HD(+), and associated species lead to significant fractionation even at 70 K, which is the assumed Orion temperature. The deuterium abundance ratios calculated at 10 K are consistent with those observed in TMC-1 for most species. However, a comparison between theory and observatiom for Orion, indicates that, for species in the ambient molecular cloud, the early-time results obtained with the old dissociative recombination branching ratios are superior if a temperature of 70 K is utilized. 60 refs

  18. Deuterium fractionation in dense interstellar clouds

    Science.gov (United States)

    Millar, T. J.; Bennett, A.; Herbst, Eric

    1989-05-01

    The time-dependent gas-phase chemistry of deuterium fractionation in dense interstellar clouds ranging in temperature between 10 and 70 K was investigated using a pseudo-time-dependent model similar to that of Brown and Rice (1986). The present approach, however, considers much more complex species, uses more deuterium fractionation reactions, and includes the use of new branching ratios for dissociative recombinations reactions. Results indicate that, in cold clouds, the major and most global source of deuterium fractionation is H2D(+) and ions derived from it, such as DCO(+) and H2DO(+). In warmer clouds, reactions of CH2D(+), C2HD(+), and associated species lead to significant fractionation even at 70 K, which is the assumed Orion temperature. The deuterium abundance ratios calculated at 10 K are consistent with those observed in TMC-1 for most species. However, a comparison between theory and observatiom for Orion, indicates that, for species in the ambient molecular cloud, the early-time results obtained with the old dissociative recombination branching ratios are superior if a temperature of 70 K is utilized.

  19. Dense module enumeration in biological networks

    Science.gov (United States)

    Tsuda, Koji; Georgii, Elisabeth

    2009-12-01

    Analysis of large networks is a central topic in various research fields including biology, sociology, and web mining. Detection of dense modules (a.k.a. clusters) is an important step to analyze the networks. Though numerous methods have been proposed to this aim, they often lack mathematical rigorousness. Namely, there is no guarantee that all dense modules are detected. Here, we present a novel reverse-search-based method for enumerating all dense modules. Furthermore, constraints from additional data sources such as gene expression profiles or customer profiles can be integrated, so that we can systematically detect dense modules with interesting profiles. We report successful applications in human protein interaction network analyses.

  20. Dense module enumeration in biological networks

    International Nuclear Information System (INIS)

    Tsuda, Koji; Georgii, Elisabeth

    2009-01-01

    Analysis of large networks is a central topic in various research fields including biology, sociology, and web mining. Detection of dense modules (a.k.a. clusters) is an important step to analyze the networks. Though numerous methods have been proposed to this aim, they often lack mathematical rigorousness. Namely, there is no guarantee that all dense modules are detected. Here, we present a novel reverse-search-based method for enumerating all dense modules. Furthermore, constraints from additional data sources such as gene expression profiles or customer profiles can be integrated, so that we can systematically detect dense modules with interesting profiles. We report successful applications in human protein interaction network analyses.

  1. Raman spectroscopy on simple molecular systems at very high density

    International Nuclear Information System (INIS)

    Schiferl, D.; LeSar, R.S.; Moore, D.S.

    1988-01-01

    We present an overview of how Raman spectroscopy is done on simple molecular substances at high pressures. Raman spectroscopy is one of the most powerful tools for studying these substances. It is often the quickest means to explore changes in crystal and molecular structures, changes in bond strength, and the formation of new chemical species. Raman measurements have been made at pressures up to 200 GPa (2 Mbar). Even more astonishing is the range of temperatures (4-5200/degree/K) achieved in various static and dynamic (shock-wave) pressure experiments. One point we particularly wish to emphasize is the need for a good theoretical understanding to properly interpret and use experimental results. This is particularly true at ultra-high pressures, where strong crystal field effects can be misinterpreted as incipient insulator-metal transitions. We have tried to point out apparatus, techniques, and results that we feel are particularly noteworthy. We have also included some of the /open quotes/oral tradition/close quotes/ of high pressure Raman spectroscopy -- useful little things that rarely or never appear in print. Because this field is rapidly expanding, we discuss a number of exciting new techniques that have been informally communicated to us, especially those that seem to open new possibilities. 58 refs., 18 figs

  2. Glaciations and dense interstellar clouds; and reply

    Energy Technology Data Exchange (ETDEWEB)

    McCrea, W H [Sussex Univ., Brighton (UK); Dennison, B; Mansfield, V N

    1976-09-16

    Reference is made to Dennison and Mansfield (Nature 261:32 (1976)) who offered comments on a previous paper by the author (Nature 255:607 (1975)), in which he suggested that a possible cause of an ice age on the Earth was the passage of the solar system through an interstellar matter compression region bordering a spiral arm of the Galaxy. Dennison and Mansfield criticised this suggestion because it led them to expect to find a dense cloud of interstellar matter still very close to the Earth, whereas no such cloud is known. It is stated here that this criticism ignores the structure of the Galaxy, that provided the basis of the suggestion. A reply by Dennison and Mansfield is appended.

  3. Equation of state of dense baryonic matter

    International Nuclear Information System (INIS)

    Weber, F.; Weigel, M.K.

    1989-01-01

    In a previous investigation we treated nuclear matter as well as neutron matter at zero and finite temperatures in the frame of different relativistic field theoretical models, but with the restriction to nucleons as the only present baryons. This approach is extended by including a larger fraction of baryons and mesons, necessary for a description of baryon matter under extreme conditions. The equation of state (EOS) is calculated in both the Hartree and Hartree-Fock (HF) approximations for dense nuclear as well as neutron matter. Self-interactions of the σ field up to fourth order have been taken into account. For the treatment of many-baryon matter in the HF approach the parameters of the theory had to be readjusted. A phase transition of both many-baryon systems (neutron as well as nuclear matter) in the high-pressure and high-energy-density region has been found. (author)

  4. Statistical mechanics of dense granular media

    International Nuclear Information System (INIS)

    Coniglio, A; Fierro, A; Nicodemi, M; Ciamarra, M Pica; Tarzia, M

    2005-01-01

    We discuss some recent results on the statistical mechanics approach to dense granular media. In particular, by analytical mean field investigation we derive the phase diagram of monodisperse and bidisperse granular assemblies. We show that 'jamming' corresponds to a phase transition from a 'fluid' to a 'glassy' phase, observed when crystallization is avoided. The nature of such a 'glassy' phase turns out to be the same as found in mean field models for glass formers. This gives quantitative evidence for the idea of a unified description of the 'jamming' transition in granular media and thermal systems, such as glasses. We also discuss mixing/segregation transitions in binary mixtures and their connections to phase separation and 'geometric' effects

  5. THE JCMT GOULD BELT SURVEY: DENSE CORE CLUSTERS IN ORION A

    Energy Technology Data Exchange (ETDEWEB)

    Lane, J.; Kirk, H.; Johnstone, D.; Mairs, S.; Francesco, J. Di [NRC Herzberg Astronomy and Astrophysics, 5071 West Saanich Road, Victoria, BC, V9E 2E7 (Canada); Sadavoy, S. [Max Planck Institute for Astronomy, Königstuhl 17, D-69117 Heidelberg (Germany); Hatchell, J. [Physics and Astronomy, University of Exeter, Stocker Road, Exeter EX4 4QL (United Kingdom); Berry, D. S. [East Asian Observatory, 660 N. A‘ohōkū Place, University Park, Hilo, Hawaii 96720 (United States); Jenness, T. [Joint Astronomy Centre, 660 N. A‘ohōkū Place, University Park, Hilo, Hawaii 96720 (United States); Hogerheijde, M. R. [Leiden Observatory, Leiden University, P.O. Box 9513, 2300 RA Leiden (Netherlands); Ward-Thompson, D. [Jeremiah Horrocks Institute, University of Central Lancashire, Preston, Lancashire, PR1 2HE (United Kingdom); Collaboration: JCMT Gould Belt Survey Team

    2016-12-10

    The Orion A molecular cloud is one of the most well-studied nearby star-forming regions, and includes regions of both highly clustered and more dispersed star formation across its full extent. Here, we analyze dense, star-forming cores identified in the 850 and 450 μ m SCUBA-2 maps from the JCMT Gould Belt Legacy Survey. We identify dense cores in a uniform manner across the Orion A cloud and analyze their clustering properties. Using two independent lines of analysis, we find evidence that clusters of dense cores tend to be mass segregated, suggesting that stellar clusters may have some amount of primordial mass segregation already imprinted in them at an early stage. We also demonstrate that the dense core clusters have a tendency to be elongated, perhaps indicating a formation mechanism linked to the filamentary structure within molecular clouds.

  6. THE JCMT GOULD BELT SURVEY: DENSE CORE CLUSTERS IN ORION A

    International Nuclear Information System (INIS)

    Lane, J.; Kirk, H.; Johnstone, D.; Mairs, S.; Francesco, J. Di; Sadavoy, S.; Hatchell, J.; Berry, D. S.; Jenness, T.; Hogerheijde, M. R.; Ward-Thompson, D.

    2016-01-01

    The Orion A molecular cloud is one of the most well-studied nearby star-forming regions, and includes regions of both highly clustered and more dispersed star formation across its full extent. Here, we analyze dense, star-forming cores identified in the 850 and 450 μ m SCUBA-2 maps from the JCMT Gould Belt Legacy Survey. We identify dense cores in a uniform manner across the Orion A cloud and analyze their clustering properties. Using two independent lines of analysis, we find evidence that clusters of dense cores tend to be mass segregated, suggesting that stellar clusters may have some amount of primordial mass segregation already imprinted in them at an early stage. We also demonstrate that the dense core clusters have a tendency to be elongated, perhaps indicating a formation mechanism linked to the filamentary structure within molecular clouds.

  7. High core count single-mode multicore fiber for dense space division multiplexing

    DEFF Research Database (Denmark)

    Aikawa, K.; Sasaki, Y.; Amma, Y.

    2016-01-01

    Multicore fibers and few-mode fibers have the potential to realize dense-space-division multiplexing systems. Several dense-space-division multiplexing system transmission experiments over multicore fibers and few-mode fibers have been demonstrated so far. Multicore fibers, including recent resul...

  8. Probing warm dense lithium by inelastic X-ray scattering

    Energy Technology Data Exchange (ETDEWEB)

    Garcia Saiz, E; Riley, D [School of Mathematics and Physics, Queen' s University of Belfast, Belfast (United Kingdom); Gregori, G [Clarendon Laboratory, University of Oxford, Parks Road, Oxford (United Kingdom); Gregori, G; Clarke, R J; Neely, D; Notley, M M; Spindloe, C [Central Laser Facility, Rutherford Appleton Laboratory, Chilton, Didcot, OX (United Kingdom); Gericke, D O; Vorberger, J; Wunsch, K [Centre for Fusion, Space and Astrophysics, Department of Physics, University of Warwick, Coventry (United Kingdom); Barbrel, B; Koenig, M [Laboratoire pour l' Utilisation des Laser Intenses, Ecole Polytechnique - Universite Paris-6, 91 - Palaiseau (France); Freeman, R R; Weber, R L; Van Woerkom, L [Department of Physics, The Ohio State University, Columbus, Ohio (United States); Glenzer, S H; Landen, O L; Neumayer, P; Price, D [Lawrence Livermore National Laboratory, Livermore, California (United States); Khattak, F Y [Department of Physics, Kohat University of Science and Technology, Kohat-26000, NWFP (Pakistan); Pelka, A; Roth, M; Schollmeier, M [Institut fur Kernphysik, Technische Universitat Darmstadt (Germany)

    2008-10-15

    One of the grand challenges of contemporary physics is understanding strongly interacting quantum systems comprising such diverse examples as ultracold atoms in traps, electrons in high-temperature superconductors and nuclear matter. Warm dense matter, defined by temperatures of a few electron volts and densities comparable with solids, is a complex state of such interacting matter. Moreover, the study of warm dense matter states has practical applications for controlled thermonuclear fusion, where it is encountered during the implosion phase, and it also represents laboratory analogues of astrophysical environments found in the core of planets and the crusts of old stars. Here we demonstrate how warm dense matter states can be diagnosed and structural properties can be obtained by inelastic X-ray scattering measurements on a compressed lithium sample. Combining experiments and ab initio simulations enables us to determine its microscopic state and to evaluate more approximate theoretical models for the ionic structure. (authors)

  9. Arbitrary electron acoustic waves in degenerate dense plasmas

    Science.gov (United States)

    Rahman, Ata-ur; Mushtaq, A.; Qamar, A.; Neelam, S.

    2017-05-01

    A theoretical investigation is carried out of the nonlinear dynamics of electron-acoustic waves in a collisionless and unmagnetized plasma whose constituents are non-degenerate cold electrons, ultra-relativistic degenerate electrons, and stationary ions. A dispersion relation is derived for linear EAWs. An energy integral equation involving the Sagdeev potential is derived, and basic properties of the large amplitude solitary structures are investigated in such a degenerate dense plasma. It is shown that only negative large amplitude EA solitary waves can exist in such a plasma system. The present analysis may be important to understand the collective interactions in degenerate dense plasmas, occurring in dense astrophysical environments as well as in laser-solid density plasma interaction experiments.

  10. Systems biology for molecular life sciences and its impact in biomedicine.

    Science.gov (United States)

    Medina, Miguel Ángel

    2013-03-01

    Modern systems biology is already contributing to a radical transformation of molecular life sciences and biomedicine, and it is expected to have a real impact in the clinical setting in the next years. In this review, the emergence of systems biology is contextualized with a historic overview, and its present state is depicted. The present and expected future contribution of systems biology to the development of molecular medicine is underscored. Concerning the present situation, this review includes a reflection on the "inflation" of biological data and the urgent need for tools and procedures to make hidden information emerge. Descriptions of the impact of networks and models and the available resources and tools for applying them in systems biology approaches to molecular medicine are provided as well. The actual current impact of systems biology in molecular medicine is illustrated, reviewing two cases, namely, those of systems pharmacology and cancer systems biology. Finally, some of the expected contributions of systems biology to the immediate future of molecular medicine are commented.

  11. Water activity in liquid food systems: A molecular scale interpretation.

    Science.gov (United States)

    Maneffa, Andrew J; Stenner, Richard; Matharu, Avtar S; Clark, James H; Matubayasi, Nobuyuki; Shimizu, Seishi

    2017-12-15

    Water activity has historically been and continues to be recognised as a key concept in the area of food science. Despite its ubiquitous utilisation, it still appears as though there is confusion concerning its molecular basis, even within simple, single component solutions. Here, by close examination of the well-known Norrish equation and subsequent application of a rigorous statistical theory, we are able to shed light on such an origin. Our findings highlight the importance of solute-solute interactions thus questioning traditional, empirically based "free water" and "water structure" hypotheses. Conversely, they support the theory of "solute hydration and clustering" which advocates the interplay of solute-solute and solute-water interactions but crucially, they do so in a manner which is free of any estimations and approximations. Copyright © 2017. Published by Elsevier Ltd.

  12. Online molecular image repository and analysis system: A multicenter collaborative open-source infrastructure for molecular imaging research and application.

    Science.gov (United States)

    Rahman, Mahabubur; Watabe, Hiroshi

    2018-05-01

    Molecular imaging serves as an important tool for researchers and clinicians to visualize and investigate complex biochemical phenomena using specialized instruments; these instruments are either used individually or in combination with targeted imaging agents to obtain images related to specific diseases with high sensitivity, specificity, and signal-to-noise ratios. However, molecular imaging, which is a multidisciplinary research field, faces several challenges, including the integration of imaging informatics with bioinformatics and medical informatics, requirement of reliable and robust image analysis algorithms, effective quality control of imaging facilities, and those related to individualized disease mapping, data sharing, software architecture, and knowledge management. As a cost-effective and open-source approach to address these challenges related to molecular imaging, we develop a flexible, transparent, and secure infrastructure, named MIRA, which stands for Molecular Imaging Repository and Analysis, primarily using the Python programming language, and a MySQL relational database system deployed on a Linux server. MIRA is designed with a centralized image archiving infrastructure and information database so that a multicenter collaborative informatics platform can be built. The capability of dealing with metadata, image file format normalization, and storing and viewing different types of documents and multimedia files make MIRA considerably flexible. With features like logging, auditing, commenting, sharing, and searching, MIRA is useful as an Electronic Laboratory Notebook for effective knowledge management. In addition, the centralized approach for MIRA facilitates on-the-fly access to all its features remotely through any web browser. Furthermore, the open-source approach provides the opportunity for sustainable continued development. MIRA offers an infrastructure that can be used as cross-boundary collaborative MI research platform for the rapid

  13. Dense sheet Z-pinches

    International Nuclear Information System (INIS)

    Tetsu, Miyamoto

    1999-01-01

    The steady state and quasi-steady processes of infinite- and finite-width sheet z-pinches are studied. The relations corresponding to the Bennett relation and Pease-Braginskii current of cylindrical fiber z-pinches depend on a geometrical factor in the sheet z-pinches. The finite-width sheet z-pinch is approximated by a segment of infinite-width sheet z-pinch, if it is wide enough, and corresponds to a number of (width/thickness) times fiber z-pinch plasmas of the diameter that equals the sheet thickness. If the sheet current equals this number times the fiber current, the plasma created in the sheet z-pinches is as dense as in the fiber z-pinches. The total energy of plasma and magnetic field per unit mass is approximately equal in both pinches. Quasi-static transient processes are different in several aspects from the fiber z-pinch. No radiation collapse occurs in the sheet z-pinch. The stability is improved in the sheet z-pinches. The fusion criterions and the experimental arrangements to produce the sheet z-pinches are also discussed. (author)

  14. STAR FORMATION IN DENSE CLUSTERS

    International Nuclear Information System (INIS)

    Myers, Philip C.

    2011-01-01

    A model of core-clump accretion with equally likely stopping describes star formation in the dense parts of clusters, where models of isolated collapsing cores may not apply. Each core accretes at a constant rate onto its protostar, while the surrounding clump gas accretes as a power of protostar mass. Short accretion flows resemble Shu accretion and make low-mass stars. Long flows resemble reduced Bondi accretion and make massive stars. Accretion stops due to environmental processes of dynamical ejection, gravitational competition, and gas dispersal by stellar feedback, independent of initial core structure. The model matches the field star initial mass function (IMF) from 0.01 to more than 10 solar masses. The core accretion rate and the mean accretion duration set the peak of the IMF, independent of the local Jeans mass. Massive protostars require the longest accretion durations, up to 0.5 Myr. The maximum protostar luminosity in a cluster indicates the mass and age of its oldest protostar. The distribution of protostar luminosities matches those in active star-forming regions if protostars have a constant birthrate but not if their births are coeval. For constant birthrate, the ratio of young stellar objects to protostars indicates the star-forming age of a cluster, typically ∼1 Myr. The protostar accretion luminosity is typically less than its steady spherical value by a factor of ∼2, consistent with models of episodic disk accretion.

  15. Observations of non-linear plasmon damping in dense plasmas

    Science.gov (United States)

    Witte, B. B. L.; Sperling, P.; French, M.; Recoules, V.; Glenzer, S. H.; Redmer, R.

    2018-05-01

    We present simulations using finite-temperature density-functional-theory molecular-dynamics to calculate dynamic dielectric properties in warm dense aluminum. The comparison between exchange-correlation functionals in the Perdew, Burke, Ernzerhof approximation, Strongly Constrained and Appropriately Normed Semilocal Density Functional, and Heyd, Scuseria, Ernzerhof (HSE) approximation indicates evident differences in the electron transition energies, dc conductivity, and Lorenz number. The HSE calculations show excellent agreement with x-ray scattering data [Witte et al., Phys. Rev. Lett. 118, 225001 (2017)] as well as dc conductivity and absorption measurements. These findings demonstrate non-Drude behavior of the dynamic conductivity above the Cooper minimum that needs to be taken into account to determine optical properties in the warm dense matter regime.

  16. Planar simplification and texturing of dense point cloud maps

    NARCIS (Netherlands)

    Ma, L.; Whelan, T.; Bondarau, Y.; With, de P.H.N.; McDonald, J.

    2013-01-01

    Dense RGB-D based SLAM techniques and highfidelity LIDAR scanners are examples from an abundant set of systems capable of providing multi-million point datasets. These large datasets quickly become difficult to process and work with due to the sheer volume of data, which typically contains

  17. Incremental and batch planar simplification of dense point cloud maps

    NARCIS (Netherlands)

    Whelan, T.; Ma, L.; Bondarev, E.; With, de P.H.N.; McDonald, J.

    2015-01-01

    Dense RGB-D SLAM techniques and high-fidelity LIDAR scanners are examples from an abundant set of systems capable of providing multi-million point datasets. These datasets quickly become difficult to process due to the sheer volume of data, typically containing significant redundant information,

  18. Interaction of ultrarelativistic electron and proton bunches with dense plasmas

    CERN Document Server

    Rukhadze, A A

    2012-01-01

    Here we discuss the possibility of employment of ultrarelativistic electron and proton bunches for generation of high plasma wakefields in dense plasmas due to the Cherenkov resonance plasma-bunch interaction. We estimate the maximum amplitude of such a wake and minimum system length at which the maximum amplitude can be generated at the given bunch parameters.

  19. Light localization in cold and dense atomic ensemble

    International Nuclear Information System (INIS)

    Sokolov, Igor

    2017-01-01

    We report on results of theoretical analysis of possibilities of light strong (Anderson) localization in a cold atomic ensemble. We predict appearance of localization in dense atomic systems in strong magnetic field. We prove that in absence of the field the light localization is impossible. (paper)

  20. Energy Flow in Dense Off-Equilibrium Plasma

    Science.gov (United States)

    2016-07-15

    brings the electron density and light emission into LTE at the measured spectral temperature while leaving the ions cold. Because of their large mass... measurements of ionization potential lowering and collision times indense plasmas, allowing us to distinguish between competing dense-plasma models...Hydrodynamic analysis of shockwaves generated by sparks yielded similar measurements ina different, more accessible system. Ultra-fast observations

  1. A grass molecular identification system for forensic botany: a critical evaluation of the strengths and limitations.

    Science.gov (United States)

    Ward, Jodie; Gilmore, Simon R; Robertson, James; Peakall, Rod

    2009-11-01

    Plant material is frequently encountered in criminal investigations but often overlooked as potential evidence. We designed a DNA-based molecular identification system for 100 Australian grasses that consisted of a series of polymerase chain reaction assays that enabled the progressive identification of grasses to different taxonomic levels. The identification system was based on DNA sequence variation at four chloroplast and two mitochondrial loci. Seventeen informative indels and 68 single-nucleotide polymorphisms were utilized as molecular markers for subfamily to species-level identification. To identify an unknown sample to subfamily level required a minimum of four markers or nine markers for species identification. The accuracy of the system was confirmed by blind tests. We have demonstrated "proof of concept" of a molecular identification system for trace botanical samples. Our evaluation suggests that the adoption of a system that combines this approach with DNA sequencing could assist the morphological identification of grasses found as forensic evidence.

  2. The rise of a novel classification system for endometrial carcinoma; integration of molecular subclasses.

    Science.gov (United States)

    McAlpine, Jessica; Leon-Castillo, Alicia; Bosse, Tjalling

    2018-04-01

    Endometrial cancer is a clinically heterogeneous disease and it is becoming increasingly clear that this heterogeneity may be a function of the diversity of the underlying molecular alterations. Recent large-scale genomic studies have revealed that endometrial cancer can be divided into at least four distinct molecular subtypes, with well-described underlying genomic aberrations. These subtypes can be reliably delineated and carry significant prognostic as well as predictive information; embracing and incorporating them into clinical practice is thus attractive. The road towards the integration of molecular features into current classification systems is not without obstacles. Collaborative studies engaging research teams from across the world are working to define pragmatic assays, improve risk stratification systems by combining molecular features and traditional clinicopathological parameters, and determine how molecular classification can be optimally utilized to direct patient care. Pathologists and clinicians caring for women with endometrial cancer need to engage with and understand the possibilities and limitations of this new approach, because integration of molecular classification of endometrial cancers is anticipated to become an essential part of gynaecological pathology practice. This review will describe the challenges in current systems of endometrial carcinoma classification, the evolution of new molecular technologies that define prognostically distinct molecular subtypes, and potential applications of molecular classification as a step towards precision medicine and refining care for individuals with the most common gynaecological cancer in the developed world. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

  3. Calculation on uranium carbon oxygen system molecular structure by DFT

    International Nuclear Information System (INIS)

    Zhang Guangfeng; Wang Xiaolin; Zou Lexi; Sun Ying; Xue Weidong; Zhu Zhenghe; Wang Hongyan

    2001-01-01

    The authors study on the possible molecular structures U-C-O, U-O-C, C-U-O (angular structure C a nd linear structure C ∞υ ) of carbon monoxide interacting on uranium metal surface by Density functional theory (DFT). The uranium atom is used RECP (Relativistic Effective Core Potential) and contracted valence basis sets (6s5p2d4f)/[3s3p2d2f], and for carbon and oxygen atoms all are 6-311G basis sets. The author presents the results of energy optimum which shows that triple and quintuple state are more stable. The authors get the electronic state, geometry structure, energy, harmonic frequency, mechanical property, etc. of these twelve triple and quintuple state relative stable structures. The normal vibrational analytical figure of angular structure (C s ) and linear structure (C ∞υ ) is given at the same time. It is indicated that angular structure has lower energy than linear structure, moreover the angular structure of U-C-O( 3 A ) has the lowest energy. The bond strength between uranium atom and carbon monoxide is weak and between uranium atom and oxygen atom is slightly stronger than between uranium atom and carbon atom which the authors can know by superposition population and bond energy analysis among atoms

  4. Molecular characterization of the thioredoxin system from Methanosarcina acetivorans

    OpenAIRE

    McCarver, Addison C.; Lessner, Daniel J.

    2014-01-01

    The thioredoxin system, composed of thioredoxin reductase (TrxR) and thioredoxin (Trx), is widely distributed in nature, where it serves key roles in electron transfer and in defense against oxidative stress. Although recent evidence reveals Trx homologues are almost universally present among the methane-producing archaea (methanogens), a complete thioredoxin system has not been characterized from any methanogen. We examined the phylogeny of Trx homologues among methanogens and characterized ...

  5. Molecular spectral imaging system for quantitative immunohistochemical analysis of early diabetic retinopathy.

    Science.gov (United States)

    Li, Qingli; Zhang, Jingfa; Wang, Yiting; Xu, Guoteng

    2009-12-01

    A molecular spectral imaging system has been developed based on microscopy and spectral imaging technology. The system is capable of acquiring molecular spectral images from 400 nm to 800 nm with 2 nm wavelength increments. The basic principles, instrumental systems, and system calibration method as well as its applications for the calculation of the stain-uptake by tissues are introduced. As a case study, the system is used for determining the pathogenesis of diabetic retinopathy and evaluating the therapeutic effects of erythropoietin. Some molecular spectral images of retinal sections of normal, diabetic, and treated rats were collected and analyzed. The typical transmittance curves of positive spots stained for albumin and advanced glycation end products are retrieved from molecular spectral data with the spectral response calibration algorithm. To explore and evaluate the protective effect of erythropoietin (EPO) on retinal albumin leakage of streptozotocin-induced diabetic rats, an algorithm based on Beer-Lambert's law is presented. The algorithm can assess the uptake by histologic retinal sections of stains used in quantitative pathology to label albumin leakage and advanced glycation end products formation. Experimental results show that the system is helpful for the ophthalmologist to reveal the pathogenesis of diabetic retinopathy and explore the protective effect of erythropoietin on retinal cells of diabetic rats. It also highlights the potential of molecular spectral imaging technology to provide more effective and reliable diagnostic criteria in pathology.

  6. Systems theoretic analysis of the central dogma of molecular biology: some recent results.

    Science.gov (United States)

    Gao, Rui; Yu, Juanyi; Zhang, Mingjun; Tarn, Tzyh-Jong; Li, Jr-Shin

    2010-03-01

    This paper extends our early study on a mathematical formulation of the central dogma of molecular biology, and focuses discussions on recent insights obtained by employing advanced systems theoretic analysis. The goal of this paper is to mathematically represent and interpret the genetic information flow at the molecular level, and explore the fundamental principle of molecular biology at the system level. Specifically, group theory was employed to interpret concepts and properties of gene mutation, and predict backbone torsion angle along the peptide chain. Finite state machine theory was extensively applied to interpret key concepts and analyze the processes related to DNA hybridization. Using the proposed model, we have transferred the character-based model in molecular biology to a sophisticated mathematical model for calculation and interpretation.

  7. Cleavage and formation of molecular dinitrogen in a single system assisted by molybdenum complexes bearing ferrocenyldiphosphine.

    Science.gov (United States)

    Miyazaki, Takamasa; Tanaka, Hiromasa; Tanabe, Yoshiaki; Yuki, Masahiro; Nakajima, Kazunari; Yoshizawa, Kazunari; Nishibayashi, Yoshiaki

    2014-10-20

    The N≡N bond of molecular dinitrogen bridging two molybdenum atoms in the pentamethylcyclopentadienyl molybdenum complexes that bear ferrocenyldiphosphine as an auxiliary ligand is homolytically cleaved under visible light irradiation at room temperature to afford two molar molybdenum nitride complexes. Conversely, the bridging molecular dinitrogen is reformed by the oxidation of the molybdenum nitride complex at room temperature. This result provides a successful example of the cleavage and formation of molecular dinitrogen induced by a pair of two different external stimuli using a single system assisted by molybdenum complexes bearing ferrocenyldiphosphine under ambient conditions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. From molecular imaging to systems diagnostics: Time for another paradigm shift?

    International Nuclear Information System (INIS)

    Li, King C.P.

    2009-01-01

    The term 'Molecular Imaging' has hit the consciousness of radiologists only in the past decade although many of the concepts that molecular imaging encompasses has been practiced in biomedical imaging, especially in nuclear medicine, for many decades. Many new imaging techniques have allowed us to interrogate biologic events at the cellular and molecular level in vivo in four dimensions but the challenge now is to translate these techniques into clinical practice in a way that will enable us to revolutionize healthcare delivery. The purpose of this article is to introduce the term 'Systems Diagnostics' and examine how radiologists can become translators of disparate sources of information into medical decisions and therapeutic actions.

  9. All-organic microelectromechanical systems integrating specific molecular recognition--a new generation of chemical sensors.

    Science.gov (United States)

    Ayela, Cédric; Dubourg, Georges; Pellet, Claude; Haupt, Karsten

    2014-09-03

    Cantilever-type all-organic microelectromechanical systems based on molecularly imprinted polymers for specific analyte recognition are used as chemical sensors. They are produced by a simple spray-coating-shadow-masking process. Analyte binding to the cantilever generates a measurable change in its resonance frequency. This allows label-free detection by direct mass sensing of low-molecular-weight analytes at nanomolar concentrations. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. DENSE GAS FRACTION AND STAR FORMATION EFFICIENCY VARIATIONS IN THE ANTENNAE GALAXIES

    Energy Technology Data Exchange (ETDEWEB)

    Bigiel, F. [Institut für theoretische Astrophysik, Zentrum für Astronomie der Universität Heidelberg, Albert-Ueberle Strasse 2, D-69120 Heidelberg (Germany); Leroy, A. K. [Department of Astronomy, The Ohio State University, 140 W 18th Street, Columbus, OH 43210 (United States); Blitz, L. [Department of Astronomy, Radio Astronomy Laboratory, University of California, Berkeley, CA 94720 (United States); Bolatto, A. D. [Department of Astronomy and Laboratory for Millimeter-Wave Astronomy, University of Maryland, College Park, MD 20742 (United States); Da Cunha, E. [Max-Planck-Institut für Astronomie, Königstuhl 17, D-69117 Heidelberg (Germany); Rosolowsky, E. [Department of Physics, University of Alberta, Edmonton, AB (Canada); Sandstrom, K. [Steward Observatory, University of Arizona, 933 North Cherry Avenue, Tucson, AZ 85721 (United States); Usero, A., E-mail: bigiel@uni-heidelberg.de [Observatorio Astronomico Nacional, Alfonso XII 3, E-28014, Madrid (Spain)

    2015-12-20

    We use the Combined Array for Research in Millimeter-wave Astronomy (CARMA) millimeter interferometer to map the Antennae Galaxies (NGC 4038/39), tracing the bulk of the molecular gas via the {sup 12}CO(1–0) line and denser molecular gas via the high density transitions HCN(1–0), HCO{sup +}(1–0), CS(2–1), and HNC(1–0). We detect bright emission from all tracers in both the two nuclei and three locales in the overlap region between the two nuclei. These three overlap region peaks correspond to previously identified “supergiant molecular clouds.” We combine the CARMA data with Herschel infrared (IR) data to compare observational indicators of the star formation efficiency (star formation rate/H{sub 2} ∝ IR/CO), dense gas fraction (HCN/CO), and dense gas star formation efficiency (IR/HCN). Regions within the Antennae show ratios consistent with those seen for entire galaxies, but these ratios vary by up to a factor of six within the galaxy. The five detected regions vary strongly in both their integrated intensities and these ratios. The northern nucleus is the brightest region in millimeter-wave line emission, while the overlap region is the brightest part of the system in the IR. We combine the CARMA and Herschel data with ALMA CO data to report line ratio patterns for each bright point. CO shows a declining spectral line energy distribution, consistent with previous studies. HCO{sup +} (1–0) emission is stronger than HCN (1–0) emission, perhaps indicating either more gas at moderate densities or higher optical depth than is commonly seen in more advanced mergers.

  11. Reaction-diffusion systems in intracellular molecular transport and control.

    Science.gov (United States)

    Soh, Siowling; Byrska, Marta; Kandere-Grzybowska, Kristiana; Grzybowski, Bartosz A

    2010-06-07

    Chemical reactions make cells work only if the participating chemicals are delivered to desired locations in a timely and precise fashion. Most research to date has focused on active-transport mechanisms, although passive diffusion is often equally rapid and energetically less costly. Capitalizing on these advantages, cells have developed sophisticated reaction-diffusion (RD) systems that control a wide range of cellular functions-from chemotaxis and cell division, through signaling cascades and oscillations, to cell motility. These apparently diverse systems share many common features and are "wired" according to "generic" motifs such as nonlinear kinetics, autocatalysis, and feedback loops. Understanding the operation of these complex (bio)chemical systems requires the analysis of pertinent transport-kinetic equations or, at least on a qualitative level, of the characteristic times of the constituent subprocesses. Therefore, in reviewing the manifestations of cellular RD, we also describe basic theory of reaction-diffusion phenomena.

  12. Simulation of Molecular Transport in Systems Containing Mobile Obstacles.

    Science.gov (United States)

    Polanowski, Piotr; Sikorski, Andrzej

    2016-08-04

    In this paper, we investigate the movement of molecules in crowded environments with obstacles undergoing Brownian motion by means of extensive Monte Carlo simulations. Our investigations were performed using the dynamic lattice liquid model, which was based on the cooperative movement concept and allowed to mimic systems at high densities where the motion of all elements (obstacles as well as moving particles) were highly correlated. The crowded environments are modeled on a two-dimensional triangular lattice containing obstacles (particles whose mobility was significantly reduced) moving by a Brownian motion. The subdiffusive motion of both elements in the system was analyzed. It was shown that the percolation transition does not exist in such systems in spite of the cooperative character of the particles' motion. The reduction of the obstacle mobility leads to the longer caging of liquid particles by mobile obstacles.

  13. A Strategy to Suppress Phonon Transport in Molecular Junctions Using pi-Stacked Systems

    DEFF Research Database (Denmark)

    Li, Qian; Strange, Mikkel; Duchemin, Ivan

    2017-01-01

    to suppress phonon transport in graphene-based molecular junctions preserving high electronic power factor, using nonbonded pi-stackal systems. Using first-principles calculations, we find that the thermal conductance of pi-stacked systems can be reduced by about 95%, compared with that of a covalently bonded...

  14. Fulminant hepatic failure following marijuana drug abuse: Molecular adsorbent recirculation system therapy

    Directory of Open Access Journals (Sweden)

    G Swarnalatha

    2013-01-01

    Full Text Available Marijuana is used for psychoactive and recreational purpose. We report a case of fulminant hepatic failure following marijuana drug abuse who recovered following artificial support systems for acute liver failure. There is no published literature of management of marijuana intoxication with molecular adsorbent recirculation system (MARS. MARS is effective and safe in patients with fulminant hepatic failure following marijuana intoxication.

  15. Relativistic Green function for atomic and molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Gruzdev, P.F.; Sherstyuk, A.I.

    1981-12-01

    The problem on Green function construction of Dirac equation is solved for a wide class of single electron potentials in the atom and molecule theory. The solution is obtained in the form of a spectrum analysis according to the total system of eigenfuctions of the generalized Dirac problem for eigenvalues. The problem possesses a purely discrete spectrum.

  16. Dense power-law networks and simplicial complexes

    Science.gov (United States)

    Courtney, Owen T.; Bianconi, Ginestra

    2018-05-01

    There is increasing evidence that dense networks occur in on-line social networks, recommendation networks and in the brain. In addition to being dense, these networks are often also scale-free, i.e., their degree distributions follow P (k ) ∝k-γ with γ ∈(1 ,2 ] . Models of growing networks have been successfully employed to produce scale-free networks using preferential attachment, however these models can only produce sparse networks as the numbers of links and nodes being added at each time step is constant. Here we present a modeling framework which produces networks that are both dense and scale-free. The mechanism by which the networks grow in this model is based on the Pitman-Yor process. Variations on the model are able to produce undirected scale-free networks with exponent γ =2 or directed networks with power-law out-degree distribution with tunable exponent γ ∈(1 ,2 ) . We also extend the model to that of directed two-dimensional simplicial complexes. Simplicial complexes are generalization of networks that can encode the many body interactions between the parts of a complex system and as such are becoming increasingly popular to characterize different data sets ranging from social interacting systems to the brain. Our model produces dense directed simplicial complexes with power-law distribution of the generalized out-degrees of the nodes.

  17. 16. Hot dense plasma atomic processes

    International Nuclear Information System (INIS)

    Werner, Dappen; Totsuji, H.; Nishii, Y.

    2002-01-01

    This document gathers 13 articles whose common feature is to deal with atomic processes in hot plasmas. Density functional molecular dynamics method is applied to the hydrogen plasma in the domain of liquid metallic hydrogen. The effects of the density gradient are taken into account in both the electronic kinetic energy and the exchange energy and it is shown that they almost cancel with each other, extending the applicability of the Thomas-Fermi-Dirac approximation to the cases where the density gradient is not negligible. Another article reports about space and time resolved M-shell X-ray measurements of a laser-produced gas jet xenon plasma. Plasma parameters have been measured by ion acoustic and electron plasma waves Thomson scattering. Photo-ionization becomes a dominant atomic process when the density and the temperature of plasmas are relatively low and when the plasma is submitted to intense external radiation. It is shown that 2 plasmas which have a very different density but have the same ionization parameters, are found in a similar ionization state. Most radiation hydrodynamics codes use radiative opacity data from available libraries of atomic data. Several articles are focused on the determination of one group Rosseland and Planck mean analytical formulas for several single elements used in inertial fusion targets. In another paper the plasma density effect on population densities, effective ionization, recombination rate coefficients and on emission lines from carbon and Al ions in hot dense plasma, is studied. The last article is devoted to a new atomic model in plasmas that considers the occupation probability of the bound state and free state density in the presence of the plasma micro-field. (A.C.)

  18. The chloroplast thylakoid membrane system is a molecular conveyor belt.

    Science.gov (United States)

    Critchley, C

    1988-10-01

    Light drives photosynthesis, but paradoxically light is also the most variable environmental factor influencing photosynthesis both qualitatively and quantitatively. The photosynthetic apparatus of higher plants is adaptable in the extreme, as exemplified by its capacity for acclimation to very bright sunny or deeply shaded conditions. It can also respond to rapid changes in light such as sunflecks. In this paper I offer a model that i) explains the thylakoid membrane organisation into grana stacks and stroma lamellae, ii) proposes a role for rapid D1 protein turnover and LHCII phosphorylation, and iii) suggests a mechanism for photoinhibition. I argue that the photosynthetic membrane system is dynamic in three dimensions, so much so that, in the light, it is in constant motion and operates in a manner somewhat analogous to a conveyor belt. D1 protein degradation is proposed to be the motor that drives this system. Photoinhibition is suggested to be due to the arrest of D1 protein turnover.

  19. Molecular pathology of systemic lupus erythematosus in Asians

    OpenAIRE

    Chai, Hwa Chia

    2017-01-01

    Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease affecting various parts of the body. Polymorphisms in genes involved in toll-like receptor (TLR)/interferon (IFN) signalling pathways have been reported previously to be associated with SLE in many populations. This study aimed to investigate the role of seven single nucleotide polymorphisms (SNPs) within TNFAIP3 (rs2230936 and rs3757173), STAT4 (rs7574865, rs10168266, and rs7601754), and IRF5 (rs4728142 and rs729302), that...

  20. Bound states and molecular structure of systems with hyperons

    International Nuclear Information System (INIS)

    Akaishi, Y.

    1992-01-01

    Microscopic calculations are done for Σ-hypernuclear few-body systems by a method named ATMS. Among two- to five-body systems, only the Σ 4 He(0 + ) and Σ 4 H(0 + ) hypernuclei are expected to be bound: The binding energy and the width of the former are calculated to be 3.7 ∼ 4.6 MeV and 4.5 ∼ 7.9 MeV, respectively. The observation of Σ 4 He at KEK is in good agreement with the above prediction. The nucleus-Σ potential has a strong Lane term and a repulsive bump at short distance. The Lane term makes the system bound and the bump suppresses the ΣN → ΛN conversion. X-ray measurement of level shifts in the 4 He-Σ - , 3 He-Σ - and 3 H-Σ - atoms can provide another information on the Lane term. In 208 Pb, there may exist a peculiar state, Coulomb-assisted (atomnucleus) hybrid state, where Σ - is trapped in the surface region by the strong interaction with the aid of the inner centrifugal repulsion and the outer Coulomb attraction. An analysis is given for new data of Ξ -.12 C atomic or nuclear systems from the emulsion-counter experiment at KEK. The double-Λ hypernucleus formation rate is calculated for a stopped Ξ - on 4 He. A high branching ratio of 37% is obtained for the ΛΛ 4 H formation from a Ξ -.4 He atom. The detection of about 2.3 MeV neutron is proposed to search for lightest double-Λ hypernucleus ΛΛ 4 H. (author)

  1. Biomedical wellness monitoring system based upon molecular markers

    Science.gov (United States)

    Ingram, Whitney

    2012-06-01

    We wish to assist caretakers with a sensor monitoring systems for tracking the physiological changes of homealone patients. One goal is seeking biomarkers and modern imaging sensors like stochastic optical reconstruction microscopy (STORM), which has achieved visible imaging at the nano-scale range. Imaging techniques like STORM can be combined with a fluorescent functional marker in a system to capture the early transformation signs from wellness to illness. By exploiting both microscopic knowledge of genetic pre-disposition and the macroscopic influence of epigenetic factors we hope to target these changes remotely. We adopt dual spectral infrared imaging for blind source separation (BSS) to detect angiogenesis changes and use laser speckle imaging for hypertension blood flow monitoring. Our design hypothesis for the monitoring system is guided by the user-friendly, veteran-preferred "4-Non" principles (noninvasive, non-contact, non-tethered, non-stop-to-measure) and by the NIH's "4Ps" initiatives (predictive, personalized, preemptive, and participatory). We augment the potential storage system with the recent know-how of video Compressive Sampling (CSp) from surveillance cameras. In CSp only major changes are saved, which reduces the manpower cost of caretakers and medical analysts. This CSp algorithm is based on smart associative memory (AM) matrix storage: change features and detailed scenes are written by the outer-product and read by the inner product without the usual Harsh index for image searching. From this approach, we attempt to design an effective household monitoring approach to save healthcare costs and maintain the quality of life of seniors.

  2. Laboratory and modeling studies of chemistry in dense molecular clouds

    Science.gov (United States)

    Huntress, W. T., Jr.; Prasad, S. S.; Mitchell, G. F.

    1980-01-01

    A chemical evolutionary model with a large number of species and a large chemical library is used to examine the principal chemical processes in interstellar clouds. Simple chemical equilibrium arguments show the potential for synthesis of very complex organic species by ion-molecule radiative association reactions.

  3. Plasmon-polariton modes of dense Au nanowire arrays

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Hongdan; Lemmens, Peter; Wulferding, Dirk; Cetin, Mehmet Fatih [IPKM, TU-BS, Braunschweig (Germany); Tornow, Sabine; Zwicknagl, Gertrud [IMP, TU-BS, Braunschweig (Germany); Krieg, Ulrich; Pfnuer, Herbert [IFP, LU Hannover (Germany); Daum, Winfried; Lilienkamp, Gerhard [IEPT, TU Clausthal (Germany); Schilling, Meinhard [EMG, TU-BS, Braunschweig (Germany)

    2011-07-01

    Using optical absorption and other techniques we study plasmon-polariton modes of dense Au nanowire arrays as function of geometrical parameters and coupling to molecular degrees of freedom. For this instance we electrochemically deposit Au nanowires in porous alumina with well controlled morphology and defect concentration. Transverse and longitudinal modes are observed in the absorption spectra resulting from the anisotropic plasmonic structure. The longitudinal mode shows a blue shift of energy with increasing length of the wires due to the more collective nature of this response. We compare our observations with model calculations and corresponding results on 2D Ag nanowire lattices.

  4. Isotopologues of dense gas tracers in NGC 1068

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Junzhi; Qiu, Jianjie [Shanghai Astronomical Observatory, Chinese Academy of Sciences, 80 Nandan Road, 200030, Shanghai (China); Zhang, Zhi-Yu [Institute for Astronomy, University of Edinburgh, Royal Observatory, Blackford Hill, Edinburgh EH9 3HJ (United Kingdom); Shi, Yong [School of Astronomy and Space Science, Nanjing University, Nanjing, 210093 (China); Zhang, Jiangshui [Center For Astrophysics, GuangZhou University, 510006, GuangZhou (China); Fang, Min, E-mail: jzwang@shao.ac.cn [ESO, Karl Schwarzschild Strasse 2, D-85748 Garching bei Munich (Germany)

    2014-11-20

    We present observations of isotopic lines of dense gas tracers toward the nuclear region of nearby Seyfert 2 galaxy NGC 1068 with the IRAM 30 m telescope and the Atacama Pathfinder Experiment (APEX) 12 m telescope. We detected four isotopic lines (H{sup 13}CN 1-0, H{sup 13}CO{sup +} 1-0, HN{sup 13}C 1-0, and HC{sup 18}O{sup +} 1-0) at the 3 mm band with the IRAM 30 m telescope and obtained upper limits of other lines. We calculated optical depths of dense gas tracers with the detected isotopic lines of HCN 1-0, HCO{sup +} 1-0, and HNC 1-0. We find that the {sup 14}N/{sup 15}N abundance ratio is greater than 420 if we adopt the upper limit of HC{sup 15}N(1-0) emission. Combining this with fluxes of 1-0 lines from IRAM 30 m observations and the upper limit of 3-2 lines from APEX 12 m observations, we also estimated the excitation condition of molecular gas in the nuclear region of NGC 1068, which is less dense than that in the extreme starburst regions of galaxies.

  5. THE GREEN BANK TELESCOPE MAPS THE DENSE, STAR-FORMING GAS IN THE NEARBY STARBURST GALAXY M82

    International Nuclear Information System (INIS)

    Kepley, Amanda A.; Frayer, David; Leroy, Adam K.; Usero, Antonio; Marvil, Josh; Walter, Fabian

    2014-01-01

    Observations of the Milky Way and nearby galaxies show that dense molecular gas correlates with recent star formation, suggesting that the formation of this gas phase may help regulate star formation. A key test of this idea requires wide-area, high-resolution maps of dense molecular gas in galaxies to explore how local physical conditions drive dense gas formation, but these observations have been limited because of the faintness of dense gas tracers like HCN and HCO + . Here we demonstrate the power of the Robert C. Byrd Green Bank Telescope (GBT)—the largest single-dish millimeter radio telescope—for mapping dense gas in galaxies by presenting the most sensitive maps yet of HCN and HCO + in the starburst galaxy M82. The HCN and HCO + in the disk of this galaxy correlates with both recent star formation and more diffuse molecular gas and shows kinematics consistent with a rotating torus. The HCO + emission extending to the north and south of the disk is coincident with the outflow previously identified in CO and traces the eastern edge of the hot outflowing gas. The central starburst region has a higher ratio of star formation to dense gas than the outer regions, pointing to the starburst as a key driver of this relationship. These results establish that the GBT can efficiently map the dense molecular gas at 90 GHz in nearby galaxies, a capability that will increase further with the 16 element feed array under construction

  6. Supra-molecular Association and Polymorphic Behaviour In Systems Containing Bile Acid Salts

    Directory of Open Access Journals (Sweden)

    Camillo La Mesa

    2007-08-01

    Full Text Available A wide number of supra-molecular association modes are observed in mixtures containing water and bile salts, BS, (with, eventually, other components. Molecular or micellar solutions transform into hydrated solids, fibres, lyotropic liquid crystals and/or gels by raising the concentration, the temperature, adding electrolytes, surfactants, lipids and proteins. Amorphous or ordered phases may be formed accordingly. The forces responsible for this very rich polymorphism presumably arise from the unusual combination of electrostatic, hydrophobic and hydrogen-bond contributions to the system stability, with subsequent control of the supra-molecular organisation modes. The stabilising effect due to hydrogen bonds does not occur in almost all surfactants or lipids and is peculiar to bile acids and salts. Some supra-molecular organisation modes, supposed to be related to malfunctions and dis-metabolic diseases in vivo, are briefly reported and discussed.

  7. Structural insight into RNA recognition motifs: versatile molecular Lego building blocks for biological systems.

    Science.gov (United States)

    Muto, Yutaka; Yokoyama, Shigeyuki

    2012-01-01

    'RNA recognition motifs (RRMs)' are common domain-folds composed of 80-90 amino-acid residues in eukaryotes, and have been identified in many cellular proteins. At first they were known as RNA binding domains. Through discoveries over the past 20 years, however, the RRMs have been shown to exhibit versatile molecular recognition activities and to behave as molecular Lego building blocks to construct biological systems. Novel RNA/protein recognition modes by RRMs are being identified, and more information about the molecular recognition by RRMs is becoming available. These RNA/protein recognition modes are strongly correlated with their biological significance. In this review, we would like to survey the recent progress on these versatile molecular recognition modules. Copyright © 2012 John Wiley & Sons, Ltd.

  8. Molecular alteration of a muscarinic acetylcholine receptor system during synaptogenesis

    International Nuclear Information System (INIS)

    Large, T.H.; Cho, N.J.; De Mello, F.G.; Klein, W.L.

    1985-01-01

    Biochemical properties of the muscarinic acetylcholine receptor system of the avian retina were found to change during the period when synapses form in ovo. Comparison of ligand binding to membranes obtained before and after synaptogenesis showed a significant increase in the affinity, but not proportion, of the high affinity agonist-binding state. There was no change in receptor sensitivity to antagonists during this period. Pirenzepine binding, which can discriminate muscarinic receptor subtypes, showed the presence of a single population of low affinity sites (M2) before and after synaptogenesis. The change in agonist binding was not due to the late development of receptor function. However, detergent-solubilization of membranes eliminated differences in agonist binding between receptors from embryos and hatched chicks, suggesting a developmental change in interactions of the receptor with functionally related membrane components. A possible basis for altered interactions was obtained from isoelectric point data showing that the muscarinic receptor population underwent a transition from a predominantly low pI form (4.25) in 13 day embryos to a predominantly high pI form (4.50) in newly hatched chicks. The possibility that biochemical changes in the muscarinic receptor play a role in differentiation of the system by controlling receptor position on the surface of nerve cells is discussed

  9. Chapter 5: Quantum Dynamics in Dissipative Molecular Systems

    Science.gov (United States)

    Zhang, Hou-Dao; Xu, J.; Xu, Rui-Xue; Yan, Y. J.

    2014-04-01

    The following sections are included: * Introduction * HEOM versus Path Integral Formalism: Background * Generic form and terminology of HEOM * Statistical mechanics description of bath influence * Feynman-Vernon influence functional formalism * General comments * Memory-Frequency Decomposition of Bath Correlation Functions * PSD of Bose function * Brownian oscillators decomposition of bath spectral density function * Optimized HEOM Theory With Accuracy Control * Construction of HEOM via path integral formalism * Accuracy control on white-noise residue ansatz * Efficient HEOM propagator: Numerical filtering and indexing algorithm * HEOM in Quantum Mechanics for Open Systems * The HEOM space and the Schrödinger picture * HEOM in the Heisenberg picture * Mixed Heisenberg-Schrödinger block-matrix dynamics in nonlinear optical response functions * Two-Dimensional Spectroscopy: Model Calculations * Concluding Remarks * Acknowledgments * References

  10. Intracellular Chemistry: Integrating Molecular Inorganic Catalysts with Living Systems.

    Science.gov (United States)

    Ngo, Anh H; Bose, Sohini; Do, Loi H

    2018-03-23

    This concept article focuses on the rapid growth of intracellular chemistry dedicated to the integration of small-molecule metal catalysts with living cells and organisms. Although biological systems contain a plethora of biomolecules that can deactivate inorganic species, researchers have shown that small-molecule metal catalysts could be engineered to operate in heterogeneous aqueous environments. Synthetic intracellular reactions have recently been reported for olefin hydrogenation, hydrolysis/oxidative cleavage, azide-alkyne cycloaddition, allylcarbamate cleavage, C-C bond cross coupling, and transfer hydrogenation. Other promising targets for new biocompatible reaction discovery will also be discussed, with a special emphasis on how such innovations could lead to the development of novel technologies and chemical tools. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Molecular dynamics coupled with a virtual system for effective conformational sampling.

    Science.gov (United States)

    Hayami, Tomonori; Kasahara, Kota; Nakamura, Haruki; Higo, Junichi

    2018-07-15

    An enhanced conformational sampling method is proposed: virtual-system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free-energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

  12. Phases of polymer systems in solution studied via molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Joshua Allen [Iowa State Univ., Ames, IA (United States)

    2009-05-01

    Polymers are amazingly versatile molecules with a tremendous range of applications. Our lives would be very different without them. There would be no multitudes of plastic encased electronic gizmos, no latex paint on the walls and no rubber tires, just to name a few of the many commonplace polymer materials. In fact, life as we know it wouldn’t exist without polymers as two of the most essential types of molecules central to cellular life, Proteins and DNA, are both polymers! [1] With their wide range of application to a variety of uses, polymers are still a very active field in basic research. Of particular current interest is the idea of combining polymers with inorganic particles to form novel composite materials. [2] As computers are becoming faster, they are becoming all the more powerful tools for modeling and simulating real systems. With recent advances in computing on graphics processing units (GPUs) [3–7], questions can now be answered via simulation that could not even be asked before. This thesis focuses on the use of computer simulations to model novel polymerinorganic composite systems in order to predict what possible phases can form and under what conditions. The goal is to provide some direction for future experiments and to gain a deeper understanding of the fundamental physics involved. Along the way, there are some interesting and essential side-tracks in the areas of equilibrating complicated phases and accelerating the available computer power with GPU computing, both of which are necessary steps to enable the study of polymer nanocomposites.

  13. Modulated molecular beam mass spectrometry: A generalized expression for the ''reaction product vector'' for linear systems

    International Nuclear Information System (INIS)

    Chang, H.; Weinberg, W.H.

    1977-01-01

    A generalized expression is developed that relates the ''reaction product vector'', epsilon exp(-iphi), to the kinetic parameters of a linear system. The formalism is appropriate for the analysis of modulated molecular beam mass spectrometry data and facilitates the correlation of experimental results to (proposed) linear models. A study of stability criteria appropriate for modulated molecular beam mass spectrometry experiments is also presented. This investigation has led to interesting inherent limitations which have not heretofore been emphasized, as well as a delineation of the conditions under which stable chemical oscillations may occur in the reacting system

  14. Potentiometric investigations of molecular heteroconjugation equilibria of substituted phenol+n-butylamine systems in dimethyl sulfoxide

    International Nuclear Information System (INIS)

    Czaja, MaIgorzata; Baginska, Katarzyna; Kozak, Anna; Makowski, Mariusz; Chmurzynski, Lech

    2005-01-01

    Molecular heteroconjugation constants, K BHA DMSO and K AHB DMSO , expressed as their logarithms, have been determined by potentiometric titration for eleven substituted phenol+n-butylamine systems in a polar protophilic aprotic solvent, dimethyl sulfoxide (DMSO). An increasing tendency towards molecular heteroconjugation in these systems without proton transfer has been found with increasing pK a DMSO (HA), i.e., with decreasing phenol acidity. Moreover, a linear correlation has been established between the determined lgK BHA DMSO values and pK a DMSO (HA). Furthermore, overall stability constants, lgK o DMSO , could be correlated linearly with pK a DMSO (HA) values

  15. A web-based personalized risk communication and decision-making tool for women with dense breasts: Design and methods of a randomized controlled trial within an integrated health care system.

    Science.gov (United States)

    Knerr, Sarah; Wernli, Karen J; Leppig, Kathleen; Ehrlich, Kelly; Graham, Amanda L; Farrell, David; Evans, Chalanda; Luta, George; Schwartz, Marc D; O'Neill, Suzanne C

    2017-05-01

    Mammographic breast density is one of the strongest risk factors for breast cancer after age and family history. Mandatory breast density disclosure policies are increasing nationally without clear guidance on how to communicate density status to women. Coupling density disclosure with personalized risk counseling and decision support through a web-based tool may be an effective way to allow women to make informed, values-consistent risk management decisions without increasing distress. This paper describes the design and methods of Engaged, a prospective, randomized controlled trial examining the effect of online personalized risk counseling and decision support on risk management decisions in women with dense breasts and increased breast cancer risk. The trial is embedded in a large integrated health care system in the Pacific Northwest. A total of 1250 female health plan members aged 40-69 with a recent negative screening mammogram who are at increased risk for interval cancer based on their 5-year breast cancer risk and BI-RADS® breast density will be randomly assigned to access either a personalized web-based counseling and decision support tool or standard educational content. Primary outcomes will be assessed using electronic health record data (i.e., chemoprevention and breast MRI utilization) and telephone surveys (i.e., distress) at baseline, six weeks, and twelve months. Engaged will provide evidence about whether a web-based personalized risk counseling and decision support tool is an effective method for communicating with women about breast density and risk management. An effective intervention could be disseminated with minimal clinical burden to align with density disclosure mandates. Clinical Trials Registration Number:NCT03029286. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Low molecular mass chitosan as carrier for hydrodynamically balanced system for sustained delivery of ciprofloxacin hydrochloride

    OpenAIRE

    VERMA, ANURAG; BANSAL, ASHOK K.; GHOSH, AMITAVA; PANDIT, JAYANTA K.

    2012-01-01

    Chitosan has become a focus of major interest in recent years due to its excellent biocompatibility, biodegradability and non-toxicity. Although this material has already been extensively investigated in the design of different types of drug delivery systems, it is still little explored for stomach specific drug delivery systems. The objective of the present investigation was to explore the potential of low molecular mass chitosan (LMCH) as carrier for a hydrodynamically balanced system (HBS)...

  17. Finding dense locations in indoor tracking data

    DEFF Research Database (Denmark)

    Ahmed, Tanvir; Pedersen, Torben Bach; Lu, Hua

    2014-01-01

    for semi-constrained indoor movement, and then uses this to map raw tracking records into mapping records representing object entry and exit times in particular locations. Then, an efficient indexing structure, the Dense Location Time Index (DLT-Index) is proposed for indexing the time intervals...... of the mapping table, along with associated construction, query processing, and pruning techniques. The DLT-Index supports very efficient aggregate point queries, interval queries, and dense location queries. A comprehensive experimental study with real data shows that the proposed techniques can efficiently......Finding the dense locations in large indoor spaces is very useful for getting overloaded locations, security, crowd management, indoor navigation, and guidance. Indoor tracking data can be very large and are not readily available for finding dense locations. This paper presents a graph-based model...

  18. Interference Coordination for Dense Wireless Networks

    DEFF Research Database (Denmark)

    Soret, Beatriz; Pedersen, Klaus I.; Jørgensen, Niels T.K.

    2015-01-01

    and dense deployment in Tokyo are compared. Evolution to DenseNets offers new opportunities for further development of downlink interference cooperation techniques. Various mechanisms in LTE and LTE-Advanced are revisited. Some techniques try to anticipate the future in a proactive way, whereas others......The promise of ubiquitous and super-fast connectivity for the upcoming years will be in large part fulfilled by the addition of base stations and spectral aggregation. The resulting very dense networks (DenseNets) will face a number of technical challenges. Among others, the interference emerges...... as an old acquaintance with new significance. As a matter of fact, the interference conditions and the role of aggressor and victim depend to a large extent on the density and the scenario. To illustrate this, downlink interference statistics for different 3GPP simulation scenarios and a more irregular...

  19. Skyrmions, dense matter and nuclear forces

    International Nuclear Information System (INIS)

    Pethick, C.J.

    1984-12-01

    A simple introduction to a number of properties of Skyrme's chiral soliton model of baryons is given. Some implications of the model for dense matter and for nuclear interactions are discussed. (orig.)

  20. Molecular evolution of peptidergic signaling systems in bilaterians

    Science.gov (United States)

    Mirabeau, Olivier; Joly, Jean-Stéphane

    2013-01-01

    Peptide hormones and their receptors are widespread in metazoans, but the knowledge we have of their evolutionary relationships remains unclear. Recently, accumulating genome sequences from many different species have offered the opportunity to reassess the relationships between protostomian and deuterostomian peptidergic systems (PSs). Here we used sequences of all human rhodopsin and secretin-type G protein-coupled receptors as bait to retrieve potential homologs in the genomes of 15 bilaterian species, including nonchordate deuterostomian and lophotrochozoan species. Our phylogenetic analysis of these receptors revealed 29 well-supported subtrees containing mixed sets of protostomian and deuterostomian sequences. This indicated that many vertebrate and arthropod PSs that were previously thought to be phyla specific are in fact of bilaterian origin. By screening sequence databases for potential peptides, we then reconstructed entire bilaterian peptide families and showed that protostomian and deuterostomian peptides that are ligands of orthologous receptors displayed some similarity at the level of their primary sequence, suggesting an ancient coevolution between peptide and receptor genes. In addition to shedding light on the function of human G protein-coupled receptor PSs, this work presents orthology markers to study ancestral neuron types that were probably present in the last common bilaterian ancestor. PMID:23671109

  1. Kinetic chemistry of dense interstellar clouds

    International Nuclear Information System (INIS)

    Graedel, T.E.; Langer, W.D.; Frerking, M.A.

    1982-01-01

    A detailed model of the time-dependent chemistry of dense interstellar clouds has been developed to study the dominant chemical processes in carbon and oxygen isotope fractionation, formation of nitrogen-containing molecules, evolution of product molecules as a function of cloud density and temperature, and other topics of interest. The full computation involves 328 individual reactions (expanded to 1067 to study carbon and oxygen isotope chemistry); photodegradation processes are unimportant in these dense clouds and are excluded

  2. Bridging the gap: linking molecular simulations and systemic descriptions of cellular compartments.

    Directory of Open Access Journals (Sweden)

    Tihamér Geyer

    Full Text Available Metabolic processes in biological cells are commonly either characterized at the level of individual enzymes and metabolites or at the network level. Often these two paradigms are considered as mutually exclusive because concepts from neither side are suited to describe the complete range of scales. Additionally, when modeling metabolic or regulatory cellular systems, often a large fraction of the required kinetic parameters are unknown. This even applies to such simple and extensively studied systems like the photosynthetic apparatus of purple bacteria. Using the chromatophore vesicles of Rhodobacter sphaeroides as a model system, we show that a consistent kinetic model emerges when fitting the dynamics of a molecular stochastic simulation to a set of time dependent experiments even though about two thirds of the kinetic parameters in this system are not known from experiment. Those kinetic parameters that were previously known all came out in the expected range. The simulation model was built from independent protein units composed of elementary reactions processing single metabolites. This pools-and-proteins approach naturally compiles the wealth of available molecular biological data into a systemic model and can easily be extended to describe other systems by adding new protein or nucleic acid types. The automated parameter optimization, performed with an evolutionary algorithm, reveals the sensitivity of the model to the value of each parameter and the relative importances of the experiments used. Such an analysis identifies the crucial system parameters and guides the setup of new experiments that would add most knowledge for a systemic understanding of cellular compartments. The successful combination of the molecular model and the systemic parametrization presented here on the example of the simple machinery for bacterial photosynthesis shows that it is actually possible to combine molecular and systemic modeling. This framework can now

  3. A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations

    KAUST Repository

    Neumann, Philipp

    2012-06-01

    We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm as well as parallel execution of the hybrid simulation. We describe the implementational concept of the tool and its parallel extensions. We particularly focus on the parallel execution of particle insertions into dense molecular systems and propose a respective parallel algorithm. Our implementations are validated for serial and parallel setups in two and three dimensions. © 2012 IEEE.

  4. Coherent Rabi oscillations in a molecular system and sub-diffraction-limited pattern generation

    International Nuclear Information System (INIS)

    Liao, Zeyang; Al-Amri, M; Zubairy, M Suhail

    2015-01-01

    The resolution of a photolithography and optical imaging system is restricted by the diffraction limit. Coherent Rabi oscillations have been shown to be able to overcome the diffraction limit in a simple two-level atomic system (Z Liao, M Al-amri, and M S Zubairy 2010 Phys. Rev. Lett. 105 183601). In this paper, we numerically calculate the wave packet dynamics of a molecular system interacting with an ultrashort laser pulse and show that coherent Rabi oscillations in a molecular system are also possible. Moreover, a sub-diffraction-limited pattern can be generated in this system by introducing spatially modulated Rabi oscillations. We also discuss several techniques to improve the visibility of the sub-diffraction-limited pattern. Our result may have important applications in super-resolution optical lithography and optical imaging. (paper)

  5. A neural network approach to the study of dynamics and structure of molecular systems

    International Nuclear Information System (INIS)

    Getino, C.; Sumpter, B.G.; Noid, D.W.

    1994-01-01

    Neural networks are used to study intramolecular energy flow in molecular systems (tetratomics to macromolecules), developing new techniques for efficient analysis of data obtained from molecular-dynamics and quantum mechanics calculations. Neural networks can map phase space points to intramolecular vibrational energies along a classical trajectory (example of complicated coordinate transformation), producing reasonably accurate values for any region of the multidimensional phase space of a tetratomic molecule. Neural network energy flow predictions are found to significantly enhance the molecular-dynamics method to longer time-scales and extensive averaging of trajectories for macromolecular systems. Pattern recognition abilities of neural networks can be used to discern phase space features. Neural networks can also expand model calculations by interpolation of costly quantum mechanical ab initio data, used to develop semiempirical potential energy functions

  6. A continuous stochastic model for non-equilibrium dense gases

    Science.gov (United States)

    Sadr, M.; Gorji, M. H.

    2017-12-01

    While accurate simulations of dense gas flows far from the equilibrium can be achieved by direct simulation adapted to the Enskog equation, the significant computational demand required for collisions appears as a major constraint. In order to cope with that, an efficient yet accurate solution algorithm based on the Fokker-Planck approximation of the Enskog equation is devised in this paper; the approximation is very much associated with the Fokker-Planck model derived from the Boltzmann equation by Jenny et al. ["A solution algorithm for the fluid dynamic equations based on a stochastic model for molecular motion," J. Comput. Phys. 229, 1077-1098 (2010)] and Gorji et al. ["Fokker-Planck model for computational studies of monatomic rarefied gas flows," J. Fluid Mech. 680, 574-601 (2011)]. The idea behind these Fokker-Planck descriptions is to project the dynamics of discrete collisions implied by the molecular encounters into a set of continuous Markovian processes subject to the drift and diffusion. Thereby, the evolution of particles representing the governing stochastic process becomes independent from each other and thus very efficient numerical schemes can be constructed. By close inspection of the Enskog operator, it is observed that the dense gas effects contribute further to the advection of molecular quantities. That motivates a modelling approach where the dense gas corrections can be cast in the extra advection of particles. Therefore, the corresponding Fokker-Planck approximation is derived such that the evolution in the physical space accounts for the dense effects present in the pressure, stress tensor, and heat fluxes. Hence the consistency between the devised Fokker-Planck approximation and the Enskog operator is shown for the velocity moments up to the heat fluxes. For validation studies, a homogeneous gas inside a box besides Fourier, Couette, and lid-driven cavity flow setups is considered. The results based on the Fokker-Planck model are

  7. Kinetic Simulations of Dense Plasma Focus Breakdown

    Science.gov (United States)

    Schmidt, A.; Higginson, D. P.; Jiang, S.; Link, A.; Povilus, A.; Sears, J.; Bennett, N.; Rose, D. V.; Welch, D. R.

    2015-11-01

    A dense plasma focus (DPF) device is a type of plasma gun that drives current through a set of coaxial electrodes to assemble gas inside the device and then implode that gas on axis to form a Z-pinch. This implosion drives hydrodynamic and kinetic instabilities that generate strong electric fields, which produces a short intense pulse of x-rays, high-energy (>100 keV) electrons and ions, and (in deuterium gas) neutrons. A strong factor in pinch performance is the initial breakdown and ionization of the gas along the insulator surface separating the two electrodes. The smoothness and isotropy of this ionized sheath are imprinted on the current sheath that travels along the electrodes, thus making it an important portion of the DPF to both understand and optimize. Here we use kinetic simulations in the Particle-in-cell code LSP to model the breakdown. Simulations are initiated with neutral gas and the breakdown modeled self-consistently as driven by a charged capacitor system. We also investigate novel geometries for the insulator and electrodes to attempt to control the electric field profile. The initial ionization fraction of gas is explored computationally to gauge possible advantages of pre-ionization which could be created experimentally via lasers or a glow-discharge. Prepared by LLNL under Contract DE-AC52-07NA27344.

  8. Borehole stability in densely welded tuffs

    International Nuclear Information System (INIS)

    Fuenkajorn, K.; Daemen, J.J.K.

    1992-07-01

    The stability of boreholes, or more generally of underground openings (i.e. including shafts, ramps, drifts, tunnels, etc.) at locations where seals or plugs are to be placed is an important consideration in seal design for a repository (Juhlin and Sandstedt, 1989). Borehole instability or borehole breakouts induced by stress redistribution could negate the effectiveness of seals or plugs. Breakout fractures along the wall of repository excavations or exploratory holes could provide a preferential flowpath for groundwater or gaseous radionuclides to bypass the plugs. After plug installation, swelling pressures exerted by a plug could induce radial cracks or could open or widen preexisting cracks in the rock at the bottom of the breakouts where the tangential compressive stresses have been released by the breakout process. The purpose of the work reported here is to determine experimentally the stability of a circular hole in a welded tuff sample subjected to various external boundary loads. Triaxial and biaxial borehole stability tests have been performed on densely welded Apache Leap tuff samples and Topopah Spring tuff samples. The nominal diameter of the test hole is 13.3 or 14.4 mm for triaxial testing, and 25.4 mm for biaxial testing. The borehole axis is parallel to one of the principal stress axes. The boreholes are drilled through the samples prior to applying external boundary loads. The boundary loads are progressively increased until breakouts occur or until the maximum load capacity of the loading system has been reached. 74 refs

  9. Large-scale molecular dynamics simulations of self-assembling systems.

    Science.gov (United States)

    Klein, Michael L; Shinoda, Wataru

    2008-08-08

    Relentless increases in the size and performance of multiprocessor computers, coupled with new algorithms and methods, have led to novel applications of simulations across chemistry. This Perspective focuses on the use of classical molecular dynamics and so-called coarse-grain models to explore phenomena involving self-assembly in complex fluids and biological systems.

  10. Origami: A Versatile Modeling System for Visualising Chemical Structure and Exploring Molecular Function

    Science.gov (United States)

    Davis, James; Leslie, Ray; Billington, Susan; Slater, Peter R.

    2010-01-01

    The use of "Origami" is presented as an accessible and transferable modeling system through which to convey the intricacies of molecular shape and highlight structure-function relationships. The implementation of origami has been found to be a versatile alternative to conventional ball-and-stick models, possessing the key advantages of being both…

  11. Molecular subtypes of systemic sclerosis in association with anti-centromere antibodies and digital ulcers

    NARCIS (Netherlands)

    Bos, C. L.; van Baarsen, L. G. M.; Timmer, T. C. G.; Overbeek, M. J.; Basoski, N. M.; Rustenburg, F.; Baggen, J. M. C.; Thiesen, H. J.; Dijkmans, B. A. C.; van der Pouw Kraan, T. C. T. M.; Voskuyl, A. E.; Verweij, C. L.

    2009-01-01

    The objective of this study was to identify molecular profiles that may distinguish clinical subtypes in systemic sclerosis (SSc). Large-scale gene expression profiling was performed on peripheral blood (PB) from 12 SSc patients and 6 healthy individuals. Significance analysis of microarrays,

  12. On the effects of transforming the vibrational spectra of molecular systems under microwave radiation

    International Nuclear Information System (INIS)

    Serikov, A.A.

    1993-01-01

    This problem is analyzed within the quantum-classical theory of molecular spectra. It is shown that the above-mentioned spectrum transformation could be, in principle, realized in macromolecular systems with strong interaction, and attention is drawn to the resonance character of the effect. (author). 19 refs., 1 fig

  13. Advances of Molecular Imaging for Monitoring the Anatomical and Functional Architecture of the Olfactory System.

    Science.gov (United States)

    Zhang, Xintong; Bi, Anyao; Gao, Quansheng; Zhang, Shuai; Huang, Kunzhu; Liu, Zhiguo; Gao, Tang; Zeng, Wenbin

    2016-01-20

    The olfactory system of organisms serves as a genetically and anatomically model for studying how sensory input can be translated into behavior output. Some neurologic diseases are considered to be related to olfactory disturbance, especially Alzheimer's disease, Parkinson's disease, multiple sclerosis, and so forth. However, it is still unclear how the olfactory system affects disease generation processes and olfaction delivery processes. Molecular imaging, a modern multidisciplinary technology, can provide valid tools for the early detection and characterization of diseases, evaluation of treatment, and study of biological processes in living subjects, since molecular imaging applies specific molecular probes as a novel approach to produce special data to study biological processes in cellular and subcellular levels. Recently, molecular imaging plays a key role in studying the activation of olfactory system, thus it could help to prevent or delay some diseases. Herein, we present a comprehensive review on the research progress of the imaging probes for visualizing olfactory system, which is classified on different imaging modalities, including PET, MRI, and optical imaging. Additionally, the probes' design, sensing mechanism, and biological application are discussed. Finally, we provide an outlook for future studies in this field.

  14. Development of Optical Molecular Imaging System for the Acquisition of Bioluminescence Signals from Small Animals

    International Nuclear Information System (INIS)

    Lee, Byeong Il; Kim, Hyeon Sik; Jeong, Hye Jin; Lee, Hyung Jae; Moon, Seung Min; Kwon, Seung Young; Jeong, Shin Young; Bom, Hee Seung; Min, Jung Joon; Choi, Eun Seo

    2009-01-01

    Optical imaging is providing great advance and improvement in genetic and molecular imaging of animals and humans. Optical imaging system consists of optical imaging devices, which carry out major function for monitoring, tracing, and imaging in most of molecular in-vivo researches. In bio-luminescent imaging, small animals containing luciferase gene locally irradiate light, and emitted photons transmitted through skin of the small animals are imaged by using a high sensitive charged coupled device (CCD) camera. In this paper, we introduced optical imaging system for the image acquisition of bio-luminescent signals emitted from small animals. In the system, Nikon lens and four LED light sources were mounted at the inside of a dark box. A cooled CCD camera equipped with a control module was used. We tested the performance of the optical imaging system using effendorf tube and light emitting bacteria which injected intravenously into CT26 tumor bearing nude mouse. The performance of implemented optical imaging system for bio-luminescence imaging was demonstrated and the feasibility of the system in small animal imaging application was proved. We anticipate this system could be a useful tool for the molecular imaging of small animals adaptable for various experimental conditions in future

  15. Propagation of monochromatic light in a hot and dense medium

    Energy Technology Data Exchange (ETDEWEB)

    Masood, Samina S. [University of Houston Clear Lake, Department of Physical and Applied Sciences, Houston, TX (United States)

    2017-12-15

    Photons, as quanta of electromagnetic fields, determine the electromagnetic properties of an extremely hot and dense medium. Considering the properties of the photons in the interacting medium of charged particles, we explicitly calculate the electromagnetic properties such as the electric permittivity, magnetic permeability, refractive index and the propagation speed of electromagnetic signals in an extremely hot and dense background. Photons acquire a dynamically generated mass in such a medium. The screening mass of the photon, the Debye shielding length and the plasma frequency are calculated as functions of the statistical parameters of the medium. We study the properties of the propagating particles in astrophysical systems of distinct statistical conditions. The modifications in the properties of the medium lead to the equation of state of the system. We mainly calculate all these parameters for extremely high temperatures of the early universe. (orig.)

  16. Propagation of monochromatic light in a hot and dense medium

    Science.gov (United States)

    Masood, Samina S.

    2017-12-01

    Photons, as quanta of electromagnetic fields, determine the electromagnetic properties of an extremely hot and dense medium. Considering the properties of the photons in the interacting medium of charged particles, we explicitly calculate the electromagnetic properties such as the electric permittivity, magnetic permeability, refractive index and the propagation speed of electromagnetic signals in an extremely hot and dense background. Photons acquire a dynamically generated mass in such a medium. The screening mass of the photon, the Debye shielding length and the plasma frequency are calculated as functions of the statistical parameters of the medium. We study the properties of the propagating particles in astrophysical systems of distinct statistical conditions. The modifications in the properties of the medium lead to the equation of state of the system. We mainly calculate all these parameters for extremely high temperatures of the early universe.

  17. Systems Biology-Driven Hypotheses Tested In Vivo: The Need to Advancing Molecular Imaging Tools.

    Science.gov (United States)

    Verma, Garima; Palombo, Alessandro; Grigioni, Mauro; La Monaca, Morena; D'Avenio, Giuseppe

    2018-01-01

    Processing and interpretation of biological images may provide invaluable insights on complex, living systems because images capture the overall dynamics as a "whole." Therefore, "extraction" of key, quantitative morphological parameters could be, at least in principle, helpful in building a reliable systems biology approach in understanding living objects. Molecular imaging tools for system biology models have attained widespread usage in modern experimental laboratories. Here, we provide an overview on advances in the computational technology and different instrumentations focused on molecular image processing and analysis. Quantitative data analysis through various open source software and algorithmic protocols will provide a novel approach for modeling the experimental research program. Besides this, we also highlight the predictable future trends regarding methods for automatically analyzing biological data. Such tools will be very useful to understand the detailed biological and mathematical expressions under in-silico system biology processes with modeling properties.

  18. Elucidation of molecular kinetic schemes from macroscopic traces using system identification.

    Directory of Open Access Journals (Sweden)

    Miguel Fribourg

    2017-02-01

    Full Text Available Overall cellular responses to biologically-relevant stimuli are mediated by networks of simpler lower-level processes. Although information about some of these processes can now be obtained by visualizing and recording events at the molecular level, this is still possible only in especially favorable cases. Therefore the development of methods to extract the dynamics and relationships between the different lower-level (microscopic processes from the overall (macroscopic response remains a crucial challenge in the understanding of many aspects of physiology. Here we have devised a hybrid computational-analytical method to accomplish this task, the SYStems-based MOLecular kinetic scheme Extractor (SYSMOLE. SYSMOLE utilizes system-identification input-output analysis to obtain a transfer function between the stimulus and the overall cellular response in the Laplace-transformed domain. It then derives a Markov-chain state molecular kinetic scheme uniquely associated with the transfer function by means of a classification procedure and an analytical step that imposes general biological constraints. We first tested SYSMOLE with synthetic data and evaluated its performance in terms of its rate of convergence to the correct molecular kinetic scheme and its robustness to noise. We then examined its performance on real experimental traces by analyzing macroscopic calcium-current traces elicited by membrane depolarization. SYSMOLE derived the correct, previously known molecular kinetic scheme describing the activation and inactivation of the underlying calcium channels and correctly identified the accepted mechanism of action of nifedipine, a calcium-channel blocker clinically used in patients with cardiovascular disease. Finally, we applied SYSMOLE to study the pharmacology of a new class of glutamate antipsychotic drugs and their crosstalk mechanism through a heteromeric complex of G protein-coupled receptors. Our results indicate that our methodology

  19. Hadronization of dense partonic matter

    Energy Technology Data Exchange (ETDEWEB)

    Fries, Rainer J [School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455 (United States)

    2006-12-15

    The parton recombination model has turned out to be a valuable tool to describe hadronization in high-energy heavy-ion collisions. I review the model and revisit recent progress in our understanding of hadron correlations. I also discuss higher Fock states in the hadrons, possible violations of the elliptic flow scaling and recombination effects in more dilute systems.

  20. Proton Radiography for the Diagnostics of a Dense Plasma

    Science.gov (United States)

    Barminova, H. Y.

    2017-12-01

    The possibility of using high-energy proton radiography for dense plasma diagnostics is discussed. The designed telescopic ion optical system for a proton radiography installation with a 1 GeV beam is presented. The schematic diagram of the proton microscope is given. It is shown that the estimate of spatial resolution for the installation obtained with consideration of chromatic aberrations of magnetic quadrupole lenses is limited from below.

  1. Studies of isotopic effects in the excited electronic states of molecular systems

    International Nuclear Information System (INIS)

    1982-01-01

    Rare gas halogen (RGH) lasers serve as convenient tools for a range of photophysical processes which exhibit isotope effects. This document summarizes progress in the production of molecular systems in their electronic excited states with the aid of RGH lasers, and the various isotopic effects one can study under these conditions. We conclude that the basic physical mechanisms involved in the isotopically sensitive characteristics of excited molecular electronic states are sufficiently selective to be useful in both the detection and separation of many atomic materials

  2. Advanced in study of cellular and molecular mechanisms of radiation effects on central nervous system

    International Nuclear Information System (INIS)

    Zhang Wei; Tu Yu; Wang Lili

    2008-01-01

    Along with radiation treatment extensively applied, radiation injury also is valued gradually. The effect of radiation to the cellular and molecular of central nervous system (CNS) is a complicated and moderately advanced process and the mechanism is remains incompletely clear yet. Inquiring into the possible mechanism of the CNS including the injury and the restoration of neuron, neuroglia cells, endotheliocyte cell and blood-brain barrier and the molecular level of change induced by radiation, so as to provide beneficial thought for preventing and curing radiation injury clinically. Some neuroprotective strategies are also addressed in the review. (authors)

  3. Energy transformation in molecular electronic systems: Comprehensive progress report, 1986--1989

    International Nuclear Information System (INIS)

    Kasha, M.

    1989-01-01

    Our research focuses on discovering the fundamental issues in proton-transfer and charge-transfer excitations in model systems, with an eye on which molecular systems will serve as the best guide to biological systems. This report addresses an intramolecular proton transfer classification system, proton-transfer potentials, proton-transfer spectroscopy of benzanilides, proton-transfer in aminosalicylates, proton-transfer in lumichrome, development of proton-transfer lasers, and triplet excitation enhancement via proton-transfer tunneling. 6 refs., 2 figs

  4. From molecular imaging to systems diagnostics: Time for another paradigm shift?

    Energy Technology Data Exchange (ETDEWEB)

    Li, King C.P. [Department of Radiology, Methodist Hospital, Weill Cornell Medical College, 6565 Fannin Street, D280 Houston, TX 77030 (United States)], E-mail: kli@tmhs.org

    2009-05-15

    The term 'Molecular Imaging' has hit the consciousness of radiologists only in the past decade although many of the concepts that molecular imaging encompasses has been practiced in biomedical imaging, especially in nuclear medicine, for many decades. Many new imaging techniques have allowed us to interrogate biologic events at the cellular and molecular level in vivo in four dimensions but the challenge now is to translate these techniques into clinical practice in a way that will enable us to revolutionize healthcare delivery. The purpose of this article is to introduce the term 'Systems Diagnostics' and examine how radiologists can become translators of disparate sources of information into medical decisions and therapeutic actions.

  5. Dynamic analysis of electron density in the course of the internal motion of molecular system

    International Nuclear Information System (INIS)

    Tachibana, A.; Hori, K.; Asai, Y.; Yamabe, T.

    1984-01-01

    The general dynamic aspect of electron density of a molecular system is studied on the basis of the general equation of the electron orbital which is formulated for the dynamic study of electronic motion. The newly defined electron orbital incorporates the dynamics of molecular vibration into the electronic structures. In this scheme, the change of electron distribution caused by excitation of vibrational state is defined as the ''dynamic electron transfer.'' The dynamic electron density is found to have the remarkable ''additive'' property. The time-dependent aspect of the dynamic electron redistribution is also analyzed on the basis of the ''coherent state.'' The new method relates the classical vibrational amplitude to the quantum number of the vibrational state. As a preliminary application of the present treatment, the dynamic electron densities of H 2 , HD, HT, HF, and HCl molecules are calculated by use of ab initio molecular orbital method

  6. Ab initio calculation of the sound velocity of dense hydrogen: implications for models of Jupiter

    NARCIS (Netherlands)

    Alavi, A.; Parrinello, M.; Frenkel, D.

    1995-01-01

    First-principles molecular dynamics simulations were used to calculate the sound velocity of dense hydrogen, and the results were compared with extrapolations of experimental data that currently conflict with either astrophysical models or data obtained from recent global oscillation measurements of

  7. Atomic and molecular sciences

    International Nuclear Information System (INIS)

    Lane, N.F.

    1989-01-01

    The theoretical atomic and molecular physics program at Rice University addresses basic questions about the collision dynamics of electrons, atoms, ions and molecules, emphasizing processes related to possible new energy technologies and other applications. The program focuses on inelastic collision processes that are important in understanding energy and ionization balance in disturbed gases and plasmas. Emphasis is placed on systems and processes where some experimental information is available or where theoretical results may be expected to stimulate new measurements. Examples of current projects include: excitation and charge-transfer processes; orientation and alignment of excited states following collisions; Rydberg atom collisions with atoms and molecules; Penning ionization and ion-pair formation in atom-atom collisions; electron-impact ionization in dense, high-temperature plasmas; electron-molecule collisions; and related topics

  8. Computing molecular fluctuations in biochemical reaction systems based on a mechanistic, statistical theory of irreversible processes.

    Science.gov (United States)

    Kulasiri, Don

    2011-01-01

    We discuss the quantification of molecular fluctuations in the biochemical reaction systems within the context of intracellular processes associated with gene expression. We take the molecular reactions pertaining to circadian rhythms to develop models of molecular fluctuations in this chapter. There are a significant number of studies on stochastic fluctuations in intracellular genetic regulatory networks based on single cell-level experiments. In order to understand the fluctuations associated with the gene expression in circadian rhythm networks, it is important to model the interactions of transcriptional factors with the E-boxes in the promoter regions of some of the genes. The pertinent aspects of a near-equilibrium theory that would integrate the thermodynamical and particle dynamic characteristics of intracellular molecular fluctuations would be discussed, and the theory is extended by using the theory of stochastic differential equations. We then model the fluctuations associated with the promoter regions using general mathematical settings. We implemented ubiquitous Gillespie's algorithms, which are used to simulate stochasticity in biochemical networks, for each of the motifs. Both the theory and the Gillespie's algorithms gave the same results in terms of the time evolution of means and variances of molecular numbers. As biochemical reactions occur far away from equilibrium-hence the use of the Gillespie algorithm-these results suggest that the near-equilibrium theory should be a good approximation for some of the biochemical reactions. © 2011 Elsevier Inc. All rights reserved.

  9. Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems.

    Science.gov (United States)

    Tanaka, Shigenori; Mochizuki, Yuji; Komeiji, Yuto; Okiyama, Yoshio; Fukuzawa, Kaori

    2014-06-14

    Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.

  10. Boundary Conditions for the Paleoenvironment: Chemical and Physical Processes in Dense Interstellar Clouds: Summary of Research

    Science.gov (United States)

    Irvine, William M.

    1999-01-01

    The basic theme of this program was the study of molecular complexity and evolution for the biogenic elements and compounds in interstellar clouds and in primitive solar system objects. Research included the detection and study of new interstellar and cometary molecules and investigation of reaction pathways for astrochemistry from a comparison of theory and observed molecular abundances. The latter includes studies of cold, dark clouds in which ion-molecule chemistry should predominate, searches for the effects of interchange of material between the gas and solid phases in interstellar clouds, unbiased spectral surveys of particular sources, and systematic investigation of the interlinked chemistry and physics of dense interstellar clouds. In addition, the study of comets has allowed a comparison between the chemistry of such minimally thermally processed objects and that of interstellar clouds, shedding light on the evolution of the biogenic elements during the process of solar system formation. One PhD dissertation on this research was completed by a graduate student at the University of Massachusetts. An additional 4 graduate students at the University of Massachusetts and 5 graduate students from other institutions participated in research supported by this grant, with 6 of these thus far receiving PhD degrees from the University of Massachusetts or their home institutions. Four postdoctoral research associates at the University of Massachusetts also participated in research supported by this grant, receiving valuable training.

  11. An analytic approach to 2D electronic PE spectra of molecular systems

    International Nuclear Information System (INIS)

    Szoecs, V.

    2011-01-01

    Graphical abstract: The three-pulse photon echo (3P-PE) spectra of finite molecular systems using direct calculation from electronic Hamiltonians allows peak classification from 3P-PE spectra dynamics. Display Omitted Highlights: → RWA approach to electronic photon echo. → A straightforward calculation of 2D electronic spectrograms in finite molecular systems. → Importance of population time dynamics in relation to inter-site coherent coupling. - Abstract: The three-pulse photon echo (3P-PE) spectra of finite molecular systems and simplified line broadening models is presented. The Fourier picture of a heterodyne detected three-pulse rephasing PE signal in the δ-pulse limit of the external field is derived in analytic form. The method includes contributions of one and two-excitonic states and allows direct calculation of Fourier PE spectrogram from corresponding Hamiltonian. As an illustration, the proposed treatment is applied to simple systems, e.g. 2-site two-level system (TLS) and n-site TLS model of photosynthetic unit. The importance of relation between Fourier picture of 3P-PE dynamics (corresponding to nonzero population time, T) and coherent inter-state coupling is emphasized.

  12. Calculation of Transport Coefficients in Dense Plasma Mixtures

    Science.gov (United States)

    Haxhimali, T.; Cabot, W. H.; Caspersen, K. J.; Greenough, J.; Miller, P. L.; Rudd, R. E.; Schwegler, E. R.

    2011-10-01

    We use classical molecular dynamics (MD) to estimate species diffusivity and viscosity in mixed dense plasmas. The Yukawa potential is used to describe the screened Coulomb interaction between the ions. This potential has been used widely, providing the basis for models of dense stellar materials, inertial confined plasmas, and colloidal particles in electrolytes. We calculate transport coefficients in equilibrium simulations using the Green- Kubo relation over a range of thermodynamic conditions including the viscosity and the self - diffusivity for each component of the mixture. The interdiffusivity (or mutual diffusivity) can then be related to the self-diffusivities by using a generalization of the Darken equation. We have also employed non-equilibrium MD to estimate interdiffusivity during the broadening of the interface between two regions each with a high concentration of either species. Here we present results for an asymmetric mixture between Ar and H. These can easily be extended to other plasma mixtures. A main motivation for this study is to develop accurate transport models that can be incorporated into the hydrodynamic codes to study hydrodynamic instabilities. We use classical molecular dynamics (MD) to estimate species diffusivity and viscosity in mixed dense plasmas. The Yukawa potential is used to describe the screened Coulomb interaction between the ions. This potential has been used widely, providing the basis for models of dense stellar materials, inertial confined plasmas, and colloidal particles in electrolytes. We calculate transport coefficients in equilibrium simulations using the Green- Kubo relation over a range of thermodynamic conditions including the viscosity and the self - diffusivity for each component of the mixture. The interdiffusivity (or mutual diffusivity) can then be related to the self-diffusivities by using a generalization of the Darken equation. We have also employed non-equilibrium MD to estimate interdiffusivity during

  13. Constitutive law of dense granular matter

    International Nuclear Information System (INIS)

    Hatano, Takahiro

    2010-01-01

    The frictional properties of dense granular matter under steady shear flow are investigated using numerical simulation. Shear flow tends to localize near the driving boundary unless the coefficient of restitution is close to zero and the driving velocity is small. The bulk friction coefficient is independent of shear rate in dense and slow flow, whereas it is an increasing function of shear rate in rapid flow. The coefficient of restitution affects the friction coefficient only in such rapid flow. Contrastingly, in dense and slow regime, the friction coefficient is independent of the coefficient of restitution and mainly determined by the elementary friction coefficient and the rotation of grains. It is found that the mismatch between the vorticity of flow and the angular frequency of grains plays a key role to the frictional properties of sheared granular matter.

  14. INTERACTIONS BETWEEN FORMING STARS AND DENSE GAS IN THE SMALL LOW-MASS CLUSTER CEDERBLAD 110

    Energy Technology Data Exchange (ETDEWEB)

    Ladd, E. F. [Department of Physics and Astronomy, Bucknell University, Lewisburg, PA 17837 (United States); Wong, T. [Department of Astronomy, University of Illinois, Urbana, IL 61801 (United States); Bourke, T. L. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Thompson, K. L., E-mail: ladd@bucknell.edu [Department of Physics and Astronomy, University of Kentucky, Lexington, KY 40506 (United States)

    2011-12-20

    We present observations of dense gas and outflow activity in the Cederblad 110 region of the Chamaeleon I dark cloud complex. The region contains nine forming low-mass stars in evolutionary stages ranging from Class 0 to Class II/III crowded into a 0.2 pc region with high surface density ({Sigma}{sub YSO} {approx} 150 pc{sup -2}). The analysis of our N{sub 2}H{sup +} (J = 1{yields}0) maps indicates the presence of 13 {+-} 3 solar masses of dense (n {approx} 10{sup 5} cm{sup -3}) gas in this region, much of which is unstable against gravitational collapse. The most unstable material is located near the Class 0 source MMS-1, which is almost certainly actively accreting material from its dense core. Smaller column densities of more stable dense gas are found toward the region's Class I sources, IRS 4, 11, and 6. Little or no dense gas is colocated with the Class II and III sources in the region. The outflow from IRS 4 is interacting with the dense core associated with MMS-1. The molecular component of the outflow, measured in the (J = 1{yields}0) line of {sup 12}CO, appears to be deflected by the densest part of the core, after which it appears to plow through some of the lower column density portions of the core. The working surface between the head of the outflow lobe and the dense core material can be seen in the enhanced velocity dispersion of the dense gas. IRS 2, the Class III source that produces the optical reflection nebula that gives the Cederblad 110 region its name, may also be influencing the dense gas in the region. A dust temperature gradient across the MMS-1 dense core is consistent with warming from IRS 2, and a sharp gradient in dense gas column density may be caused by winds from this source. Taken together, our data indicate that this region has been producing several young stars in the recent past, and that sources which began forming first are interacting with the remaining dense gas in the region, thereby influencing current and future star

  15. Time-dependent theoretical treatments of the dynamics of electrons and nuclei in molecular systems

    International Nuclear Information System (INIS)

    Deumens, E.; Diz, A.; Longo, R.; Oehrn, Y.

    1994-01-01

    An overview is presented of methods for time-dependent treatments of molecules as systems of electrons and nuclei. The theoretical details of these methods are reviewed and contrasted in the light of a recently developed time-dependent method called electron-nuclear dynamics. Electron-nuclear dynamics (END) is a formulation of the complete dynamics of electrons and nuclei of a molecular system that eliminates the necessity of constructing potential-energy surfaces. Because of its general formulation, it encompasses many aspects found in other formulations and can serve as a didactic device for clarifying many of the principles and approximations relevant in time-dependent treatments of molecular systems. The END equations are derived from the time-dependent variational principle applied to a chosen family of efficiently parametrized approximate state vectors. A detailed analysis of the END equations is given for the case of a single-determinantal state for the electrons and a classical treatment of the nuclei. The approach leads to a simple formulation of the fully nonlinear time-dependent Hartree-Fock theory including nuclear dynamics. The nonlinear END equations with the ab initio Coulomb Hamiltonian have been implemented at this level of theory in a computer program, ENDyne, and have been shown feasible for the study of small molecular systems. Implementation of the Austin Model 1 semiempirical Hamiltonian is discussed as a route to large molecular systems. The linearized END equations at this level of theory are shown to lead to the random-phase approximation for the coupled system of electrons and nuclei. The qualitative features of the general nonlinear solution are analyzed using the results of the linearized equations as a first approximation. Some specific applications of END are presented, and the comparison with experiment and other theoretical approaches is discussed

  16. MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems.

    Directory of Open Access Journals (Sweden)

    Sophie S Abby

    Full Text Available Biologists often wish to use their knowledge on a few experimental models of a given molecular system to identify homologs in genomic data. We developed a generic tool for this purpose.Macromolecular System Finder (MacSyFinder provides a flexible framework to model the properties of molecular systems (cellular machinery or pathway including their components, evolutionary associations with other systems and genetic architecture. Modelled features also include functional analogs, and the multiple uses of a same component by different systems. Models are used to search for molecular systems in complete genomes or in unstructured data like metagenomes. The components of the systems are searched by sequence similarity using Hidden Markov model (HMM protein profiles. The assignment of hits to a given system is decided based on compliance with the content and organization of the system model. A graphical interface, MacSyView, facilitates the analysis of the results by showing overviews of component content and genomic context. To exemplify the use of MacSyFinder we built models to detect and class CRISPR-Cas systems following a previously established classification. We show that MacSyFinder allows to easily define an accurate "Cas-finder" using publicly available protein profiles.MacSyFinder is a standalone application implemented in Python. It requires Python 2.7, Hmmer and makeblastdb (version 2.2.28 or higher. It is freely available with its source code under a GPLv3 license at https://github.com/gem-pasteur/macsyfinder. It is compatible with all platforms supporting Python and Hmmer/makeblastdb. The "Cas-finder" (models and HMM profiles is distributed as a compressed tarball archive as Supporting Information.

  17. Projective block Lanczos algorithm for dense, Hermitian eigensystems

    International Nuclear Information System (INIS)

    Webster, F.; Lo, G.C.

    1996-01-01

    Projection operators are used to effect open-quotes deflation by restrictionclose quotes and it is argued that this is an optimal Lanczos algorithm for memory minimization. Algorithmic optimization is constrained to dense, Hermitian eigensystems where a significant number of the extreme eigenvectors must be obtained reliably and completely. The defining constraints are operator algebra without a matrix representation and semi-orthogonalization without storage of Krylov vectors. other semi-orthogonalization strategies for Lanczos algorithms and conjugate gradient techniques are evaluated within these constraints. Large scale, sparse, complex numerical experiments are performed on clusters of magnetic dipoles, a quantum many-body system that is not block-diagonalizable. Plane-wave, density functional theory of beryllium clusters provides examples of dense complex eigensystems. Use of preconditioners and spectral transformations is evaluated in a preprocessor prior to a high accuracy self-consistent field calculation. 25 refs., 3 figs., 5 tabs

  18. Temperature Measurements of Dense Plasmas by Detailed Balance

    International Nuclear Information System (INIS)

    Holl, A; Redmer, R; Ropke, G; Reinholz, H; Thiele, R; Fortmann, C; Forster, E; Cao, L; Tschentscher, T; Toleikis, S; Glenzer, S H

    2006-01-01

    Plasmas at high electron densities of n e = 10 20 - 10 26 cm -3 and moderate temperatures T e = 1 - 20 eV are important for laboratory astrophysics, high energy density science and inertial confinement fusion. These plasmas are usually referred to as Warm Dense Matter (WDM) and are characterized by a coupling parameter of Λ ∼> 1 where correlations become important. The characterization of such plasmas is still a challenging task due to the lack of direct measurement techniques for temperatures and densities. They propose to measure the Thomson scattering spectrum of vacuum-UV radiation off density fluctuations in the plasma. Collective Thomson scattering provides accurate data for the electron temperature applying first principles. Further, this method takes advantage of the spectral asymmetry resulting from detailed balance and is independent of collisional effects in these dense systems

  19. Nucleon structure and properties of dense matter

    International Nuclear Information System (INIS)

    Kutschera, M.; Pethick, C.J.; Illinois Univ., Urbana, IL

    1988-01-01

    We consider the properties of dense matter in a framework of the Skyrme soliton model and the chiral bag model. The influence of the nucleon structure on the equation of state of dense matter is emphasized. We find that in both models the energy per unit volume is proportional to n 4/3 , n being the baryon number density. We discuss the properties of neutron stars with a derived equation of state. The role of many-body effects is investigated. The effect of including higher order terms in the chiral lagrangian is examined. The phase transition to quark matter is studied. 29 refs., 6 figs. (author)

  20. [Motivation and Emotional States: Structural Systemic, Neurochemical, Molecular and Cellular Mechanisms].

    Science.gov (United States)

    Bazyan, A S

    2016-01-01

    The structural, systemic, neurochemical, molecular and cellular mechanisms of organization and coding motivation and emotional states are describe. The GABA and glutamatergic synaptic systems of basal ganglia form a neural network and participate in the implementation of voluntary behavior. Neuropeptides, neurohormones and paracrine neuromodulators involved in the organization of motivation and emotional states, integrated with synaptic systems, controlled by neural networks and organizing goal-directed behavior. Structural centers for united and integrated of information in voluntary and goal-directed behavior are globus pallidus. Substantia nigra pars reticulata switches the information from corticobasal networks to thalamocortical networks, induces global dopaminergic (DA) signal and organize interaction of mesolimbic and nigostriatnoy DA systems controlled by prefrontal and motor cortex. Together with the motor cortex, substantia nigra displays information in the brainstem and spinal cord to implementation of behavior. Motivation states are formed in the interaction of neurohormonal and neuropeptide systems by monoaminergic systems of brain. Emotional states are formed by monoaminergic systems of the mid-brain, where the leading role belongs to the mesolimbic DA system. The emotional and motivation state of the encoded specific epigenetic molecular and chemical pattern of neuron.

  1. A molecular beam/quadrupole mass spectrometer system with synchronized beam modulation and digital waveform analysis

    Science.gov (United States)

    Pellett, G. L.; Adams, B. R.

    1983-01-01

    A performance evaluation is conducted for a molecular beam/mass spectrometer (MB/MS) system, as applied to a 1-30 torr microwave-discharge flow reactor (MWFR) used in the formation of the methylperoxy radical and a study of its subsequent destruction in the presence or absence of NO(x). The modulated MB/MS system is four-staged and differentially pumped. The results obtained by the MWFR study is illustrative of overall system performance, including digital waveform analysis; significant improvements over previous designs are noted in attainable S/N ratio, detection limit, and accuracy.

  2. Radiopharmaceuticals: nanoparticles like multi-functional systems for the obtaining in vivo of molecular images

    International Nuclear Information System (INIS)

    Ferro F, G.; Ramirez de la Cruz, F. M.; Ocampo G, B. E.; Morales A, E.; Santos C, C. L.; Mendoza S, A. N.

    2010-01-01

    The techniques of obtaining direct or indirect molecular images detect and register the space-temporary distribution of molecular or cellular processes for biochemical, biological, diagnostic and therapeutic applications. The advanced techniques of image like the nuclear magnetic resonance, the single photon emission computed tomography, the positron emission tomography and the images of optic fluorescence have been used successfully to detect these processes. On the other hand, the utility of the nanoparticles for any application is dependent of the physicochemical properties that present, being possible to modify their surface when making them react with different biomolecules what allows the formation of conjugates with specific molecular recognition. The joint of various protein molecules, peptides or oligonucleotides to the surface of a nanoparticle produce a multi-functional system able to increase the multivalent joints from the nanoparticles-biomolecules to their receivers for the obtaining of molecular images in vivo. The peptides stimulate, regulate or inhibit numerous functions of the life, acting mainly as information transmitters and activity coordinators of several tissues in the organism. The receivers of regulator peptides are over represented in numerous types of cancer cells and they are protein structures. These receivers have been used as white molecular of marked peptides, to locate primary malignant tumors and their metastasis, using the diagnostic techniques of molecular image mentioned above, which consist basically on the radio peptides use and conjugated peptides to fluoro chromes, to metallic nanoparticles and nano crystals. A summary of the work is presented carried out by the personnel of the Radio-active Materials and Chemistry Departments of the Instituto Nacional de Investigaciones Nucleares in this field. (Author)

  3. Potentiometric investigations of molecular heteroconjugation equilibria of substituted phenol+n-butylamine systems in dimethyl sulfoxide

    Energy Technology Data Exchange (ETDEWEB)

    Czaja, MaIgorzata [Department of General Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland); Baginska, Katarzyna [Department of General Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland); Kozak, Anna [Department of General Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland); Makowski, Mariusz [Department of General Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland); Chmurzynski, Lech [Department of General Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland)]. E-mail: lech@chem.univ.gda.pl

    2005-08-15

    Molecular heteroconjugation constants, K{sub BHA}{sup DMSO} and K{sub AHB}{sup DMSO}, expressed as their logarithms, have been determined by potentiometric titration for eleven substituted phenol+n-butylamine systems in a polar protophilic aprotic solvent, dimethyl sulfoxide (DMSO). An increasing tendency towards molecular heteroconjugation in these systems without proton transfer has been found with increasing pK{sub a}{sup DMSO} (HA), i.e., with decreasing phenol acidity. Moreover, a linear correlation has been established between the determined lgK{sub BHA}{sup DMSO} values and pK{sub a}{sup DMSO} (HA). Furthermore, overall stability constants, lgK{sub o}{sup DMSO}, could be correlated linearly with pK{sub a}{sup DMSO} (HA) values.

  4. Hybrid artificial photosynthetic systems comprising semiconductors as light harvesters and biomimetic complexes as molecular cocatalysts.

    Science.gov (United States)

    Wen, Fuyu; Li, Can

    2013-11-19

    Solar fuel production through artificial photosynthesis may be a key to generating abundant and clean energy, thus addressing the high energy needs of the world's expanding population. As the crucial components of photosynthesis, the artificial photosynthetic system should be composed of a light harvester (e.g., semiconductor or molecular dye), a reduction cocatalyst (e.g., hydrogenase mimic, noble metal), and an oxidation cocatalyst (e.g., photosystem II mimic for oxygen evolution from water oxidation). Solar fuel production catalyzed by an artificial photosynthetic system starts from the absorption of sunlight by the light harvester, where charge separation takes place, followed by a charge transfer to the reduction and oxidation cocatalysts, where redox reaction processes occur. One of the most challenging problems is to develop an artificial photosynthetic solar fuel production system that is both highly efficient and stable. The assembly of cocatalysts on the semiconductor (light harvester) not only can facilitate the charge separation, but also can lower the activation energy or overpotential for the reactions. An efficient light harvester loaded with suitable reduction and oxidation cocatalysts is the key for high efficiency of artificial photosynthetic systems. In this Account, we describe our strategy of hybrid photocatalysts using semiconductors as light harvesters with biomimetic complexes as molecular cocatalysts to construct efficient and stable artificial photosynthetic systems. We chose semiconductor nanoparticles as light harvesters because of their broad spectral absorption and relatively robust properties compared with a natural photosynthesis system. Using biomimetic complexes as cocatalysts can significantly facilitate charge separation via fast charge transfer from the semiconductor to the molecular cocatalysts and also catalyze the chemical reactions of solar fuel production. The hybrid photocatalysts supply us with a platform to study the

  5. Bayesian quantification of thermodynamic uncertainties in dense gas flows

    International Nuclear Information System (INIS)

    Merle, X.; Cinnella, P.

    2015-01-01

    A Bayesian inference methodology is developed for calibrating complex equations of state used in numerical fluid flow solvers. Precisely, the input parameters of three equations of state commonly used for modeling the thermodynamic behavior of the so-called dense gas flows, – i.e. flows of gases characterized by high molecular weights and complex molecules, working in thermodynamic conditions close to the liquid–vapor saturation curve – are calibrated by means of Bayesian inference from reference aerodynamic data for a dense gas flow over a wing section. Flow thermodynamic conditions are such that the gas thermodynamic behavior strongly deviates from that of a perfect gas. In the aim of assessing the proposed methodology, synthetic calibration data – specifically, wall pressure data – are generated by running the numerical solver with a more complex and accurate thermodynamic model. The statistical model used to build the likelihood function includes a model-form inadequacy term, accounting for the gap between the model output associated to the best-fit parameters and the true phenomenon. Results show that, for all of the relatively simple models under investigation, calibrations lead to informative posterior probability density distributions of the input parameters and improve the predictive distribution significantly. Nevertheless, calibrated parameters strongly differ from their expected physical values. The relationship between this behavior and model-form inadequacy is discussed. - Highlights: • Development of a Bayesian inference procedure for calibrating dense-gas flow solvers. • Complex thermodynamic models calibrated by using aerodynamic data for the flow. • Preliminary Sobol analysis used to reduce parameter space. • Piecewise polynomial surrogate model constructed to reduce computational cost. • Calibration results show the crucial role played by model-form inadequacies

  6. Quantitative computational models of molecular self-assembly in systems biology.

    Science.gov (United States)

    Thomas, Marcus; Schwartz, Russell

    2017-05-23

    Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.

  7. A Pilot-Scale System for Carbon Molecular Sieve Hollow Fiber Membrane Manufacturing

    KAUST Repository

    Karvan, O.

    2012-12-21

    Carbon molecular sieve (CMS) membranes offer advantages over traditional polymeric membrane materials, but scale-up of manufacturing systems has not received much attention. In the recent decade, there has been a dramatic increase in fundamental research on these materials with a variety of applications being studied. The results from a pilot-scale CMS production system are presented. This system was designed based on extensive laboratory research, and hollow fiber membranes produced in this system show similar performance compared to membranes produced using a smaller bench-scale system. After optimizing the system design, a 93% recovery of the precursor fibers for use in membrane module preparation were obtained. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Dense high temperature ceramic oxide superconductors

    Science.gov (United States)

    Landingham, Richard L.

    1993-01-01

    Dense superconducting ceramic oxide articles of manufacture and methods for producing these articles are described. Generally these articles are produced by first processing these superconducting oxides by ceramic processing techniques to optimize materials properties, followed by reestablishing the superconducting state in a desired portion of the ceramic oxide composite.

  9. Dense high-temperature plasma transport processes

    International Nuclear Information System (INIS)

    Giniyatova, Sh.G.

    2002-01-01

    In this work the transport processes in dense high-temperature semiclassical plasma are studied on the base of the kinetic equation, where the semiclassical potential was used, in its collision integral. The coefficient of plasma electrical conductivity, viscosity and thermal conductivity were received. There were compared with the other authors' results. The Grad's method was used obtaining of viscosity and thermal coefficients. (author)

  10. The electronic pressure in dense plasmas

    International Nuclear Information System (INIS)

    Pozwolski, A.E.

    1982-01-01

    A thermodynamic calculation of the electronic pressure in a dense plasma is given. Approximations involved by the use of the Debye length are avoided, so the above theory remains valid even if the Debye length is smaller than the interionic distance. (author)

  11. APT: Action localization Proposals from dense Trajectories

    NARCIS (Netherlands)

    van Gemert, J.C.; Jain, M.; Gati, E.; Snoek, C.G.M.; Xie, X.; Jones, M.W.; Tam, G.K.L.

    2015-01-01

    This paper is on action localization in video with the aid of spatio-temporal proposals. To alleviate the computational expensive video segmentation step of existing proposals, we propose bypassing the segmentations completely by generating proposals directly from the dense trajectories used to

  12. Dense Alternating Sign Matrices and Extensions

    Czech Academy of Sciences Publication Activity Database

    Fiedler, Miroslav; Hall, F.J.; Stroev, M.

    2014-01-01

    Roč. 444, 1 March (2014), s. 219-226 ISSN 0024-3795 Institutional support: RVO:67985807 Keywords : alternating sign matrix * dense matrix * totally unimodular matrix * combined matrix * generalized complementary basic matrix Subject RIV: BA - General Mathematics Impact factor: 0.939, year: 2014

  13. Coalescence preference in dense packing of bubbles

    Science.gov (United States)

    Kim, Yeseul; Gim, Bopil; Gim, Bopil; Weon, Byung Mook

    2015-11-01

    Coalescence preference is the tendency that a merged bubble from the contact of two original bubbles (parent) tends to be near to the bigger parent. Here, we show that the coalescence preference can be blocked by densely packing of neighbor bubbles. We use high-speed high-resolution X-ray microscopy to clearly visualize individual coalescence phenomenon which occurs in micro scale seconds and inside dense packing of microbubbles with a local packing fraction of ~40%. Previous theory and experimental evidence predict a power of -5 between the relative coalescence position and the parent size. However, our new observation for coalescence preference in densely packed microbubbles shows a different power of -2. We believe that this result may be important to understand coalescence dynamics in dense packing of soft matter. This work (NRF-2013R1A22A04008115) was supported by Mid-career Researcher Program through NRF grant funded by the MEST and also was supported by Ministry of Science, ICT and Future Planning (2009-0082580) and by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry and Education, Science and Technology (NRF-2012R1A6A3A04039257).

  14. Probing dense matter with strange hadrons

    CERN Document Server

    Rafelski, Johann; Rafelski, Johann; Letessier, Jean

    2002-01-01

    Analysis of hadron production experimental data allows to understand the properties of the dense matter fireball produced in relativistic heavy ion collisions. We interpret the analysis results and argue that color deconfined state has been formed at highest CERN-SPS energies and at BNL-RHIC.

  15. Synthesis of Heteroaromatic Compounds by Oxidative Aromatization Using an Activated Carbon/Molecular Oxygen System

    Directory of Open Access Journals (Sweden)

    Masahiko Hayashi

    2009-08-01

    Full Text Available A variety of heteroaromatic compounds, such as substituted pyridines, pyrazoles, indoles, 2-substituted imidazoles, 2-substituted imidazoles, 2-arylbenzazoles and pyrimidin-2(1H-ones are synthesized by oxidative aromatization using the activated carbon and molecular oxygen system. Mechanistic study focused on the role of activated carbon in the synthesis of 2-arylbenzazoles is also discussed. In the final section, we will disclose the efficient synthesis of substituted 9,10-anthracenes via oxidative aromatization.

  16. AUTOMR: An automatic processing program system for the molecular replacement method

    International Nuclear Information System (INIS)

    Matsuura, Yoshiki

    1991-01-01

    An automatic processing program system of the molecular replacement method AUTMR is presented. The program solves the initial model of the target crystal structure using a homologous molecule as the search model. It processes the structure-factor calculation of the model molecule, the rotation function, the translation function and the rigid-group refinement successively in one computer job. Test calculations were performed for six protein crystals and the structures were solved in all of these cases. (orig.)

  17. Gene expression-based molecular diagnostic system for malignant gliomas is superior to histological diagnosis.

    Science.gov (United States)

    Shirahata, Mitsuaki; Iwao-Koizumi, Kyoko; Saito, Sakae; Ueno, Noriko; Oda, Masashi; Hashimoto, Nobuo; Takahashi, Jun A; Kato, Kikuya

    2007-12-15

    Current morphology-based glioma classification methods do not adequately reflect the complex biology of gliomas, thus limiting their prognostic ability. In this study, we focused on anaplastic oligodendroglioma and glioblastoma, which typically follow distinct clinical courses. Our goal was to construct a clinically useful molecular diagnostic system based on gene expression profiling. The expression of 3,456 genes in 32 patients, 12 and 20 of whom had prognostically distinct anaplastic oligodendroglioma and glioblastoma, respectively, was measured by PCR array. Next to unsupervised methods, we did supervised analysis using a weighted voting algorithm to construct a diagnostic system discriminating anaplastic oligodendroglioma from glioblastoma. The diagnostic accuracy of this system was evaluated by leave-one-out cross-validation. The clinical utility was tested on a microarray-based data set of 50 malignant gliomas from a previous study. Unsupervised analysis showed divergent global gene expression patterns between the two tumor classes. A supervised binary classification model showed 100% (95% confidence interval, 89.4-100%) diagnostic accuracy by leave-one-out cross-validation using 168 diagnostic genes. Applied to a gene expression data set from a previous study, our model correlated better with outcome than histologic diagnosis, and also displayed 96.6% (28 of 29) consistency with the molecular classification scheme used for these histologically controversial gliomas in the original article. Furthermore, we observed that histologically diagnosed glioblastoma samples that shared anaplastic oligodendroglioma molecular characteristics tended to be associated with longer survival. Our molecular diagnostic system showed reproducible clinical utility and prognostic ability superior to traditional histopathologic diagnosis for malignant glioma.

  18. A field-deployable mobile molecular diagnostic system for malaria at the point of need.

    Science.gov (United States)

    Choi, Gihoon; Song, Daniel; Shrestha, Sony; Miao, Jun; Cui, Liwang; Guan, Weihua

    2016-11-01

    In response to the urgent need of a field-deployable and highly sensitive malaria diagnosis, we developed a standalone, "sample-in-answer-out" molecular diagnostic system (AnyMDx) to enable quantitative molecular analysis of blood-borne malaria in low resource areas. The system consists of a durable battery-powered analyzer and a disposable microfluidic compact disc loaded with reagents ready for use. A low power thermal module and a novel fluorescence-sensing module are integrated into the analyzer for real-time monitoring of loop-mediated isothermal nucleic acid amplification (LAMP) of target parasite DNA. With 10 μL of raw blood sample, the AnyMDx system automates the nucleic acid sample preparation and subsequent LAMP and real-time detection. Under laboratory conditions with whole-blood samples spiked with cultured Plasmodium falciparum, we achieved a detection limit of ∼0.6 parasite per μL, much lower than those for the conventional microscopy and rapid diagnostic tests (∼50-100 parasites per μL). The turnaround time from sample to answer is less than 40 minutes. The AnyMDx is user-friendly requiring minimal technological training. The analyzer and the disposable reagent compact discs are cost-effective, making AnyMDx a potential tool for malaria molecular diagnosis under field settings for malaria elimination.

  19. Resolution of identity approximation for the Coulomb term in molecular and periodic systems

    Science.gov (United States)

    Burow, Asbjörn M.; Sierka, Marek; Mohamed, Fawzi

    2009-12-01

    A new formulation of resolution of identity approximation for the Coulomb term is presented, which uses atom-centered basis and auxiliary basis functions and treats molecular and periodic systems of any dimensionality on an equal footing. It relies on the decomposition of an auxiliary charge density into charged and chargeless components. Applying the Coulomb metric under periodic boundary conditions constrains the explicit form of the charged part. The chargeless component is determined variationally and converged Coulomb lattice sums needed for its determination are obtained using chargeless linear combinations of auxiliary basis functions. The lattice sums are partitioned in near- and far-field portions which are treated through an analytical integration scheme employing two- and three-center electron repulsion integrals and multipole expansions, respectively, operating exclusively in real space. Our preliminary implementation within the TURBOMOLE program package demonstrates consistent accuracy of the method across molecular and periodic systems. Using common auxiliary basis sets the errors of the approximation are small, in average about 20 μhartree per atom, for both molecular and periodic systems.

  20. High Molecular Weight Isoforms of Growth Hormone In Cells of the Immune System

    Science.gov (United States)

    Weigent, Douglas A.

    2013-01-01

    A substantial body of research exists to support the idea that cells of the immune system produce growth hormone (GH). However, the structure and mechanism of action of lymphocyte-derived GH continues to remain largely unknown. Here we present the results of Western analysis of whole cell extracts showing that different molecular weight isoforms of GH of approximately 100 kDa, 65 kDa, and 48 kDa can be detected in primary mouse cells of the immune system and in the mouse EL4 cell line. The identity of the 65 kDa and 48 kDa isoforms of GH were confirmed by mass spectrometry. The various isoforms were detected in both enriched T and B spleen cell populations. The large molecular weight isoform appears to reside primarily in the cytoplasm whereas the lower molecular weight 65 kDa and 48 kDa isoforms were detected primarily in the nucleus. These results also suggest that GH isoforms are induced by oxidative stress. In EL4 cells overexpressing GH, the expression of luciferase controlled by a promoter containing the antioxidant response element is increased almost three-fold above control. The data suggest that the induction of isoforms of the GH molecule in cells of the immune system may be an important mechanism of adaptation and/or protection of lymphoid cells under conditions of oxidative stress. PMID:21741628

  1. Rheology of dense suspensions of non colloidal particles

    Science.gov (United States)

    Guazzelli, Élisabeth

    2017-06-01

    Dense suspensions are materials with broad applications both in industrial processes (e.g. waste disposal, concrete, drilling muds, metalworking chip transport, and food processing) and in natural phenomena (e.g. flows of slurries, debris, and lava). Despite its long research history and its practical relevance, the mechanics of dense suspensions remain poorly understood. The major difficulty is that the grains interact both by hydrodynamic interactions through the liquid and by mechanical contact. These systems thus belong to an intermediate regime between pure suspensions and granular flows. We show that we can unify suspension and granular rheology under a common framework by transferring the frictional approach of dry granular media to wet suspensions of spherical particles. We also discuss non-Newtonian behavior such as normal-stress differences and shear-induced migration. Beyond the classical problem of dense suspension of hard spheres which is far from being completely resolved, there are also entirely novel avenues of study concerning more complex mixtures of particles and fluids such as those involving other types of particles (e.g. fibers) or non-Newtonian fluids that we will also address.

  2. Rheology of dense suspensions of non colloidal particles

    Directory of Open Access Journals (Sweden)

    Guazzelli Élisabeth

    2017-01-01

    Full Text Available Dense suspensions are materials with broad applications both in industrial processes (e.g. waste disposal, concrete, drilling muds, metalworking chip transport, and food processing and in natural phenomena (e.g. flows of slurries, debris, and lava. Despite its long research history and its practical relevance, the mechanics of dense suspensions remain poorly understood. The major difficulty is that the grains interact both by hydrodynamic interactions through the liquid and by mechanical contact. These systems thus belong to an intermediate regime between pure suspensions and granular flows. We show that we can unify suspension and granular rheology under a common framework by transferring the frictional approach of dry granular media to wet suspensions of spherical particles. We also discuss non-Newtonian behavior such as normal-stress differences and shear-induced migration. Beyond the classical problem of dense suspension of hard spheres which is far from being completely resolved, there are also entirely novel avenues of study concerning more complex mixtures of particles and fluids such as those involving other types of particles (e.g. fibers or non-Newtonian fluids that we will also address.

  3. Molecular machines in living cells. Seibutsu no bunshi kikai to sono system

    Energy Technology Data Exchange (ETDEWEB)

    Osawa, F. (Aichi Inst. of Tech., Nagoya (Japan))

    1992-12-20

    At first, flagellar motors of bacteria are reviewed as a typical example of molecular machines in living cells. A rotational motor is embedded in the cell membrane at the root of the flagellum. The driving power of the rotation is the flow of hydrogen ion from the inside to the outside of the cell. In a normal state of a bacterium, potential difference of about 0.2 V is produced by the ion pump existing in the cell membrane. A molecular motor of sliding motion of muscle attracts the attention on the relation of the input and output of the molecular motor. The mechanism of the smooth motion without fluctuation in the fluctuated environment and the fluctuated input is unknown. Next, the motion of Paramecium is discussed as an example of a system composed of a number of molecular machines. Paramecium moves to a place of a suitable temperature when placed in a water tank with temperature gradient, however, it does not stop the motion at the place of the suitable temperature and increases a probability to change the direction when leaving, that is it takes a method of indirect probabilistic control. 12 refs., 8 figs.

  4. On the theory of frequency-shifted secondary emission of light-harvesting molecular systems

    International Nuclear Information System (INIS)

    Morozov, V.A.

    2001-01-01

    The expressions are obtained for the intensity of the frequency-shifted secondary emission of a chromophore playing the role of a reaction center in the simplest model three-chromophore molecular 'light-harvesting' antenna, which is constructed and oriented in space so that the incident photons coherently excite two of its chromophore pigments. The quantum-field formalism was used, which takes into account the generalized (quantum-electrodynamic) dipole-dipole, as well as radiative and nonradiative dissipative interactions between pigments and the reaction center of the antenna. The special features of the excitation spectrum of the Raman scattering line and the frequency-shifted fluorescence spectrum of the reaction center of the molecular antenna under study are discussed. A comparison of the expressions obtained for the excitation and fluorescence spectra and with the corresponding expressions obtained for a bichromophore molecular system, which differs from a three-chromophore antenna by the absence of one of the pigments, revealed the properties of the mechanism of action of light-harvesting molecular antennas that have not been found earlier. In particular, it is shown that 'the light-harvesting' caused by the collective dissipative interactions of pigments with the reaction center of the antenna can substantially exceed a sum of contributions from separate pigments

  5. An approach towards understanding the structure of complex molecular systems: the case of lower aliphatic alcohols

    Energy Technology Data Exchange (ETDEWEB)

    Vrhovsek, Aleksander; Gereben, Orsolya; Pothoczki, Szilvia; Pusztai, Laszlo [Research Institute for Solid State Physics and Optics, Hungarian Academy of Sciences, H-1525 Budapest, PO Box 49 (Hungary); Tomsic, Matija; Jamnik, Andrej [Faculty of Chemistry and Chemical Technology, University of Ljubljana, Askerceva 5, SI-1001 Ljubljana (Slovenia); Kohara, Shinji, E-mail: aleksander.vrhovsek@gmail.co [Research and Utilization Division, Japan Synchrotron Radiation Research Institute (JASRI, SPring-8), 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan)

    2010-10-13

    An extensive study of liquid aliphatic alcohols methanol, ethanol, and propanol, applying reverse Monte Carlo modelling as a method of interpretation of diffraction data, is presented. The emphasis is on the evaluation of several computational strategies in view of their suitability to obtain high quality molecular models via the reverse Monte Carlo procedure. A consistent set of distances of closest approach and fixed neighbour constraints applicable to all three investigated systems was developed. An all-atom description is compared with a united-atom approach. The potentialities of employment of neutron diffraction data of completely deuterated and isotopically substituted samples, x-ray diffraction data, and results of either molecular dynamics or Monte Carlo calculations were investigated. Results show that parallel application of x-ray and neutron diffraction data, the latter being from completely deuterated samples, within an all-atom reverse Monte Carlo procedure is the most successful strategy towards attaining reliable, detailed, and well-structured molecular models, especially if the models are subsequently refined with the results of molecular dynamics simulations.

  6. Net emission coefficient for CO–H2 thermal plasmas with the consideration of molecular systems

    International Nuclear Information System (INIS)

    Billoux, T.; Cressault, Y.; Gleizes, A.

    2015-01-01

    This paper deals with the calculation of net emission coefficients (NECs) for CO–H 2 thermal plasmas. This task required the elaboration of a complete spectroscopic database including atoms and molecules formed by carbon, oxygen and hydrogen elements. We have used a systematic line by line method to calculate all the main radiative contributions which are the atomic and molecular continua, the atomic lines and the molecular (diatomic and polyatomic) lines. The main diatomic electronic systems for CO–H 2 plasmas and the triatomic molecular bands were considered. We present some variations of the net emission coefficient versus temperature, for various pressures and for two relative proportions of the components. The role of the diatomic molecules is important at temperatures lower than 5000 K whereas the net emission coefficient presents an unusual peak at temperature around 1000 K, due to the presence of the CO 2 molecule presenting a strong infrared radiation. Finally, the results show that the NEC slightly depends on the relative proportion of CO and H 2 . - highlights: • We calculate radiative losses from CO–H 2 thermal plasmas. • We use the up-to-date atomic and molecular databases. • The influence of CO 2 molecule is very important at low temperature. • The relative maximum of the net emission coefficient at low temperature is unusual

  7. Characterization of the hydrogen bond in molecular systems of biological interest by neutron scattering

    International Nuclear Information System (INIS)

    Cavillon, F.

    2004-10-01

    This work presents a methodology for the analysis of the scattering spectra of neutrons on molecular liquids. This method is based on the adjustment of the molecular form factor concerning great momentum transfer. The subtraction of the intra-molecular contributions gives access to information on inter-molecular interactions such as the hydrogen bond. 3 systems with increasing levels of difficulty have been studied: the ammonia molecule, the N-methyl-formamide (NMF) and the N-methyl-acetamide (NMA). The value we get for the N-D intermolecular distance of the liquid ammonia molecule is 1.7 angstrom, this value is different from the value generally admitted (2.3 angstrom) but we have validated it by studying the isotopic substitution N 14 /N 15 . The adjustment to the NMF is obtained with a good accuracy but the characterization of the hydrogen bound is more delicate to infer. A preliminary study of the NMA molecule shows that this method can give relevant results on complex molecules

  8. From Molecular Classification to Targeted Therapeutics: The Changing Face of Systemic Therapy in Metastatic Gastroesophageal Cancer

    Directory of Open Access Journals (Sweden)

    Adrian Murphy

    2015-01-01

    Full Text Available Histological classification of adenocarcinoma or squamous cell carcinoma for esophageal cancer or using the Lauren classification for intestinal and diffuse type gastric cancer has limited clinical utility in the management of advanced disease. Germline mutations in E-cadherin (CDH1 or mismatch repair genes (Lynch syndrome were identified many years ago but given their rarity, the identification of these molecular alterations does not substantially impact treatment in the advanced setting. Recent molecular profiling studies of upper GI tumors have added to our knowledge of the underlying biology but have not led to an alternative classification system which can guide clinician’s therapeutic decisions. Recently the Cancer Genome Atlas Research Network has proposed four subtypes of gastric cancer dividing tumors into those positive for Epstein-Barr virus, microsatellite unstable tumors, genomically stable tumors, and tumors with chromosomal instability. Unfortunately to date, many phase III clinical trials involving molecularly targeted agents have failed to meet their survival endpoints due to their use in unselected populations. Future clinical trials should utilize molecular profiling of individual tumors in order to determine the optimal use of targeted therapies in preselected patients.

  9. Intelligent Techniques Using Molecular Data Analysis in Leukaemia: An Opportunity for Personalized Medicine Support System.

    Science.gov (United States)

    Banjar, Haneen; Adelson, David; Brown, Fred; Chaudhri, Naeem

    2017-01-01

    The use of intelligent techniques in medicine has brought a ray of hope in terms of treating leukaemia patients. Personalized treatment uses patient's genetic profile to select a mode of treatment. This process makes use of molecular technology and machine learning, to determine the most suitable approach to treating a leukaemia patient. Until now, no reviews have been published from a computational perspective concerning the development of personalized medicine intelligent techniques for leukaemia patients using molecular data analysis. This review studies the published empirical research on personalized medicine in leukaemia and synthesizes findings across studies related to intelligence techniques in leukaemia, with specific attention to particular categories of these studies to help identify opportunities for further research into personalized medicine support systems in chronic myeloid leukaemia. A systematic search was carried out to identify studies using intelligence techniques in leukaemia and to categorize these studies based on leukaemia type and also the task, data source, and purpose of the studies. Most studies used molecular data analysis for personalized medicine, but future advancement for leukaemia patients requires molecular models that use advanced machine-learning methods to automate decision-making in treatment management to deliver supportive medical information to the patient in clinical practice.

  10. Molecular stratification and precision medicine in systemic sclerosis from genomic and proteomic data.

    Science.gov (United States)

    Martyanov, Viktor; Whitfield, Michael L

    2016-01-01

    The goal of this review is to summarize recent advances into the pathogenesis and treatment of systemic sclerosis (SSc) from genomic and proteomic studies. Intrinsic gene expression-driven molecular subtypes of SSc are reproducible across three independent datasets. These subsets are a consistent feature of SSc and are found in multiple end-target tissues, such as skin and esophagus. Intrinsic subsets as well as baseline levels of molecular target pathways are potentially predictive of clinical response to specific therapeutics, based on three recent clinical trials. A gene expression-based biomarker of modified Rodnan skin score, a measure of SSc skin severity, can be used as a surrogate outcome metric and has been validated in a recent trial. Proteome analyses have identified novel biomarkers of SSc that correlate with SSc clinical phenotypes. Integrating intrinsic gene expression subset data, baseline molecular pathway information, and serum biomarkers along with surrogate measures of modified Rodnan skin score provides molecular context in SSc clinical trials. With validation, these approaches could be used to match patients with the therapies from which they are most likely to benefit and thus increase the likelihood of clinical improvement.

  11. Synthesis of Dense and Chiral Dendritic Polyols Using Glyconanosynthon Scaffolds

    Directory of Open Access Journals (Sweden)

    Tze Chieh Shiao

    2016-04-01

    Full Text Available Most classical dendrimers are frequently built-up from identical repeating units of low valency (usually AB2 monomers. This strategy necessitates several generations to achieve a large number of surface functionalities. In addition, these typical monomers are achiral. We propose herein the use of sugar derivatives consisting of several and varied functionalities with their own individual intrinsic chirality as both scaffolds/core as well as repeating units. This approach allows the construction of chiral, dense dendrimers with a large number of surface groups at low dendrimer generations. Perpropargylated β-D-glucopyranoside, serving as an A5 core, together with various derivatives, such as 2-azidoethyl tetra-O-allyl-β-D-glucopyranoside, serving as an AB4 repeating moiety, were utilized to construct chiral dendrimers using “click chemistry” (CuAAC reaction. These were further modified by thiol-ene and thiol-yne click reactions with alcohols to provide dendritic polyols. Molecular dynamic simulation supported the assumption that the resulting polyols have a dense structure.

  12. Stochastic entangled chain dynamics of dense polymer solutions.

    Science.gov (United States)

    Kivotides, Demosthenes; Wilkin, S Louise; Theofanous, Theo G

    2010-10-14

    We propose an adjustable-parameter-free, entangled chain dynamics model of dense polymer solutions. The model includes the self-consistent dynamics of molecular chains and solvent by describing the former via coarse-grained polymer dynamics that incorporate hydrodynamic interaction effects, and the latter via the forced Stokes equation. Real chain elasticity is modeled via the inclusion of a Pincus regime in the polymer's force-extension curve. Excluded volume effects are taken into account via the combined action of coarse-grained intermolecular potentials and explicit geometric tracking of chain entanglements. We demonstrate that entanglements are responsible for a new (compared to phantom chain dynamics), slow relaxation mode whose characteristic time scale agrees very well with experiment. Similarly good agreement between theory and experiment is also obtained for the equilibrium chain size. We develop methods for the solution of the model in periodic flow domains and apply them to the computation of entangled polymer solutions in equilibrium. We show that the number of entanglements Π agrees well with the number of entanglements expected on the basis of tube theory, satisfactorily reproducing the latter's scaling of Π with the polymer volume fraction φ. Our model predicts diminishing chain size with concentration, thus vindicating Flory's suggestion of excluded volume effects screening in dense solutions. The predicted scaling of chain size with φ is consistent with the heuristic, Flory theory based value.

  13. Chemical potential calculations in dense liquids using metadynamics

    Science.gov (United States)

    Perego, C.; Giberti, F.; Parrinello, M.

    2016-10-01

    The calculation of chemical potential has traditionally been a challenge in atomistic simulations. One of the most used approaches is Widom's insertion method in which the chemical potential is calculated by periodically attempting to insert an extra particle in the system. In dense systems this method fails since the insertion probability is very low. In this paper we show that in a homogeneous fluid the insertion probability can be increased using metadynamics. We test our method on a supercooled high density binary Lennard-Jones fluid. We find that we can obtain efficiently converged results even when Widom's method fails.

  14. The effects of ecstasy on neurotransmitter systems: a review on the findings of molecular imaging studies.

    Science.gov (United States)

    Vegting, Yosta; Reneman, Liesbeth; Booij, Jan

    2016-10-01

    Ecstasy is a commonly used psychoactive drug with 3,4-methylenedioxymethamphetamine (MDMA) as the main content. Importantly, it has been suggested that use of MDMA may be neurotoxic particularly for serotonergic (5-hydroxytryptamine (5-HT)) neurons. In the past decades, several molecular imaging studies examined directly in vivo the effects of ecstasy/MDMA on neurotransmitter systems. The objective of the present study is to review the effects of ecstasy/MDMA on neurotransmitter systems as assessed by molecular imaging studies in small animals, non-human primates and humans. A search in PubMed was performed. Eighty-eight articles were found on which inclusion and exclusion criteria were applied. Thirty-three studies met the inclusion criteria; all were focused on the 5-HT or dopamine (DA) system. Importantly, 9 out of 11 of the animal studies that examined the effects of MDMA on 5-HT transporter (SERT) availability showed a significant loss of binding potential. In human studies, this was the case for 14 out of 16 studies, particularly in heavy users. In abstinent users, significant recovery of SERT binding was found over time. Most imaging studies in humans that focused on the DA system did not find any significant effect of ecstasy/MDMA use. Preclinical and clinical molecular imaging studies on the effects of ecstasy/MDMA use/administration on neurotransmitter systems show quite consistent alterations of the 5-HT system. Particularly, in human studies, loss of SERT binding was observed in heavy ecstasy users, which might reflect 5-HT neurotoxicity, although alternative explanations (e.g. down-regulation of the SERT) cannot be excluded.

  15. Reclamation of a molecular beam epitaxy system and conversion for oxide epitaxy

    International Nuclear Information System (INIS)

    Carver, Alexander G.; Henderson, Walter; Doolittle, W. Alan

    2008-01-01

    An early 1980s vintage molecular beam epitaxy system, a Varian Gen II system, originally used for HgCdTe epitaxy, was converted into a system capable of growing thin-film complex metal oxides. The nature of some of the alternative oxides requires a thorough cleaning and, in some cases, complete replacement of system components. Details are provided regarding the chemistry of the etchants used, safety requirements for properly handling, and disposal of large quantities of etchants and etch by-products, and components that can be reused versus components that require replacement are given. Following the given procedures, an ultimate base pressure of 2x10 -10 Torr was obtained. Films grown in the system after reclamation contained no evidence of previously present materials down to the detection limit of secondary ion mass spectrometry

  16. Mathematical models of non-linear phenomena, processes and systems: from molecular scale to planetary atmosphere

    CERN Document Server

    2013-01-01

    This book consists of twenty seven chapters, which can be divided into three large categories: articles with the focus on the mathematical treatment of non-linear problems, including the methodologies, algorithms and properties of analytical and numerical solutions to particular non-linear problems; theoretical and computational studies dedicated to the physics and chemistry of non-linear micro-and nano-scale systems, including molecular clusters, nano-particles and nano-composites; and, papers focused on non-linear processes in medico-biological systems, including mathematical models of ferments, amino acids, blood fluids and polynucleic chains.

  17. Unraveling the effect of the hydration level on the molecular mobility of nanolayered polymeric systems.

    Science.gov (United States)

    Borges, João; Caridade, Sofia G; Silva, Joana M; Mano, João F

    2015-02-01

    This work investigates the influence of the hydration level on the molecular mobility and glass transition dynamics of freestanding chitosan/alginate (CHT/ALG) nanolayered systems. Nonconventional dynamic mechanical analysis identifies two relaxation processes assigned to the α-relaxation of the two biopolymers, respectively, CHT and ALG, when immersed in water/ethanol mixtures. This phenomenon explains the shape memory properties of the multilayered systems induced by hydration, thus constituting promising smart materials that would be of paramount importance in a plethora of research fields, including in the biomedical and biotechnological fields. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Optical activity of oriented molecular systems in terms of the magnetoelectric tensor of gyrotropy

    International Nuclear Information System (INIS)

    Arteaga, Oriol

    2014-01-01

    The optical activity of oriented molecular systems is investigated using bianisotropic material constitutives for Maxwell's equations. It is shown that the circular birefringence and circular dichroism for an oriented system can be conveniently expressed in terms of the two components of the symmetric magnetoelectric tensor of gyrotropy that are perpendicular to this direction of light propagation. This description establishes a direct link between the optical activity measured at a certain direction and the tensors that describe the oscillating electric and magnetic dipole and electric quadrupole moments induced by the optical wave. (paper)

  19. Preliminary Design of Molecular Sieve for Removing Organic Iodide in Containment Filtered Venting System

    Energy Technology Data Exchange (ETDEWEB)

    Park, Tong Kyu; Shin, So Eun; Lee, Byung Chul [Heungdeok IT Valley Bldg., Yongin (Korea, Republic of); Kim, Hong Hyun; Lee, Kyung Jun [Gemvax and KAEL Inc., Daejeon (Korea, Republic of)

    2014-05-15

    In this paper, to increase the DF for gaseous iodine species, especially organic iodide, molecular sieve filled by silver exchanged zeolites is proposed and designed preliminarily. Its aerodynamic analysis is also performed and presented. In order to increase the DF for gaseous organic iodide, deep-bed type molecular sieve was proposed and designed preliminarily. Total 1,620kg of silver exchanged zeolites were filled evenly in 10 beds of the molecular sieve. The safety factor in the case of 20m{sup 3}/s will be smaller than the counterpart of the standard case (6m{sup 3}/s). However, if the adsorption capacity of the zeolites is larger than 3.09mg/g when the residence time is 0.09 second, the designed molecular sieve can be used at 20m3/s of volumetric flow rate. The removal efficiency for organic iodide should be considered as well as economical aspects in the design of molecular sieve. In the event of nuclear power plant (NPP) severe accident, the nuclear reactor containment might suffer damage resulting from overpressure caused by decay heat. In order to prevent this containment damage, containment venting has been considered as one of effective methods. However, since vented gases contain radioactive fission products, they should be filtered to be released to environment. Generally, containment filtered venting system (CFVS) is installed on NPP to achieve this aim. Even though great amount of efforts have been devoted to developing the CFVS using various filtering methods, the decontaminant factor (DF) for radioactive gaseous iodide is still unsatisfactory while DFs for radioactive aerosols and elemental iodine are very high.

  20. Quantum statistical mechanics of dense partially ionized hydrogen.

    Science.gov (United States)

    Dewitt, H. E.; Rogers, F. J.

    1972-01-01

    The theory of dense hydrogenic plasmas beginning with the two component quantum grand partition function is reviewed. It is shown that ionization equilibrium and molecular dissociation equilibrium can be treated in the same manner with proper consideration of all two-body states. A quantum perturbation expansion is used to give an accurate calculation of the equation of state of the gas for any degree of dissociation and ionization. In this theory, the effective interaction between any two charges is the dynamic screened potential obtained from the plasma dielectric function. We make the static approximation; and we carry out detailed numerical calculations with the bound and scattering states of the Debye potential, using the Beth-Uhlenbeck form of the quantum second virial coefficient. We compare our results with calculations from the Saha equation.

  1. Molecular depth profiling of multi-layer systems with cluster ion sources

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Juan [Department of Chemistry, Penn State University, University Park, PA 16802 (United States); Winograd, Nicholas [Department of Chemistry, Penn State University, University Park, PA 16802 (United States)]. E-mail: nxw@psu.edu

    2006-07-30

    Cluster bombardment of molecular films has created new opportunities for SIMS research. To more quantitatively examine the interaction of cluster beams with organic materials, we have developed a reproducible platform consisting of a well-defined sugar film (trehalose) doped with peptides. Molecular depth profiles have been acquired with these systems using C{sub 60} {sup +} bombardment. In this study, we utilize this platform to determine the feasibility of examining buried interfaces for multi-layer systems. Using C{sub 60} {sup +} at 20 keV, several systems have been tested including Al/trehalose/Si, Al/trehalose/Al/Si, Ag/trehalose/Si and ice/trehalose/Si. The results show that there can be interactions between the layers during the bombardment process that prevent a simple interpretation of the depth profile. We find so far that the best results are obtained when the mass of the overlayer atoms is less than or nearly equal to the mass of the atoms in buried molecules. In general, these observations suggest that C{sub 60} {sup +} bombardment can be successfully applied to interface characterization of multi-layer systems if the systems are carefully chosen.

  2. Novel insights into systemic autoimmune rheumatic diseases using shared molecular signatures and an integrative analysis.

    Science.gov (United States)

    Hudson, Marie; Bernatsky, Sasha; Colmegna, Ines; Lora, Maximilien; Pastinen, Tomi; Klein Oros, Kathleen; Greenwood, Celia M T

    2017-06-03

    We undertook this study to identify DNA methylation signatures of three systemic autoimmune rheumatic diseases (SARDs), namely rheumatoid arthritis, systemic lupus erythematosus, and systemic sclerosis, compared to healthy controls. Using a careful design to minimize confounding, we restricted our study to subjects with incident disease and performed our analyses on purified CD4 + T cells, key effector cells in SARD. We identified differentially methylated (using the Illumina Infinium HumanMethylation450 BeadChip array) and expressed (using the Illumina TruSeq stranded RNA-seq protocol) sites between cases and controls, and investigated the biological significance of this SARD signature using gene annotation databases. We recruited 13 seropositive rheumatoid arthritis, 19 systemic sclerosis, 12 systemic lupus erythematosus subjects, and 8 healthy controls. We identified 33 genes that were both differentially methylated and expressed (26 over- and 7 under-expressed) in SARD cases versus controls. The most highly overexpressed gene was CD1C (log fold change in expression = 1.85, adjusted P value = 0.009). In functional analysis (Ingenuity Pathway Analysis), the top network identified was lipid metabolism, molecular transport, small molecule biochemistry. The top canonical pathways included the mitochondrial L-carnitine shuttle pathway (P = 5E-03) and PTEN signaling (P = 8E-03). The top upstream regulator was HNF4A (P = 3E-05). This novel SARD signature contributes to ongoing work to further our understanding of the molecular mechanisms underlying SARD and provides novel targets of interest.

  3. System geometry optimization for molecular breast tomosynthesis with focusing multi-pinhole collimators

    Science.gov (United States)

    van Roosmalen, Jarno; Beekman, Freek J.; Goorden, Marlies C.

    2018-01-01

    Imaging of 99mTc-labelled tracers is gaining popularity for detecting breast tumours. Recently, we proposed a novel design for molecular breast tomosynthesis (MBT) based on two sliding focusing multi-pinhole collimators that scan a modestly compressed breast. Simulation studies indicate that MBT has the potential to improve the tumour-to-background contrast-to-noise ratio significantly over state-of-the-art planar molecular breast imaging. The aim of the present paper is to optimize the collimator-detector geometry of MBT. Using analytical models, we first optimized sensitivity at different fixed system resolutions (ranging from 5 to 12 mm) by tuning the pinhole diameters and the distance between breast and detector for a whole series of automatically generated multi-pinhole designs. We evaluated both MBT with a conventional continuous crystal detector with 3.2 mm intrinsic resolution and with a pixelated detector with 1.6 mm pixels. Subsequently, full system simulations of a breast phantom containing several lesions were performed for the optimized geometry at each system resolution for both types of detector. From these simulations, we found that tumour-to-background contrast-to-noise ratio was highest for systems in the 7 mm-10 mm system resolution range over which it hardly varied. No significant differences between the two detector types were found.

  4. Positron annihilation lifetime spectroscopy (PALS): a probe for molecular organisation in self-assembled biomimetic systems.

    Science.gov (United States)

    Fong, Celesta; Dong, Aurelia W; Hill, Anita J; Boyd, Ben J; Drummond, Calum J

    2015-07-21

    Positron annihilation lifetime spectroscopy (PALS) has been shown to be highly sensitive to conformational, structural and microenvironmental transformations arising from subtle geometric changes in molecular geometry in self-assembling biomimetic systems. The ortho-positronium (oPs) may be considered an active probe that can provide information on intrinsic packing and mobility within low molecular weight solids, viscous liquids, and soft matter systems. In this perspective we provide a critical overview of the literature in this field, including the evolution of analysis software and experimental protocols with commentary upon the practical utility of PALS. In particular, we discuss how PALS can provide unique insight into the macroscopic transport properties of several porous biomembrane-like nanostructures and suggest how this insight may provide information on the release of drugs from these matrices to aid in developing therapeutic interventions. We discuss the potentially exciting and fruitful application of this technique to membrane dynamics, diffusion and permeability. We propose that PALS can provide novel molecular level information that is complementary to conventional characterisation techniques.

  5. A neural network approach to the study of internal energy flow in molecular systems

    International Nuclear Information System (INIS)

    Sumpter, B.G.; Getino, C.; Noid, D.W.

    1992-01-01

    Neural networks are used to develop a new technique for efficient analysis of data obtained from molecular-dynamics calculations and is applied to the study of mode energy flow in molecular systems. The methodology is based on teaching an appropriate neural network the relationship between phase-space points along a classical trajectory and mode energies for stretch, bend, and torsion vibrations. Results are discussed for reactive and nonreactive classical trajectories of hydrogen peroxide (H 2 O 2 ) on a semiempirical potential-energy surface. The neural-network approach is shown to produce reasonably accurate values for the mode energies, with average errors between 1% and 12%, and is applicable to any region within the 24-dimensional phase space of H 2 O 2 . In addition, the generic knowledge learned by the neural network allows calculations to be made for other molecular systems. Results are discussed for a series of tetratomic molecules: H 2 X 2 , X=C, N, O, Si, S, or Se, and preliminary results are given for energy flow predictions in macromolecules

  6. Theoretical study on the molecular tautomerism of the 3-hydroxy-pyridin-4-one system

    Science.gov (United States)

    Zborowski, Krzysztof K.; Mohammadpour, Mehrdad; Sadeghi, Amir; Proniewicz, Leonard M.

    2013-04-01

    3-hydroxy-pyridin-4-one is a parent molecule for the family of hydroxypyridinones that are known in coordination chemistry as efficient metal ions chelators. In this work, relative stabilities of some possible tautomers were investigated using several quantum chemical methods: CBS (complete basis set methods), Gn, DFT (density functional theory), Hartree-Fock and MP2. Performed calculations show that the system under consideration exists as a mixture of two tautomers with comparable energies. Among them, the hydroxypyridinone structure of the studied molecular system seems to be a bit more stable than the o-dihydroxypyridine one, by a few kJ/mol only. Aromaticity and intra-molecular hydrogen bonding are the main effects influencing the stability of the studied tautomeric structures. Consequently, aromatic effects were calculated using several indices of aromaticity: HOMA (harmonic oscillator model of aromaticity), NICS (nucleus independent chemical shift), H, PDI (para delocalisation index), MCI (multi-centre index) and ASE (aromatic stabilisation energy). The strength of possible intra-molecular hydrogen bonds (H-bonds) was determined by means of the AIM (atoms-in-molecules) method and by calculating enthalpies for theoretical reactions that do or do not involve H-bonds. The AIM method was employed to understand how variations in atomic energies influence the stability of different tautomeric structures.

  7. A Protoplast Transient Expression System to Enable Molecular, Cellular, and Functional Studies in Phalaenopsis orchids

    Directory of Open Access Journals (Sweden)

    Hsiang-Yin Lin

    2018-06-01

    Full Text Available The enigmatic nature of the specialized developmental programs of orchids has fascinated plant biologists for centuries. The recent releases of orchid genomes indicate that orchids possess new gene families and family expansions and contractions to regulate a diverse suite of developmental processes. However, the extremely long orchid life cycle and lack of molecular toolkit have hampered the advancement of orchid biology research. To overcome the technical difficulties and establish a platform for rapid gene regulation studies, in this study, we developed an efficient protoplast isolation and transient expression system for Phalaenopsis aphrodite. This protocol was successfully applied to protein subcellular localization and protein–protein interaction studies. Moreover, it was confirmed to be useful in delineating the PaE2F/PaDP-dependent cell cycle pathway and studying auxin response. In summary, the established orchid protoplast transient expression system provides a means to functionally characterize orchid genes at the molecular level allowing assessment of transcriptome responses to transgene expression and widening the scope of molecular studies in orchids.

  8. MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations.

    Science.gov (United States)

    Ohmura, Itta; Morimoto, Gentaro; Ohno, Yousuke; Hasegawa, Aki; Taiji, Makoto

    2014-08-06

    We are developing the MDGRAPE-4, a special-purpose computer system for molecular dynamics (MD) simulations. MDGRAPE-4 is designed to achieve strong scalability for protein MD simulations through the integration of general-purpose cores, dedicated pipelines, memory banks and network interfaces (NIFs) to create a system on chip (SoC). Each SoC has 64 dedicated pipelines that are used for non-bonded force calculations and run at 0.8 GHz. Additionally, it has 65 Tensilica Xtensa LX cores with single-precision floating-point units that are used for other calculations and run at 0.6 GHz. At peak performance levels, each SoC can evaluate 51.2 G interactions per second. It also has 1.8 MB of embedded shared memory banks and six network units with a peak bandwidth of 7.2 GB s(-1) for the three-dimensional torus network. The system consists of 512 (8×8×8) SoCs in total, which are mounted on 64 node modules with eight SoCs. The optical transmitters/receivers are used for internode communication. The expected maximum power consumption is 50 kW. While MDGRAPE-4 software has still been improved, we plan to run MD simulations on MDGRAPE-4 in 2014. The MDGRAPE-4 system will enable long-time molecular dynamics simulations of small systems. It is also useful for multiscale molecular simulations where the particle simulation parts often become bottlenecks.

  9. Tripolar vortex formation in dense quantum plasma with ion-temperature-gradients

    Science.gov (United States)

    Qamar, Anisa; Ata-ur-Rahman, Mirza, Arshad M.

    2012-05-01

    We have derived system of nonlinear equations governing the dynamics of low-frequency electrostatic toroidal ion-temperature-gradient mode for dense quantum magnetoplasma. For some specific profiles of the equilibrium density, temperature, and ion velocity gradients, the nonlinear equations admit a stationary solution in the form of a tripolar vortex. These results are relevant to understand nonlinear structure formation in dense quantum plasmas in the presence of equilibrium ion-temperature and density gradients.

  10. Tripolar vortex formation in dense quantum plasma with ion-temperature-gradients

    Energy Technology Data Exchange (ETDEWEB)

    Qamar, Anisa; Ata-ur-Rahman [Institute of Physics and Electronics, University of Peshawar, Khyber Pakhtoon Khwa 25000 (Pakistan); National Center for Physics Shahdrah Valley Road, Islamabad 44000 (Pakistan); Mirza, Arshad M. [Theoretical Plasma Physics Group, Physics Department, Quaid-i-Azam University, Islamabad 45320 (Pakistan)

    2012-05-15

    We have derived system of nonlinear equations governing the dynamics of low-frequency electrostatic toroidal ion-temperature-gradient mode for dense quantum magnetoplasma. For some specific profiles of the equilibrium density, temperature, and ion velocity gradients, the nonlinear equations admit a stationary solution in the form of a tripolar vortex. These results are relevant to understand nonlinear structure formation in dense quantum plasmas in the presence of equilibrium ion-temperature and density gradients.

  11. Tripolar vortex formation in dense quantum plasma with ion-temperature-gradients

    International Nuclear Information System (INIS)

    Qamar, Anisa; Ata-ur-Rahman; Mirza, Arshad M.

    2012-01-01

    We have derived system of nonlinear equations governing the dynamics of low-frequency electrostatic toroidal ion-temperature-gradient mode for dense quantum magnetoplasma. For some specific profiles of the equilibrium density, temperature, and ion velocity gradients, the nonlinear equations admit a stationary solution in the form of a tripolar vortex. These results are relevant to understand nonlinear structure formation in dense quantum plasmas in the presence of equilibrium ion-temperature and density gradients.

  12. CAST: a new program package for the accurate characterization of large and flexible molecular systems.

    Science.gov (United States)

    Grebner, Christoph; Becker, Johannes; Weber, Daniel; Bellinger, Daniel; Tafipolski, Maxim; Brückner, Charlotte; Engels, Bernd

    2014-09-15

    The presented program package, Conformational Analysis and Search Tool (CAST) allows the accurate treatment of large and flexible (macro) molecular systems. For the determination of thermally accessible minima CAST offers the newly developed TabuSearch algorithm, but algorithms such as Monte Carlo (MC), MC with minimization, and molecular dynamics are implemented as well. For the determination of reaction paths, CAST provides the PathOpt, the Nudge Elastic band, and the umbrella sampling approach. Access to free energies is possible through the free energy perturbation approach. Along with a number of standard force fields, a newly developed symmetry-adapted perturbation theory-based force field is included. Semiempirical computations are possible through DFTB+ and MOPAC interfaces. For calculations based on density functional theory, a Message Passing Interface (MPI) interface to the Graphics Processing Unit (GPU)-accelerated TeraChem program is available. The program is available on request. Copyright © 2014 Wiley Periodicals, Inc.

  13. Self-consistent field theory based molecular dynamics with linear system-size scaling

    Energy Technology Data Exchange (ETDEWEB)

    Richters, Dorothee [Institute of Mathematics and Center for Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 9, D-55128 Mainz (Germany); Kühne, Thomas D., E-mail: kuehne@uni-mainz.de [Institute of Physical Chemistry and Center for Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 7, D-55128 Mainz (Germany); Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn (Germany)

    2014-04-07

    We present an improved field-theoretic approach to the grand-canonical potential suitable for linear scaling molecular dynamics simulations using forces from self-consistent electronic structure calculations. It is based on an exact decomposition of the grand canonical potential for independent fermions and does neither rely on the ability to localize the orbitals nor that the Hamilton operator is well-conditioned. Hence, this scheme enables highly accurate all-electron linear scaling calculations even for metallic systems. The inherent energy drift of Born-Oppenheimer molecular dynamics simulations, arising from an incomplete convergence of the self-consistent field cycle, is circumvented by means of a properly modified Langevin equation. The predictive power of the present approach is illustrated using the example of liquid methane under extreme conditions.

  14. Carbon molecular sieve membranes derived from Matrimid® polyimide for nitrogen/methane separation

    KAUST Repository

    Ning, Xue; Koros, William J.

    2014-01-01

    A commercial polyimide, Matrimid® 5218, was pyrolyzed under an inert argon atmosphere to produce carbon molecular sieve (CMS) dense film membranes for nitrogen/methane separation. The resulting CMS dense film separation performance was evaluated

  15. A molecular dynamics simulation of sodium pentadecyl sulphonate (SPDS)/water system

    International Nuclear Information System (INIS)

    Arsenyan, L.H.; Poghosyan, A.H.; Shahinyan, A.A.

    2008-07-01

    We have carried out a molecular dynamics simulation of a sodium pentadecylsulfonate (SPDS)/water system consisting of 64PDS/1200water and 512PDS/9000water molecules, correspondingly. The overall simulation time for both cases reaches up to 60ns and the simulation was performed using the NAMD code with CHARMM27 force field. The main parameters of the system have been calculated and compared with available X-ray diffraction findings. For large system, after a couple of ns, we receive the molecule's hydrocarbon chains tilt in the opposite sense in layers and reducing the system size leads to the decrease of the average angle between bilayer normal and chain vector. At the end of 50ns of a simulation run we achieve the crystalline-like structure of hydrocarbon packing. For both cases, we obtain tilted hydrocarbon chains packing and the average angle between bilayer normal and chain vector is estimated to be about 13 deg. and 10 deg. (author)

  16. Molecular Mechanisms Underlying Renin-Angiotensin-Aldosterone System Mediated Regulation of BK Channels

    Directory of Open Access Journals (Sweden)

    Zhen-Ye Zhang

    2017-09-01

    Full Text Available Large-conductance calcium-activated potassium channels (BK channels belong to a family of Ca2+-sensitive voltage-dependent potassium channels and play a vital role in various physiological activities in the human body. The renin-angiotensin-aldosterone system is acknowledged as being vital in the body's hormone system and plays a fundamental role in the maintenance of water and electrolyte balance and blood pressure regulation. There is growing evidence that the renin-angiotensin-aldosterone system has profound influences on the expression and bioactivity of BK channels. In this review, we focus on the molecular mechanisms underlying the regulation of BK channels mediated by the renin-angiotensin-aldosterone system and its potential as a target for clinical drugs.

  17. Dense Output for Strong Stability Preserving Runge–Kutta Methods

    KAUST Repository

    Ketcheson, David I.

    2016-12-10

    We investigate dense output formulae (also known as continuous extensions) for strong stability preserving (SSP) Runge–Kutta methods. We require that the dense output formula also possess the SSP property, ideally under the same step-size restriction as the method itself. A general recipe for first-order SSP dense output formulae for SSP methods is given, and second-order dense output formulae for several optimal SSP methods are developed. It is shown that SSP dense output formulae of order three and higher do not exist, and that in any method possessing a second-order SSP dense output, the coefficient matrix A has a zero row.

  18. Dense plasma focus - a literature review

    International Nuclear Information System (INIS)

    Tendys, J.

    1976-01-01

    The dense plasma focus (DPF) is a convenient source of short, intense neutron pulses, and dense, high temperature plasma. This review of the literature on the DPF indicates that its operation is still not understood, and attempts to show where the present data is either inadequate or inconsistent. Because the plasma conditions and neutron and x-ray fluxes vary from shot to shot, it is maintained that, to resolve inconsistencies in the present data, spectra need to be measured with energy and time resolution simultaneously, and cannot be built up from a large number of shots. Time resolutions of the order of 1 nsec for pulse lengths of about 100 nsec make these requirements especially difficult. Some theoretical models are presented for the neutron output and its spectrum, but no self-consistent description of the plasma in the focus region is likely for some time. (author)

  19. Highly Dense Isolated Metal Atom Catalytic Sites

    DEFF Research Database (Denmark)

    Chen, Yaxin; Kasama, Takeshi; Huang, Zhiwei

    2015-01-01

    -ray diffraction. A combination of electron microscopy images with X-ray absorption spectra demonstrated that the silver atoms were anchored on five-fold oxygen-terminated cavities on the surface of the support to form highly dense isolated metal active sites, leading to excellent reactivity in catalytic oxidation......Atomically dispersed noble-metal catalysts with highly dense active sites are promising materials with which to maximise metal efficiency and to enhance catalytic performance; however, their fabrication remains challenging because metal atoms are prone to sintering, especially at a high metal...... loading. A dynamic process of formation of isolated metal atom catalytic sites on the surface of the support, which was achieved starting from silver nanoparticles by using a thermal surface-mediated diffusion method, was observed directly by using in situ electron microscopy and in situ synchrotron X...

  20. Anomalous properties of hot dense nonequilibrium plasmas

    International Nuclear Information System (INIS)

    Ferrante, G; Zarcone, M; Uryupin, S A

    2005-01-01

    A concise overview of a number of anomalous properties of hot dense nonequilibrium plasmas is given. The possibility of quasistationary megagauss magnetic field generation due to Weibel instability is discussed for plasmas created in atom tunnel ionization. The collisionless absorption and reflection of a test electromagnetic wave normally impinging on the plasma with two-temperature bi-maxwellian electron velocity distribution function are studied. Due to the wave magnetic field influence on the electron kinetics in the skin layer the wave absorption and reflection significantly depend on the degree of the electron temperature anisotropy. The linearly polarized impinging wave during reflection transforms into an elliptically polarized one. The problem of transmission of an ultrashort laser pulse through a layer of dense plasma, formed as a result of ionization of a thin foil, is considered. It is shown that the strong photoelectron distribution anisotropy yields an anomalous penetration of the wave field through the foil

  1. Deterministic dense coding with partially entangled states

    Science.gov (United States)

    Mozes, Shay; Oppenheim, Jonathan; Reznik, Benni

    2005-01-01

    The utilization of a d -level partially entangled state, shared by two parties wishing to communicate classical information without errors over a noiseless quantum channel, is discussed. We analytically construct deterministic dense coding schemes for certain classes of nonmaximally entangled states, and numerically obtain schemes in the general case. We study the dependency of the maximal alphabet size of such schemes on the partially entangled state shared by the two parties. Surprisingly, for d>2 it is possible to have deterministic dense coding with less than one ebit. In this case the number of alphabet letters that can be communicated by a single particle is between d and 2d . In general, we numerically find that the maximal alphabet size is any integer in the range [d,d2] with the possible exception of d2-1 . We also find that states with less entanglement can have a greater deterministic communication capacity than other more entangled states.

  2. DEVELOPMENT OF SEPARATION SYSTEMS FOR POLYNUCLEAR AROMATIC HYDROCARBON ENVIRONMENTAL CONTAMINANTS USING MICELLAR ELECTROKINETIC CHROMATOGRAPHY WITH MOLECULAR MICELLES AND FREE ZONE ELECTROPHORESIS

    Science.gov (United States)

    Of four systems available from the literature, based on cyclodextrins, dioctylsulfosuccinate, bile salts, and molecular micelles consisting of oligomers of undecylenic acid, the most successful separation system in our hands is based on the molecular micelles, oligomers of sodiu...

  3. A Systems Biology Approach Reveals Converging Molecular Mechanisms that Link Different POPs to Common Metabolic Diseases.

    Science.gov (United States)

    Ruiz, Patricia; Perlina, Ally; Mumtaz, Moiz; Fowler, Bruce A

    2016-07-01

    A number of epidemiological studies have identified statistical associations between persistent organic pollutants (POPs) and metabolic diseases, but testable hypotheses regarding underlying molecular mechanisms to explain these linkages have not been published. We assessed the underlying mechanisms of POPs that have been associated with metabolic diseases; three well-known POPs [2,3,7,8-tetrachlorodibenzodioxin (TCDD), 2,2´,4,4´,5,5´-hexachlorobiphenyl (PCB 153), and 4,4´-dichlorodiphenyldichloroethylene (p,p´-DDE)] were studied. We used advanced database search tools to delineate testable hypotheses and to guide laboratory-based research studies into underlying mechanisms by which this POP mixture could produce or exacerbate metabolic diseases. For our searches, we used proprietary systems biology software (MetaCore™/MetaDrug™) to conduct advanced search queries for the underlying interactions database, followed by directional network construction to identify common mechanisms for these POPs within two or fewer interaction steps downstream of their primary targets. These common downstream pathways belong to various cytokine and chemokine families with experimentally well-documented causal associations with type 2 diabetes. Our systems biology approach allowed identification of converging pathways leading to activation of common downstream targets. To our knowledge, this is the first study to propose an integrated global set of step-by-step molecular mechanisms for a combination of three common POPs using a systems biology approach, which may link POP exposure to diseases. Experimental evaluation of the proposed pathways may lead to development of predictive biomarkers of the effects of POPs, which could translate into disease prevention and effective clinical treatment strategies. Ruiz P, Perlina A, Mumtaz M, Fowler BA. 2016. A systems biology approach reveals converging molecular mechanisms that link different POPs to common metabolic diseases. Environ

  4. Information theory and signal transduction systems: from molecular information processing to network inference.

    Science.gov (United States)

    Mc Mahon, Siobhan S; Sim, Aaron; Filippi, Sarah; Johnson, Robert; Liepe, Juliane; Smith, Dominic; Stumpf, Michael P H

    2014-11-01

    Sensing and responding to the environment are two essential functions that all biological organisms need to master for survival and successful reproduction. Developmental processes are marshalled by a diverse set of signalling and control systems, ranging from systems with simple chemical inputs and outputs to complex molecular and cellular networks with non-linear dynamics. Information theory provides a powerful and convenient framework in which such systems can be studied; but it also provides the means to reconstruct the structure and dynamics of molecular interaction networks underlying physiological and developmental processes. Here we supply a brief description of its basic concepts and introduce some useful tools for systems and developmental biologists. Along with a brief but thorough theoretical primer, we demonstrate the wide applicability and biological application-specific nuances by way of different illustrative vignettes. In particular, we focus on the characterisation of biological information processing efficiency, examining cell-fate decision making processes, gene regulatory network reconstruction, and efficient signal transduction experimental design. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. The GBT 3mm Survey of Infall and Fragmentation of Dense Cores in Taurus

    Science.gov (United States)

    Seo, Youngmin; Goldsmith, Paul; Shirley, Yancy L.; Church, Sara; Frayer, David

    2018-01-01

    We present preliminary results of the infall and fragmentation survey toward a complete population of prestellar cores in Taurus that was carried out with the 16-element W-band focal plane array receiver (Argus) on the 100m Green Bank Telescope. The survey is designed take advantage of the 8.5” angular resolution and high sensitivity of Argus on the GBT to trace infall motions in HCN 1-0 & HCO+ 1-0 and find any evidence of fragmentation in N2H+ & NH2D within prestellar cores ranging in size from 0.05 pc to 0.0075 pc (1500 AU), which is a typical size scale of individual planetary systems. The scientific goal is to estimate the fraction of infall candidates from a complete population of prestellar cores and to understand internal velocity structure during the final gravitational collapse before forming stars. The survey started in the winter of 2016 and is to continue to the end of January 2018. So far, we observed 23 prestellar cores out of 65 targets in HCN 1-0 and HCO+ 1-0. We have so far found only two prestellar cores (L1495A-N, L1521D) out of 23 observed that show infall signatures, which is a fraction of infalling cores less than half of that reported by the previous surveys toward the bright, dense cores in various molecular clouds (Lee et al. 2004; Sohn et al. 2007). We also found that L1495A-N has a highly asymmetric infall motion which does not fit to a conventional model of dense core collapse, while L1521D has a slow infall motion similar to L1544.

  6. Dense-plasma research using ballistic compressors

    International Nuclear Information System (INIS)

    Hess, H.

    1986-01-01

    An introduction is given to research on dense (or nonideal) plasmas which can be generated to advantage by ballistic compressors. Some properties of ballistic compressors are discussed especially in comparison with shock tubes. A short review is given on the history of these devices for high-pressure plasma generation. The present state of the art is reported including research on the two ZIE (Central Institute for Electron Physics) ballistic compressors. (author)

  7. Studying dense plasmas with coherent XUV pulses

    International Nuclear Information System (INIS)

    Stabile, H.

    2006-12-01

    The investigation of dense plasma dynamic requires the development of diagnostics able to ensure the measurement of electronic density with micro-metric space resolution and sub-nanosecond, or even subpicosecond, time resolution (indeed this must be at least comparable with the characteristic tune scale of plasma evolution). In contrast with low-density plasmas, dense plasmas cannot be studied using optical probes in the visible domain, the density range accessible being limited to the critical density (N c equals 1.1*10 21 λ -2 (μm) ∼ 10 21 cm -3 for infrared). In addition, light is reflected even at smaller densities if the medium exhibits sharp density gradients. Hence probing of dense plasmas, for instance those produced by laser irradiation of solids, requires using shorter wavelength radiation. Thanks to their physical properties, high order harmonics generated in rare gases are particularly adapted to the study of dense plasmas. Indeed, they can naturally be synchronized with the generating laser and their pulse duration is very short, which makes it possible to use them in pump-probe experiments. Moreover, they exhibit good spatial and temporal coherencies. Two types of diagnostics were developed during this thesis. The first one was used to study the instantaneous creation of hot-solid-density plasma generated by focusing a femtosecond high-contrast laser on an ultra-thin foil (100 nm) in the 10 18 W/cm 2 intensity regime. The use of high order harmonics, providing a probe beam of sufficiently short wavelengths to penetrate such a medium, enables the study of its dynamics on the 100 fs time scale. The second one uses the harmonics beam as probe beam (λ equals 32 nm) within an interferometric device. This diagnostic was designed to ensure a micro-metric spatial resolution and a temporal resolution in the femtosecond range. The first results in presence of plasma created by irradiation of an aluminum target underline the potentialities of this new

  8. Leeuwpan fine coal dense medium plant

    CSIR Research Space (South Africa)

    Lundt, M

    2010-11-01

    Full Text Available Beneficiation 2010, 4–6 May 2010. 671The Journal of The Southern African Institute of Mining and Metallurgy VOLUME 110 NOVEMBER 2010 L Leeuwpan fine coal dense medium plant mixed with magnetite in the launder and enters... with production. Plant equipment operational changes Cyclone spigot changes In an attempt to lower the cut-point density, the spigot on the L 672 NOVEMBER 2010 VOLUME 110 The Journal of The Southern African Institute of Mining and Metallurgy Figure 1...

  9. Hybrid-Based Dense Stereo Matching

    Science.gov (United States)

    Chuang, T. Y.; Ting, H. W.; Jaw, J. J.

    2016-06-01

    Stereo matching generating accurate and dense disparity maps is an indispensable technique for 3D exploitation of imagery in the fields of Computer vision and Photogrammetry. Although numerous solutions and advances have been proposed in the literature, occlusions, disparity discontinuities, sparse texture, image distortion, and illumination changes still lead to problematic issues and await better treatment. In this paper, a hybrid-based method based on semi-global matching is presented to tackle the challenges on dense stereo matching. To ease the sensitiveness of SGM cost aggregation towards penalty parameters, a formal way to provide proper penalty estimates is proposed. To this end, the study manipulates a shape-adaptive cross-based matching with an edge constraint to generate an initial disparity map for penalty estimation. Image edges, indicating the potential locations of occlusions as well as disparity discontinuities, are approved by the edge drawing algorithm to ensure the local support regions not to cover significant disparity changes. Besides, an additional penalty parameter 𝑃𝑒 is imposed onto the energy function of SGM cost aggregation to specifically handle edge pixels. Furthermore, the final disparities of edge pixels are found by weighting both values derived from the SGM cost aggregation and the U-SURF matching, providing more reliable estimates at disparity discontinuity areas. Evaluations on Middlebury stereo benchmarks demonstrate satisfactory performance and reveal the potency of the hybrid-based dense stereo matching method.

  10. Multiscale simulations of patchy particle systems combining Molecular Dynamics, Path Sampling and Green's Function Reaction Dynamics

    Science.gov (United States)

    Bolhuis, Peter

    Important reaction-diffusion processes, such as biochemical networks in living cells, or self-assembling soft matter, span many orders in length and time scales. In these systems, the reactants' spatial dynamics at mesoscopic length and time scales of microns and seconds is coupled to the reactions between the molecules at microscopic length and time scales of nanometers and milliseconds. This wide range of length and time scales makes these systems notoriously difficult to simulate. While mean-field rate equations cannot describe such processes, the mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. The recently developed multiscale Molecular Dynamics Green's Function Reaction Dynamics (MD-GFRD) approach combines GFRD for simulating the system at the mesocopic scale where particles are far apart, with microscopic Molecular (or Brownian) Dynamics, for simulating the system at the microscopic scale where reactants are in close proximity. The association and dissociation of particles are treated with rare event path sampling techniques. I will illustrate the efficiency of this method for patchy particle systems. Replacing the microscopic regime with a Markov State Model avoids the microscopic regime completely. The MSM is then pre-computed using advanced path-sampling techniques such as multistate transition interface sampling. I illustrate this approach on patchy particle systems that show multiple modes of binding. MD-GFRD is generic, and can be used to efficiently simulate reaction-diffusion systems at the particle level, including the orientational dynamics, opening up the possibility for large-scale simulations of e.g. protein signaling networks.

  11. Coherent scattering of neutrinos by 'nuclear pasta' in dense matter

    International Nuclear Information System (INIS)

    Sonoda, Hidetaka

    2007-01-01

    We examine coherent scattering cross section of neutrino and nucleon systems via weak-neutral current at subnuclear densities, which will be important in supernova cores. Below melting density and temparature of nuclei, nuclear shape becomes rodlike and slablike; this is called nuclear 'pasta'. Transition of structure will greatly influence coherent effects which can not easily be predicted. We calculate static structure factor of nuclear matter using data of several nuclear models, and discuss the effects of existence of nuclear pasta on neutrino opacity in hot dense matter

  12. The role of triplet correlation function in dense fluids

    International Nuclear Information System (INIS)

    Rashid, R.I.M.A.

    1993-09-01

    In the theory of dense liquids, one usually introduces various correlation functions for describing properties of such systems. It has proved impossible to solve these correlation functions exactly and as such one often resorts to some meaningful approximations for their solutions. It is well known that unless proper precautions are taken, the approximate solutions will violate some useful sum rules and thermodynamic consistency conditions. Here the general rules for generating thermodynamically consistent approximate correlation functions are discussed. The role of triplet correlation is elucidated further by calculating a residual correction to the vacancy formation energy via three-particle correlation in rare gas solids. (author). 16 refs, 4 figs, 1 tab

  13. Proteomic approach toward molecular backgrounds of drug resistance of osteosarcoma cells in spheroid culture system.

    Science.gov (United States)

    Arai, Kazuya; Sakamoto, Ruriko; Kubota, Daisuke; Kondo, Tadashi

    2013-08-01

    Chemoresistance is one of the most critical prognostic factors in osteosarcoma, and elucidation of the molecular backgrounds of chemoresistance may lead to better clinical outcomes. Spheroid cells resemble in vivo cells and are considered an in vitro model for the drug discovery. We found that spheroid cells displayed more chemoresistance than conventional monolayer cells across 11 osteosarcoma cell lines. To investigate the molecular mechanisms underlying the resistance to chemotherapy, we examined the proteomic differences between the monolayer and spheroid cells by 2D-DIGE. Of the 4762 protein species observed, we further investigated 435 species with annotated mass spectra in the public proteome database, Genome Medicine Database of Japan Proteomics. Among the 435 protein species, we found that 17 species exhibited expression level differences when the cells formed spheroids in more than five cell lines and four species out of these 17 were associated with spheroid-formation associated resistance to doxorubicin. We confirmed the upregulation of cathepsin D in spheroid cells by western blotting. Cathepsin D has been implicated in chemoresistance of various malignancies but has not previously been implemented in osteosarcoma. Our study suggested that the spheroid system may be a useful tool to reveal the molecular backgrounds of chemoresistance in osteosarcoma. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Molecular transformation, gene cloning, and gene expression systems for filamentous fungi

    Science.gov (United States)

    Gold, Scott E.; Duick, John W.; Redman, Regina S.; Rodriguez, Rusty J.

    2001-01-01

    This chapter discusses the molecular transformation, gene cloning, and gene expression systems for filamentous fungi. Molecular transformation involves the movement of discrete amounts of DNA into cells, the expression of genes on the transported DNA, and the sustainable replication of the transforming DNA. The ability to transform fungi is dependent on the stable replication and expression of genes located on the transforming DNA. Three phenomena observed in bacteria, that is, competence, plasmids, and restriction enzymes to facilitate cloning, were responsible for the development of molecular transformation in fungi. Initial transformation success with filamentous fungi, involving the complementation of auxotrophic mutants by exposure to sheared genomic DNA or RNA from wt isolates, occurred with low transformation efficiencies. In addition, it was difficult to retrieve complementing DNA fragments and isolate genes of interest. This prompted the development of transformation vectors and methods to increase efficiencies. The physiological studies performed with fungi indicated that the cell wall could be removed to generate protoplasts. It was evident that protoplasts could be transformed with significantly greater efficiencies than walled cells.

  15. Solar fuels generation and molecular systems: is it homogeneous or heterogeneous catalysis?

    Science.gov (United States)

    Artero, Vincent; Fontecave, Marc

    2013-03-21

    Catalysis is a key enabling technology for solar fuel generation. A number of catalytic systems, either molecular/homogeneous or solid/heterogeneous, have been developed during the last few decades for both the reductive and oxidative multi-electron reactions required for fuel production from water or CO(2) as renewable raw materials. While allowing for a fine tuning of the catalytic properties through ligand design, molecular approaches are frequently criticized because of the inherent fragility of the resulting catalysts, when exposed to extreme redox potentials. In a number of cases, it has been clearly established that the true catalytic species is heterogeneous in nature, arising from the transformation of the initial molecular species, which should rather be considered as a pre-catalyst. Whether such a situation is general or not is a matter of debate in the community. In this review, covering water oxidation and reduction catalysts, involving noble and non-noble metal ions, we limit our discussion to the cases in which this issue has been directly and properly addressed as well as those requiring more confirmation. The methodologies proposed for discriminating homogeneous and heterogeneous catalysis are inspired in part by those previously discussed by Finke in the case of homogeneous hydrogenation reaction in organometallic chemistry [J. A. Widegren and R. G. Finke, J. Mol. Catal. A, 2003, 198, 317-341].

  16. Parametric sensitivity analysis for stochastic molecular systems using information theoretic metrics

    Energy Technology Data Exchange (ETDEWEB)

    Tsourtis, Anastasios, E-mail: tsourtis@uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete, Crete (Greece); Pantazis, Yannis, E-mail: pantazis@math.umass.edu; Katsoulakis, Markos A., E-mail: markos@math.umass.edu [Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts 01003 (United States); Harmandaris, Vagelis, E-mail: harman@uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete, and Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), GR-70013 Heraklion, Crete (Greece)

    2015-07-07

    In this paper, we present a parametric sensitivity analysis (SA) methodology for continuous time and continuous space Markov processes represented by stochastic differential equations. Particularly, we focus on stochastic molecular dynamics as described by the Langevin equation. The utilized SA method is based on the computation of the information-theoretic (and thermodynamic) quantity of relative entropy rate (RER) and the associated Fisher information matrix (FIM) between path distributions, and it is an extension of the work proposed by Y. Pantazis and M. A. Katsoulakis [J. Chem. Phys. 138, 054115 (2013)]. A major advantage of the pathwise SA method is that both RER and pathwise FIM depend only on averages of the force field; therefore, they are tractable and computable as ergodic averages from a single run of the molecular dynamics simulation both in equilibrium and in non-equilibrium steady state regimes. We validate the performance of the extended SA method to two different molecular stochastic systems, a standard Lennard-Jones fluid and an all-atom methane liquid, and compare the obtained parameter sensitivities with parameter sensitivities on three popular and well-studied observable functions, namely, the radial distribution function, the mean squared displacement, and the pressure. Results show that the RER-based sensitivities are highly correlated with the observable-based sensitivities.

  17. Improved Fab presentation on phage surface with the use of molecular chaperone coplasmid system.

    Science.gov (United States)

    Loh, Qiuting; Leong, Siew Wen; Tye, Gee Jun; Choong, Yee Siew; Lim, Theam Soon

    2015-05-15

    The low presentation efficiency of Fab (fragment antigen binding) fragments during phage display is largely due to the complexity of disulphide bond formation. This can result in the presentation of Fab fragments devoid of a light chain during phage display. Here we propose the use of a coplasmid system encoding several molecular chaperones (DsbA, DsbC, FkpA, and SurA) to improve Fab packaging. A comparison was done using the Fab fragment from IgG and IgD. We found that the use of the coplasmid during phage packaging was able to improve the presentation efficiency of the Fab fragment on phage surfaces. A modified version of panning using the coplasmid system was evaluated and was successful at enriching Fab binders. Therefore, the coplasmid system would be an attractive alternative for improved Fab presentation for phage display. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Molecular players involved in the interaction between beneficial bacteria and the immune system

    Directory of Open Access Journals (Sweden)

    Arancha eHevia

    2015-11-01

    Full Text Available The human gastrointestinal tract is a very complex ecosystem, in which there is a continuous interaction between nutrients, host cells, and microorganisms. The gut microbiota comprises trillions of microbes that have been selected during evolution on the basis of their functionality and capacity to survive in, and adapt to, the intestinal environment. Host bacteria and our immune system constantly sense and react to one another. In this regard, commensal microbes contribute to gut homeostasis, whereas the necessary responses are triggered against enteropathogens. Some representatives of our gut microbiota have beneficial effects on human health. Some of the most important roles of these microbes are to help to maintain the integrity of the mucosal barrier, to provide nutrients such as vitamins, or to protect against pathogens. In addition, the interaction between commensal microbiota and the mucosal immune system is crucial for proper immune function. This process is mainly performed via the pattern recognition receptors of epithelial cells, such as Toll-like or Nod-like receptors, which are able to recognize the molecular effectors that are produced by intestinal microbes. These effectors mediate processes that can ameliorate certain inflammatory gut disorders, discriminate between beneficial and pathogenic bacteria, or increase the number of immune cells or their pattern recognition receptors. This review intends to summarize the molecular players produced by probiotic bacteria, notably Lactobacillus and Bifidobacterium strains, but also other very promising potential probiotics, which affect the human immune system.

  19. Generalized Langevin equation: An efficient approach to nonequilibrium molecular dynamics of open systems

    Science.gov (United States)

    Stella, L.; Lorenz, C. D.; Kantorovich, L.

    2014-04-01

    The generalized Langevin equation (GLE) has been recently suggested to simulate the time evolution of classical solid and molecular systems when considering general nonequilibrium processes. In this approach, a part of the whole system (an open system), which interacts and exchanges energy with its dissipative environment, is studied. Because the GLE is derived by projecting out exactly the harmonic environment, the coupling to it is realistic, while the equations of motion are non-Markovian. Although the GLE formalism has already found promising applications, e.g., in nanotribology and as a powerful thermostat for equilibration in classical molecular dynamics simulations, efficient algorithms to solve the GLE for realistic memory kernels are highly nontrivial, especially if the memory kernels decay nonexponentially. This is due to the fact that one has to generate a colored noise and take account of the memory effects in a consistent manner. In this paper, we present a simple, yet efficient, algorithm for solving the GLE for practical memory kernels and we demonstrate its capability for the exactly solvable case of a harmonic oscillator coupled to a Debye bath.

  20. Non-linear optical techniques and optical properties of condensed molecular systems

    Science.gov (United States)

    Citroni, Margherita

    2013-06-01

    Structure, dynamics, and optical properties of molecular systems can be largely modified by the applied pressure, with remarkable consequences on their chemical stability. Several examples of selective reactions yielding technologically attractive products can be cited, which are particularly efficient when photochemical effects are exploited in conjunction with the structural conditions attained at high density. Non-linear optical techniques are a basic tool to unveil key aspects of the chemical reactivity and dynamic properties of molecules. Their application to high-pressure samples is experimentally challenging, mainly because of the small sample dimensions and of the non-linear effects generated in the anvil materials. In this talk I will present results on the electronic spectra of several aromatic crystals obtained through two-photon induced fluorescence and two-photon excitation profiles measured as a function of pressure (typically up to about 25 GPa), and discuss the relationship between the pressure-induced modifications of the electronic structure and the chemical reactivity at high pressure. I will also present the first successful pump-probe infrared measurement performed as a function of pressure on a condensed molecular system. The system under examination is liquid water, in a sapphire anvil cell, up to 1 GPa along isotherms at 298 and 363 K. These measurements give a new enlightening insight into the dynamical properties of low- and high-density water allowing a definition of the two structures.