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...... a kinetic algorithm, CRISP, that greatly enhances the sampling efficiency in all-atom MC simulations of dense systems. The algorithm is based on an exact analytical solution to the classic chain-closure problem, making it possible to express the interdependencies among degrees of freedom in the molecule...

  2. Subtle Monte Carlo Updates in Dense Molecular Systems.

    Science.gov (United States)

    Bottaro, Sandro; Boomsma, Wouter; E Johansson, Kristoffer; Andreetta, Christian; Hamelryck, Thomas; Ferkinghoff-Borg, Jesper

    2012-02-14

    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 a kinetic algorithm, CRISP, that greatly enhances the sampling efficiency in all-atom MC simulations of dense systems. The algorithm is based on an exact analytical solution to the classic chain-closure problem, making it possible to express the interdependencies among degrees of freedom in the molecule 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.

  3. Role of multipole moments in electric-field-induced order of dense molecular systems.

    Science.gov (United States)

    Acebal, Pablo; Carretero, Luis; Blaya, Salvador

    2010-07-12

    A new model is developed to describe the orientational order of dense molecular systems under an applied external electric field as a function of the n-particle distribution functions of a system under no external perturbation. From an approximation of this expression, the effects of several variables on this orientational order, such as the microscopic properties of the oriented molecules (the molecular geometry and multipole moments) and the solvent or matrix properties, are studied. The theoretical predictions show that, for a correct description of the orientational order, quadrupole and octupole moments must be included, as they play an important role in the orientational order achieved, depending on the molecular geometry. Furthermore, to verify the validity of the model, theoretical predictions are compared with experimental results, and show a good concordance.

  4. Molecular systems under shock compression into the dense plasma regime: carbon dioxide and hydrocarbon polymers

    Science.gov (United States)

    Mattsson, Thomas R.; Cochrane, Kyle R.; Root, Seth; Carpenter, John H.

    2013-10-01

    Density Functional Theory (DFT) has proven remarkably accurate in predicting properties of matter under shock compression into the dense plasma regime. Materials where chemistry plays a role are of interest for many applications, including planetary science and inertial confinement fusion (ICF). As examples of systems where chemical reactions are important, and demonstration of the high fidelity possible for these both structurally and chemically complex systems, we will discuss shock- and re-shock of liquid carbon dioxide (CO2) in the range 100 to 800 GPa and shock compression of hydrocarbon polymers, including GDP (glow discharge polymer) which is used as an ablator in laser ICF experiments. Experimental results from Sandia's Z machine validate the DFT simulations at extreme conditions and the combination of experiment and DFT provide reliable data for evaluating existing and constructing future wide-range equations of state models for molecular compounds. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Company, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  5. Hybrid particle-field molecular dynamics simulations for dense polymer systems.

    Science.gov (United States)

    Milano, Giuseppe; Kawakatsu, Toshihiro

    2009-06-07

    We propose a theoretical scheme for a hybrid simulation technique where self-consistent field theory and molecular dynamics simulation are combined (MD-SCF). We describe the detail of the main implementation issues on the evaluation of a smooth three-dimensional spatial density distribution and its special gradient based on the positions of particles. The treatments of our multiscale model system on an atomic scale or on a specific coarse-grained scale are carefully discussed. We perform a series of test simulations on this hybrid model system and compare the structural correlations on the atomic scale with those of classical MD simulations. The results are very encouraging and open a way to an efficient strategy that possess the main advantages common to the SCF and the atomistic approaches, while avoiding the disadvantages of each of the treatments.

  6. Molecular mobility in dense protein systems: an investigation through 1H NMR relaxometry and diffusometry.

    Science.gov (United States)

    Bouchoux, Antoine; Schorr, Diane; Daffé, Awa; Cambert, Mireille; Gésan-Guiziou, Geneviève; Mariette, François

    2012-09-27

    Understanding how proteins behave in highly concentrated systems is a major issue in many fields of research, including biology, biophysics, and chemical engineering. In this paper, we provide a comprehensive (1)H NMR study of molecular mobility in dilute to highly concentrated dispersions of the exact same protein (casein) but organized in two distinct supramolecular forms: spongelike casein micelles or soft casein aggregates. Both relaxometry and diffusometry experiments were performed, so that three different parameters are reported: spin-spin relaxation rates of non-water protons (1/T(2,ne)), spin-spin relaxation rates of water protons (1/T(2,e+w)), and water self-diffusion coefficients (D(w)). The results are discussed in an effort to understand the respective effects of protein crowding and protein supramolecular organization on each mobility indicator. We also examine if connections exist between the observed changes in molecular mobility and the already documented changes in rheological and osmotic properties of casein dispersions as concentration is increased.

  7. Molecular Dynamics for Dense Matter

    CERN Document Server

    Maruyama, Toshiki; Chiba, Satoshi

    2012-01-01

    We review a molecular dynamics method for nucleon many-body systems called the quantum molecular dynamics (QMD) and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to the 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 on 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 the 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 increase of density, a crystalline solid of spherical nuclei change to a triangular lattice of rods by connecting neighboring nuclei. Finally, we dis...

  8. Quantum molecular dynamics simulations of dense matter

    Energy Technology Data Exchange (ETDEWEB)

    Collins, L.; Kress, J.; Troullier, N.; Lenosky, T.; Kwon, I. [Los Alamos National Lab., Albuquerque, NM (United States)

    1997-12-31

    The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB, which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.

  9. 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

  10. Experimental and molecular dynamics characterization of dense microemulsion 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

  11. Experimental and molecular dynamics characterization of dense microemulsion 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 exper

  12. Dense Molecular Gas: A Sensitive Probe of Stellar Feedback Models

    CERN Document Server

    Hopkins, Philip F; Murray, Norman; Quataert, Eliot

    2012-01-01

    We show that the mass fraction of GMC gas (n>100 cm^-3) in dense (n>>10^4 cm^-3) star-forming clumps, observable in dense molecular tracers (L_HCN/L_CO(1-0)), is a sensitive probe of the strength and mechanism(s) of stellar feedback. Using high-resolution galaxy-scale simulations with pc-scale resolution and explicit models for feedback from radiation pressure, photoionization heating, stellar winds, and supernovae (SNe), we make predictions for the dense molecular gas tracers as a function of GMC and galaxy properties and the efficiency of stellar feedback. In models with weak/no feedback, much of the mass in GMCs collapses into dense sub-units, predicting L_HCN/L_CO(1-0) ratios order-of-magnitude larger than observed. By contrast, models with feedback properties taken directly from stellar evolution calculations predict dense gas tracers in good agreement with observations. Changing the strength or timing of SNe tends to move systems along, rather than off, the L_HCN-L_CO relation (because SNe heat lower-de...

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

    Science.gov (United States)

    Blake, Geoffrey 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.

  14. Dense Molecular Cores Being Externally Heated

    CERN Document Server

    Kim, Gwanjeong; Gopinathan, Maheswar; Jeong, Woong-Seob; Kim, Mi-Ryang

    2016-01-01

    We present results of our study on eight dense cores, previously classified as starless, using infrared (3-160 {\\micron}) imaging observations with \\textit{AKARI} telescope and molecular line (HCN and N$_2$H$^+$) mapping observations with \\textit{KVN} telescope. Combining our results with the archival IR to mm continuum data, we examined the starless nature of these eight cores. Two of the eight cores are found to harbor faint protostars having luminosity of $\\sim0.3-4.4$ L$_{\\odot}$. The other six cores are found to remain as 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 towards 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 over-dominance of red asymmetric line profiles over the cores may indicate that the cores are set into either an expansion or an oscillatory mot...

  15. 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)

  16. 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.

  17. Molecular Description of Yield in Densely Crosslinked Epoxy Thermosets

    Science.gov (United States)

    Chattaraj, Sandipan; Pant, Prita; Pawaskar, Dnyanesh; Nanavati, Hemant

    In densely crosslinked networks, macroscopic yield is a transition from deformations of bond lengths and angles, to cooperative deformation of multiple effective network chains via bond torsions. In this work, we examine this yield in terms of the ''activation number'', ν, of microscopic effective chains between crosslinks. ν is the number of effective network chains, in one Eyring activation volume, V*. It is thus a measure of the number of network chains 'activated' at yield, for cooperative deformation. Microcompression experiments have been performed on SU-8 micropillars, to determine its V* value. SU-8 is an important epoxy thermoset, which is used extensively in the microelectronics industry, in microfluidics and microelectromechanical systems (MEMS). The effective chain length based on Arruda and Boyce's 8-chain model, compares well with the rms length, obtained by chain conformer analyses. We find that ν ~ 2-4, at room temperature, for DGEBA-based epoxies including SU-8 and DGEBA-amine networks, over a range of network junction functionalities and V*. That ν corresponds very well with the reduced temperature, T/Tg, also demonstrates its viability as a molecular descriptor of yield in densely crosslinked thermosets.

  18. Kinetic theory molecular dynamics and hot dense matter: theoretical foundations.

    Science.gov (United States)

    Graziani, F R; Bauer, J D; Murillo, M S

    2014-09-01

    Electrons are weakly coupled in hot, dense matter that is created in high-energy-density experiments. They are also mildly quantum mechanical and the ions associated with them are classical and may be strongly coupled. In addition, the dynamical evolution of plasmas under these hot, dense matter conditions involve a variety of transport and energy exchange processes. Quantum kinetic theory is an ideal tool for treating the electrons but it is not adequate for treating the ions. Molecular dynamics is perfectly suited to describe the classical, strongly coupled ions but not the electrons. We develop a method that combines a Wigner kinetic treatment of the electrons with classical molecular dynamics for the ions. We refer to this hybrid method as "kinetic theory molecular dynamics," or KTMD. The purpose of this paper is to derive KTMD from first principles and place it on a firm theoretical foundation. The framework that KTMD provides for simulating plasmas in the hot, dense regime is particularly useful since current computational methods are generally limited by their inability to treat the dynamical quantum evolution of the electronic component. Using the N-body von Neumann equation for the electron-proton plasma, three variations of KTMD are obtained. Each variant is determined by the physical state of the plasma (e.g., collisional versus collisionless). The first variant of KTMD yields a closed set of equations consisting of a mean-field quantum kinetic equation for the electron one-particle distribution function coupled to a classical Liouville equation for the protons. The latter equation includes both proton-proton Coulombic interactions and an effective electron-proton interaction that involves the convolution of the electron density with the electron-proton Coulomb potential. The mean-field approach is then extended to incorporate equilibrium electron-proton correlations through the Singwi-Tosi-Land-Sjolander (STLS) ansatz. This is the second variant of KTMD

  19. 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.

  20. Contraction Signatures Toward Dense Cores in the Perseus Molecular Cloud

    CERN Document Server

    Campbell, J L; Martin, P G; Caselli, P; Kauffmann, J; Pineda, J E

    2016-01-01

    We report the results of an HCO+ (3-2) and N2D+ (3-2) molecular line survey performed toward 91 dense cores in the Perseus molecular cloud using the James Clerk Maxwell Telescope, to identify the fraction of starless and protostellar cores with systematic radial motions. We quantify the HCO+ asymmetry using a dimensionless asymmetry parameter $\\delta_v$, and identify 20 cores with significant blue or red line asymmetries in optically-thick emission indicative of collapsing or expanding motions, respectively. We separately fit the HCO+ profiles with an analytic collapse model and determine contraction (expansion) speeds toward 22 cores. Comparing the $\\delta_v$ and collapse model results, we find that $\\delta_v$ is a good tracer of core contraction if the optically-thin emission is aligned with the model-derived systemic velocity. The contraction speeds range from subsonic (0.03 km/s) to supersonic (0.4 km/s), where the supersonic contraction speeds may trace global rather than local core contraction. Most cor...

  1. Active fluidization in dense glassy systems.

    Science.gov (United States)

    Mandal, Rituparno; Bhuyan, Pranab Jyoti; Rao, Madan; Dasgupta, Chandan

    2016-07-20

    Dense soft glasses show strong collective caging behavior at sufficiently low temperatures. Using molecular dynamics simulations of a model glass former, we show that the incorporation of activity or self-propulsion, f0, can induce cage breaking and fluidization, resulting in the disappearance of the glassy phase beyond a critical f0. The diffusion coefficient crosses over from being strongly to weakly temperature dependent as f0 is increased. In addition, we demonstrate that activity induces a crossover from a fragile to a strong glass and a tendency of active particles to cluster. Our results are of direct relevance to the collective dynamics of dense active colloidal glasses and to recent experiments on tagged particle diffusion in living cells.

  2. Strategies for Dense Optical CDMA Communication Systems

    Institute of Scientific and Technical Information of China (English)

    WANG Yu-bao; LIN Jin-tong

    2005-01-01

    In this paper,we have formulated a strategy that the limited available code sequences in pure Direct-Sequence(DS)or Frequency-Hopping(FH)system can be reused to realize dense optical CDMA:the strategy of novel hybrid DS/FH system.In which,the case that there are n users employing the same FH pattern but different DS code patterns is considered.On the condition that the impact of channel noises is neglected,the upper bound probability of error is evaluated based on the stationary random process theory.The results show that the hybrid system is suitable for Dense Optical CDMA(DOCDMA)communication.Moreover,the problems such as the link-impairment,dispersion of group velocity,etc.in the pure(DS or FH)system can be solved effectively.

  3. Wave packet molecular dynamics simulations of warm dense hydrogen

    CERN Document Server

    Knaup, M; Toepffer, C; Zwicknagel, G

    2003-01-01

    Recent shock-wave experiments with deuterium in a regime where a plasma phase-transition has been predicted and their theoretical interpretation are the matter of a controversial discussion. In this paper, we apply 'wave packet molecular dynamics' (WPMD) simulations to investigate warm dense hydrogen. The WPMD method was originally used by Heller for a description of the scattering of composite particles such as simple atoms and molecules; later it was applied to Coulomb systems by Klakow et al. In the present version of our model the protons are treated as classical point-particles, whereas the electrons are represented by a completely anti-symmetrized Slater sum of periodic Gaussian wave packets. We present recent results for the equation of state of hydrogen at constant temperature T = 300 K and of deuterium at constant Hugoniot E - E sub 0 + 1/2(1/n - 1/n sub 0)(p + p sub 0) = 0, and compare them with the experiments and several theoretical approaches.

  4. Contraction Signatures toward Dense Cores in the Perseus Molecular Cloud

    Science.gov (United States)

    Campbell, J. L.; Friesen, R. K.; Martin, P. G.; Caselli, P.; Kauffmann, J.; Pineda, J. E.

    2016-03-01

    We report the results of an HCO+ (3-2) and N2D+ (3-2) molecular line survey performed toward 91 dense cores in the Perseus molecular cloud using the James Clerk Maxwell Telescope, to identify the fraction of starless and protostellar cores with systematic radial motions. We quantify the HCO+ asymmetry using a dimensionless asymmetry parameter δv, and identify 20 cores with significant blue or red line asymmetries in optically thick emission indicative of collapsing or expanding motions, respectively. We separately fit the HCO+ profiles with an analytic collapse model and determine contraction (expansion) speeds toward 22 cores. Comparing the δv and collapse model results, we find that δv is a good tracer of core contraction if the optically thin emission is aligned with the model-derived systemic velocity. The contraction speeds range from subsonic (0.03 km s-1) to supersonic (0.4 km s-1), where the supersonic contraction speeds may trace global rather than local core contraction. Most cores have contraction speeds significantly less than their free-fall speeds. Only 7 of 28 starless cores have spectra well-fit by the collapse model, which more than doubles (15 of 28) for protostellar cores. Starless cores with masses greater than the Jeans mass (M/MJ > 1) are somewhat more likely to show contraction motions. We find no trend of optically thin non-thermal line width with M/MJ, suggesting that any undetected contraction motions are small and subsonic. Most starless cores in Perseus are either not in a state of collapse or expansion, or are in a very early stage of collapse.

  5. CONTRACTION SIGNATURES TOWARD DENSE CORES IN THE PERSEUS MOLECULAR CLOUD

    Energy Technology Data Exchange (ETDEWEB)

    Campbell, J. L. [Department of Astronomy and Astrophysics, University of Toronto, 50 St. George St., Toronto, Ontario, M5S 3H4 (Canada); Friesen, R. K. [Dunlap Institute for Astronomy and Astrophysics, University of Toronto, 50 St. George St., Toronto, Ontario, M5S 3H4 (Canada); Martin, P. G. [Canadian Institute for Theoretical Astrophysics, University of Toronto, 60 St. George St., Toronto, Ontario, M5S 3H8 (Canada); Caselli, P.; Pineda, J. E. [Max-Planck-Institut für extraterrestrische Physik (MPE), Gießenbachstrasse 1, D-85741 Garching (Germany); Kauffmann, J., E-mail: jessicalynn.campbell@mail.utoronto.ca [Max-Planck-Institut für Radioastronomie, Auf dem Hügel 69, D-53121 Bonn (Germany)

    2016-03-10

    We report the results of an HCO{sup +} (3–2) and N{sub 2}D{sup +} (3–2) molecular line survey performed toward 91 dense cores in the Perseus molecular cloud using the James Clerk Maxwell Telescope, to identify the fraction of starless and protostellar cores with systematic radial motions. We quantify the HCO{sup +} asymmetry using a dimensionless asymmetry parameter δ{sub v}, and identify 20 cores with significant blue or red line asymmetries in optically thick emission indicative of collapsing or expanding motions, respectively. We separately fit the HCO{sup +} profiles with an analytic collapse model and determine contraction (expansion) speeds toward 22 cores. Comparing the δ{sub v} and collapse model results, we find that δ{sub v} is a good tracer of core contraction if the optically thin emission is aligned with the model-derived systemic velocity. The contraction speeds range from subsonic (0.03 km s{sup −1}) to supersonic (0.4 km s{sup −1}), where the supersonic contraction speeds may trace global rather than local core contraction. Most cores have contraction speeds significantly less than their free-fall speeds. Only 7 of 28 starless cores have spectra well-fit by the collapse model, which more than doubles (15 of 28) for protostellar cores. Starless cores with masses greater than the Jeans mass (M/M{sub J} > 1) are somewhat more likely to show contraction motions. We find no trend of optically thin non-thermal line width with M/M{sub J}, suggesting that any undetected contraction motions are small and subsonic. Most starless cores in Perseus are either not in a state of collapse or expansion, or are in a very early stage of collapse.

  6. Dense circum-nuclear molecular gas in starburst galaxies

    CERN Document Server

    Green, Claire-Elise; Green, James A; Dawson, Joanne R; Jones, Paul A; López-Sánchez, Ángel R; Verdes-Montenegro, Lourdes; Henkel, Christian; Baan, Willem A; Martín, Sergio

    2016-01-01

    We present results from a study of the dense circum-nuclear molecular gas of starburst galaxies. The study aims to investigate the interplay between starbursts, active galactic nuclei and molecular gas. We characterise the dense gas traced by HCN, HCO$^{+}$ and HNC and examine its kinematics in the circum-nuclear regions of nine starburst galaxies observed with the Australia Telescope Compact Array. We detect HCN (1$-$0) and HCO$^{+}$ (1$-$0) in seven of the nine galaxies and HNC (1$-$0) in four. Approximately 7 arcsec resolution maps of the circum-nuclear molecular gas are presented. The velocity integrated intensity ratios, HCO$^{+}$ (1$-$0)/HCN (1$-$0) and HNC (1$-$0)/HCN (1$-$0), are calculated. Using these integrated intensity ratios and spatial intensity ratio maps we identify photon dominated regions (PDRs) in NGC 1097, NGC 1365 and NGC 1808. We find no galaxy which shows the PDR signature in only one part of the observed nuclear region. We also observe unusually strong HNC emission in NGC 5236, but it...

  7. Coupling lattice Boltzmann and molecular dynamics models for dense fluids

    Science.gov (United States)

    Dupuis, A.; Kotsalis, E. M.; Koumoutsakos, P.

    2007-04-01

    We propose a hybrid model, coupling lattice Boltzmann (LB) and molecular dynamics (MD) models, for the simulation of dense fluids. Time and length scales are decoupled by using an iterative Schwarz domain decomposition algorithm. The MD and LB formulations communicate via the exchange of velocities and velocity gradients at the interface. We validate the present LB-MD model in simulations of two- and three-dimensional flows of liquid argon past and through a carbon nanotube. Comparisons with existing hybrid algorithms and with reference MD solutions demonstrate the validity of the present approach.

  8. Dense gas in high-latitude molecular clouds

    Science.gov (United States)

    Reach, William T.; Pound, Marc W.; Wilner, David J.; Lee, Youngung

    1995-01-01

    The nearby molecular clouds MBM 7, 12, 30, 32, 40, 41, and 55 were surveyed for tracers of dense gas, including the (1-0), (2-1), and (3-2) rotational lines of CS and the (1-0) lines of HCO(+) and HCN. MBM 7 and MBM 12 contain dense cores, while the other clouds contain little or no traces of dense gas. Comparison of the emission from dense gas tracers to that of (13)CO reveals that the former are more compact in angular size as well as line width. An extensive CS(2-1) survey of part of MBM 12 reveals that the emission is characterized by clumps on approximately 3 min scales as well as extended emission. Observations of the CS(1-0) and (3-2) lines using telescopes with matched beam sizes reveal that the volume density must be at least approximately 10(exp 4.5)/cc within the (3-2) emitting regions, which are approximately 0.03 pc in radius. Electron excitation of the CS rotational levels is ruled out (in the cores) by comparing the (3-2)/(1-0) line ratios with models including H2 and electron collisions. The volume density in the cores is substantially larger than in the portions of the cloud traced by CO emission. The density increases into the cores as r(exp -2), suggesting dynamical collapse. The masses of the cores are close to the virial mass, suggesting they are dynamically bound. The cores in MBM 7 and MBM 12 are thus likely to form stars; they are the nearest sites of star formation.

  9. The ALMA View of Dense Molecular Gas in 30 Doradus

    Science.gov (United States)

    Bittle, Lauren E.; Indebetouw, Remy; Brogan, Crystal L.; Hunter, Todd R.; Leroy, Adam

    2017-01-01

    At a distance of 50 kpc, the 30 Doradus region within the Large Magellanic Cloud (LMC) hosts several sites of star formation including R136, a starburst region home to dozens of evolved O stars. The intense radiation from R136 creates an extreme environment for nearby star formation in such a low-metallicity, low mass galaxy. We have targeted a star-forming region ~15 pc away from R136 within 30 Doradus using the Atacama Large Millimeter/submillimeter Array (ALMA) to map the molecular gas to study the sites of star formation. We are conducting a clump-by-clump analysis of the intensities and line ratios of dense gas (HCO+, HCN, CS, H13CO+, H13CN) and diffuse gas (CO, 13CO, C18O) tracers at sub-parsec resolution. We identify and characterize ~100 molecular clumps within the region. With the observed molecular species, we aim to determine the physical conditions of each clump (e.g. size, internal turbulence, molecular abundance). We compare the intensities and line ratios to non-LTE Radex model grids of the excitation temperature, molecular column density, and volume density of the H2 collider to determine the physical excitation conditions within the clumps. We compare these properties of each clump to both associated and embedded star formation properties to quantify the relative importance of internal feedback from the star formation itself versus external feedback processes from R136 and determine which process dominates in this region.

  10. Evolution of Binaries in Dense Stellar Systems

    CERN Document Server

    Ivanova, Natalia

    2011-01-01

    In contrast to the field, the binaries in dense stellar systems are frequently not primordial, and could be either dynamically formed or significantly altered from their primordial states. Destruction and formation of binaries occur in parallel all the time. The destruction, which constantly removes soft binaries from a binary pool, works as an energy sink and could be a reason for cluster entering the binary-burning phase. The true binary fraction is greater than observed, as a result, the observable binary fraction evolves differently from the predictions. Combined measurements of binary fractions in globular clusters suggest that most of the clusters are still core-contracting. The formation, on other hand, affects most the more evolutionary advanced stars, which significantly enhances the population of X-ray sources in globular clusters. The formation of binaries with a compact objects proceeds mainly through physical collisions, binary-binary and single-binary encounters; however, it is the dynamical for...

  11. 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.

  12. Dense Molecular Gas and Star Formation in Nearby Seyfert Galaxies

    CERN Document Server

    Kohno, K; Vila-Vilaro, B; Okumura, S K; Shibatsuka, T; Okiura, M; Ishizuki, S; Kawabe, R

    2002-01-01

    An imaging survey of CO(1-0), HCN(1-0), and HCO$^+$(1-0) lines in the centers of nearby Seyfert galaxies has been conducted using the Nobeyama Millimeter Array and the RAINBOW interferometer. Preliminary results reveal that 3 Seyferts out of 7 show abnormally high HCN/CO and HCN/HCO$^+$ ratios, which cannot occur even in nuclear starburst galaxies. We suggest that the enhanced HCN emission originated from X-ray irradiated dense obscuring tori, and that these molecular line ratios can be a new diagnostic tool to search for ``pure'' AGNs. According to our HCN diagram, we suggest that NGC 1068, NGC 1097, and NGC 5194 host ``pure'' AGNs, whereas Seyfert nuclei of NGC 3079, NGC 6764, and NGC 7469 may be ``composite'' in nature.

  13. On the formation of glycolaldehyde in dense molecular cores

    CERN Document Server

    Woods, Paul M; 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 10K 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 CH3OH + HCO being favoured. However, when we consider the feasibility of these mechanisms from a reaction chemistry perspective, the second grain-surface route looks more promising, H3CO + HCO.

  14. The JCMT dense gas survey in dense molecular clouds: an HCO+/HCN comparison

    Science.gov (United States)

    Walker-Smith, Samantha; Richer, John; Buckle, Jane; Salji, Carl; Hatchell, Jennifer; Drabek, Emily

    2013-07-01

    We present the results of a large-scale survey of the very dense molecular gas in Perseus, Orion A and B, Serpens and Ophiuchus using HCO+ and HCN (J = 4 - 3) transitions. We have used this emission to trace the structure and kinematics of gas at the extremely high densities found in pre- and protostellar cores; as well as tracing outflows powered by these early star-forming cores. We present a comparison of the HCO+/HCN data, highlighting regions where there is a marked discrepancy in the spectra of the two emission lines. This is particularly noticeable in some of the more powerful outflows driven by Class 0 sources, where the HCN is greatly enhanced in the linewings in comparison with HCO+. We also use the HCO+ to positively identify protostellar outflows and their driving sources. We present a statistical analysis of the outflow properties that we derive from this tracer. We show that our results are comparable to those obtained from similar outflow analyses using 12CO.

  15. Characterising the Dense Molecular Gas in Exceptional Local Galaxies

    Science.gov (United States)

    Tunnard, Richard C. A.

    2016-08-01

    The interferometric facilities now coming online (the Atacama Large Millimetre Array (ALMA) and the NOrthern Extended Millimeter Array (NOEMA)) and those planned for the coming decade (the Next Generation Very Large Array (ngVLA) and the Square Kilometre Array (SKA)) in the radio to sub-millimetre regimes are opening a window to the molecular gas in high-redshift galaxies. However, our understanding of similar galaxies in the local universe is still far from complete and the data analysis techniques and tools needed to interpret the observations in consistent and comparable ways are yet to be developed. I first describe the Monte Carlo Markov Chain (MCMC) script developed to empower a public radiative transfer code. I characterise both the public code and MCMC script, including an exploration of the effect of observing molecular lines at high redshift where the Cosmic Microwave Background (CMB) can provide a significant background, as well as the effect this can have on well-known local correlations. I present two studies of ultraluminous infrared galaxies (ULIRGs) in the local universe making use of literature and collaborator data. In the first of these, NGC6240, I use the wealth of available data and the geometry of the source to develop a multi-phase, multi-species model, finding evidence for a complex medium of hot diffuse and cold dense gas in pressure equilibrium. Next, I study the prototypical ULIRG Arp 220; an extraordinary galaxy rendered especially interesting by the controversy over the power source of the western of the two merger nuclei and its immense luminosity and dust obscuration. Using traditional grid based methods I explore the molecular gas conditions within the nuclei and find evidence for chemical differentiation between the two nuclei, potentially related to the obscured power source. Finally, I investigate the potential evolution of proto-clusters over cosmic time with sub-millimetre observations of 14 radio galaxies, unexpectedly finding

  16. Dense gas in high-latitude molecular clouds

    Energy Technology Data Exchange (ETDEWEB)

    Reach, W.R.; Pound, M.W.; Wilner, D.J. (Univ. of California, Berkeley (United States)); Lee, Y.

    1992-01-01

    The authors have surveyed high-latitude molecular clouds (MBM 12, 7, 55, 40) in spectral lines that are believed to be dense-gas' tracers due to the high H[sub 2] volume density required for collisional excitation. An extensive CS (2-1) line map of MBM 12 revealed emission that is not confined to clumps. Less than 20% of the integrated line emission from the cloud originates in clearly identified clumps with size between 0.2 pc and 0.02 pc in the integrated line map. The bulk of the emission originates from a relatively smooth horseshoe' structure about 0.1 pc wide and 1 pc long. The CS (2-1) map correlates with the published Bell Labs [sup 13] CO map, with significant [sup 13] CO emission even where the CS emission is undetectable. Within the central core, the C[sup 18]O(1-0) and CS(2-1) lines are positively correlated with significant scatter. There is some indication of higher CS/[sup 13]CO in the cores than the horseshoe'. The observed correlations suggest that both the diffuse CS and [sup 13]CO originate from either numerous, unresolved clumps, or the diffuse parts of the cloud. High-spatial-resolution observations of HCO[sup +] from MBM 12 obtained with the BIMA Hat Creek array demonstrated that the main core emission is primarily on spatial scales greater than 0.004 pc. It appears that the authors have resolved most of the spatial structure of the dense-gas' tracers and have found that the emission is primarily diffuse. To understand the excitation mechanism of the CS rotational levels, a multitransitional study of the 1-0, 2-1, and 3-2 lines is being performed. The CS excitation may be governed by electron collisions in regions with H[sub 2] column densities an order of magnitude lower than the critical density' of [approx gt] 2 [times] 10[sup 4] cm[sup -3]. If electron collisions are populating the CS levels, then the CS and [sup 13]CO lines can both be produced in the outer parts of the cloud, explaining their positive correlation

  17. An unbiased survey for dense cores in the Lynds 1630 molecular cloud

    Science.gov (United States)

    Lada, Elizabeth A.; Bally, John; Stark, Antony A.

    1991-01-01

    An unbiased, systematic survey for dense cores within the L1630 (Orion B) molecular cloud has been completed. This survey provides the first complete census of dense (n greater tha 10,000/cu cm) cores within a molecular cloud. To identify the dense gas, 3.6 square degrees of the L1630 cloud were surveyed in the J = 2-1 transition of CS. CS emission was detected over 10 percent of the area surveyed, and this emission is not uniformly distributed throughout the cloud but is confined to 42 dense cores. The size, shape, velocity dispersion, and mass of these cores are examined. Comparison of the mass contained within dense cores with the total gas mass within the surveyed region, estimated from CO emission, reveals that the dense cores constitute only a small fraction (not greater than 19 percent) of the total cloud mass.

  18. The Dynamics of Dense Cores in the Perseus Molecular Cloud II: The Relationship Between Dense Cores and the Cloud

    CERN Document Server

    Kirk, Helen; Johnstone, Doug; Goodman, Alyssa

    2010-01-01

    We utilize the extensive datasets available for the Perseus molecular cloud to analyze the relationship between the kinematics of small-scale dense cores and the larger structures in which they are embedded. The kinematic measures presented here can be used in conjunction with those discussed in our previous work as strong observational constraints that numerical simulations (or analytic models) of star formation should match. We find that dense cores have small motions with respect to the 13CO gas, about one third of the 13CO velocity dispersion along the same line of sight. Within each extinction region, the core-to-core velocity dispersion is about half of the total (13CO) velocity dispersion seen in the region. Large-scale velocity gradients account for roughly half of the total velocity dispersion in each region, similar to what is predicted from large-scale turbulent modes following a power spectrum of P(k) ~ k^{-4}.

  19. 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

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

    Science.gov (United States)

    Privon, G. C.; Aalto, S.; Falstad, N.; Muller, S.; González-Alfonso, E.; Sliwa, K.; Treister, E.; Costagliola, F.; Armus, L.; Evans, A. S.; Garcia-Burillo, S.; Izumi, T.; Sakamoto, K.; van der Werf, P.; Chu, J. K.

    2017-02-01

    We present new Atacama Large Millimeter/submillimeter Array Band 7 (∼340 GHz) observations of the dense gas tracers HCN, HCO+, and CS in the local, single-nucleus, ultraluminous infrared galaxy IRAS 13120–5453. We find centrally enhanced HCN (4–3) emission, relative to HCO+ (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‑1, the high HCN/HCO+ 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 ΣIR of 4.7 × 1012 L⊙ kpc‑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 H2O lines and find a nuclear dust temperature of ∼40 K. IRAS 13120–5453 has a lower dust temperature and ΣIR 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.

  1. Elastic and thermal expansion asymmetry in dense molecular materials.

    Science.gov (United States)

    Burg, Joseph A; Dauskardt, Reinhold H

    2016-09-01

    The elastic modulus and coefficient of thermal expansion are fundamental properties of elastically stiff molecular materials and are assumed to be the same (symmetric) under both tension and compression loading. We show that molecular materials can have a marked asymmetric elastic modulus and coefficient of thermal expansion that are inherently related to terminal chemical groups that limit molecular network connectivity. In compression, terminal groups sterically interact to stiffen the network, whereas in tension they interact less and disconnect the network. The existence of asymmetric elastic and thermal expansion behaviour has fundamental implications for computational approaches to molecular materials modelling and practical implications on the thermomechanical strains and associated elastic stresses. We develop a design space to control the degree of elastic asymmetry in molecular materials, a vital step towards understanding their integration into device technologies.

  2. Elastic and thermal expansion asymmetry in dense molecular materials

    Science.gov (United States)

    Burg, Joseph A.; Dauskardt, Reinhold H.

    2016-09-01

    The elastic modulus and coefficient of thermal expansion are fundamental properties of elastically stiff molecular materials and are assumed to be the same (symmetric) under both tension and compression loading. We show that molecular materials can have a marked asymmetric elastic modulus and coefficient of thermal expansion that are inherently related to terminal chemical groups that limit molecular network connectivity. In compression, terminal groups sterically interact to stiffen the network, whereas in tension they interact less and disconnect the network. The existence of asymmetric elastic and thermal expansion behaviour has fundamental implications for computational approaches to molecular materials modelling and practical implications on the thermomechanical strains and associated elastic stresses. We develop a design space to control the degree of elastic asymmetry in molecular materials, a vital step towards understanding their integration into device technologies.

  3. A new mechanism for dendritic pattern formation in dense systems

    Science.gov (United States)

    Oikawa, Noriko; Kurita, Rei

    2016-06-01

    Patterns are often formed when particles cluster: Since patterns reflect the connectivity of different types of material, the emergence of patterns affects the physical and chemical properties of systems and shares a close relationship to their macroscopic functions. A radial dendritic pattern (RDP) is observed in many systems such as snow crystals, polymer crystals and biological systems. Although most of these systems are considered as dense particle suspensions, the mechanism of RDP formation in dense particle systems is not yet understood. It should be noted that the diffusion limited aggregation model is not applicable to RDP formation in dense systems, but in dilute particle systems. Here, we propose a simple model that exhibits RDP formation in a dense particle system. The model potential for the inter-particle interaction is composed of two parts, a repulsive and an attractive force. The repulsive force is applied to all the particles all the time and the attractive force is exerted only among particles inside a circular domain, which expands at a certain speed as a wave front propagating from a preselected centre. It is found that an RDP is formed if the velocity of the wave front that triggers the attractive interaction is of the same order of magnitude as the time scale defined by the aggregation speed.

  4. MALT90 Kinematic Distances to Dense Molecular Clumps

    Science.gov (United States)

    Whitaker, J. Scott; Jackson, James M.; Rathborne, J. M.; Foster, J. B.; Contreras, Y.; Sanhueza, Patricio; Stephens, Ian W.; Longmore, S. N.

    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 μm 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+, HNC, and N2H+ (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. High resolution ALMA observations of dense molecular medium in the central regions of active galaxies

    CERN Document Server

    Kohno, Kotaro; Taniguchi, Akio; Izumi, Takuma; Tosaki, Tomoka

    2016-01-01

    In the central regions of active galaxies, dense molecular medium are exposed to various types of radiation and energy injections, such as UV, X-ray, cosmic ray, and shock dissipation. With the rapid progress of chemical models and implementation of new-generation mm/submm interferometry, we are now able to use molecules as powerful diagnostics of the physical and chemical processes in galaxies. Here we give a brief overview on the recent ALMA results to demonstrate how molecules can reveal underlying physical and chemical processes in galaxies. First, new detections of Galactic molecular absorption systems with elevated HCO/H$^{13}$CO$^+$ column density ratios are reported, indicating that these molecular media are irradiated by intense UV fields. Second, we discuss the spatial distributions of various types of shock tracers including HNCO, CH$_3$OH and SiO in NGC 253 and NGC 1068. Lastly, we provide an overview of proposed diagnostic methods of nuclear energy sources using ALMA, with an emphasis on the syne...

  6. ALMA high spatial resolution observations of the dense molecular region of NGC 6302

    CERN Document Server

    Santander-García, M; Alcolea, J; Castro-Carrizo, A; Sánchez-Contreras, C; Quintana-Lacaci, G; Corradi, R L M; Neri, R

    2016-01-01

    The mechanism behind the shaping of bipolar planetary nebulae is still poorly understood. Accurately tracing the molecule-rich equatorial regions of post-AGB stars can give valuable insight into the ejection mechanisms at work. We investigate the physical conditions, structure and velocity field of the dense molecular region of the planetary nebula NGC 6302 by means of ALMA band 7 interferometric maps. The high spatial resolution of the $^{12}$CO and $^{13}$CO J=3-2 ALMA data allows for an analysis of the geometry of the ejecta in unprecedented detail. We built a spatio-kinematical model of the molecular region with the software SHAPE and performed detailed non-LTE calculations of excitation and radiative transfer with the SHAPEMOL plug-in. We find that the molecular region consists of a massive ring out of which a system of fragments of lobe walls emerge and enclose the base of the lobes visible in the optical. The general properties of this region are in agreement with previous works, although the much grea...

  7. Sandqvist 187 - A dense molecular cloud in Norma

    Science.gov (United States)

    Alvarez, H.; Bronfman, L.; Cohen, R.; Garay, G.; Graham, J.; Thaddeus, P.

    1986-01-01

    Observations of Sandqvist 187, an elongated dust cloud in the southern constellation Norma are presented and discussed. The cloud contains two Herbig-Haro objects, HH 56 and HH 57. HH 57 currently displays on its NE edge a 17th mag variable star of the FU Ori type. Using the Columbia University 1.2 m millimeter-wave telescope at Cerro Tololo, the region is mapped and an extended CO cloud which envelops and is elongated along the optical dust cloud is found. The position of maximum CO emission coincides with HH 56 and HH 57. Assuming a distance of 0.7 kpc, the total mass of the cloud is found to be close to 500 solar masses. The CO spectra show evidence of a molecular flow. Photographs and CCD images obtained mostly with the CTIO 4 m telescope show the detailed optical structure of the dark cloud's core region. The Herbig-Haro object HH 56 appears to be related to an emission-line star embedded in the small nebula Reipurth 13, not to the FU Ori star in HH 57.

  8. Sandqvist 187 - A dense molecular cloud in Norma

    Science.gov (United States)

    Alvarez, H.; Bronfman, L.; Cohen, R.; Garay, G.; Graham, J.; Thaddeus, P.

    1986-01-01

    Observations of Sandqvist 187, an elongated dust cloud in the southern constellation Norma are presented and discussed. The cloud contains two Herbig-Haro objects, HH 56 and HH 57. HH 57 currently displays on its NE edge a 17th mag variable star of the FU Ori type. Using the Columbia University 1.2 m millimeter-wave telescope at Cerro Tololo, the region is mapped and an extended CO cloud which envelops and is elongated along the optical dust cloud is found. The position of maximum CO emission coincides with HH 56 and HH 57. Assuming a distance of 0.7 kpc, the total mass of the cloud is found to be close to 500 solar masses. The CO spectra show evidence of a molecular flow. Photographs and CCD images obtained mostly with the CTIO 4 m telescope show the detailed optical structure of the dark cloud's core region. The Herbig-Haro object HH 56 appears to be related to an emission-line star embedded in the small nebula Reipurth 13, not to the FU Ori star in HH 57.

  9. Molecular dynamics of spherical nanoparticles in dense polymer melts.

    Science.gov (United States)

    Patti, Alessandro

    2014-04-03

    By performing molecular dynamics simulations, we investigate the structural and dynamical properties of polymer melts containing probe spherical nanoparticles. Generally speaking, the behavior of these polymer nanocomposites is strongly affected by the interaction strength established between the nanoparticles and the chain monomers and by the nanoparticle sizes. We highlight that this dependence is not always evident and some intriguing properties, such as the heterogeneous dynamics of both polymer chains and nanoparticles and their nonGaussian behavior at short and long timescales, are not particularly influenced by the degree of attraction between nanoparticles and polymer for the range of interactions we study (up to 6 kBT). We find the existence of weakly ordered interdigitated structures with sequential arrangements of particles and polymer chains, which separate each other and hence inhibit the formation of nanoparticle clusters. This is especially evident with big nanoparticles, being less prone to aggregate than small ones, even when their interaction with the polymer chain is as low as 0.5 kBT. Moreover, by integrating the stress-tensor autocorrelation functions, we estimate the shear viscosity and determine its dependence on the strength of the polymer-nanoparticle interactions and on the nanoparticle size. By acting as plasticizers, small nanoparticles decrease the viscosity, especially at low-to-moderate interactions with the polymer. By contrast, big nanoparticles that establish strongly attractive interactions with the polymer chains behave as thickening agents and significantly increase the viscosity. This complex and perhaps still scantily understood balance between the geometry of nanoparticles and their interaction with the polymer is key to predict and fully control the macroscopic response of nanocomposite materials and hence suitably tailor their mechanical properties.

  10. 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.

  11. Molecular dynamics of a dense fluid of polydisperse hard spheres

    OpenAIRE

    Sear, Richard P.

    2000-01-01

    Slow dynamics in a fluid are studied in one of the most basic systems possible: polydisperse hard spheres. Monodisperse hard spheres cannot be studied as the slow down in dynamics as the density is increased is preempted by crystallisation. As the dynamics slow they become more heterogeneous, the spread in the distances traveled by different particles in the same time increases. However, the dynamics appears to be less heterogeneous than in hard-sphere-like colloids at the same volume fractio...

  12. Molecular observations of HH34 - Does NH3 accurately trace dense molecular gas near young stars?

    Science.gov (United States)

    Davis, C. J.; Dent, W. R. F.

    1993-03-01

    Single-dish observations in HCO(+) J = 4-3 are presented of the regions around HH34 and around HH34IRS. The former is one of the best examples of the association between Herbig-Haro shocks, optical jets, and young stellar objects. The HCO(+) and CS maps peak toward the outflow source HH34IRS and suggest the presence of a hot dense molecular core. The NH3 is confined to a peak about 4-0 arcsec east of HH34IRS and to a ridge which extends in a north-south direction and peaks about 20 arcsec south of the end of the optical jet. Thus, the NH3 observations do not trace the underlying gas density and temperature in this outflow source. Toward HH34IRS the NH3 column density is less by a factor of about 10 than toward the NH3 peak position is the HH34 region, providing evidence that the NH3 is underabundant towards the central exciting stars. This underabundance may explain the toroidal structures often seen in NH3 observations of other outflow sources.

  13. Molecular dynamics simulations of microscopic structure of ultra strong shock waves in dense helium

    Science.gov (United States)

    Liu, Hao; Kang, Wei; Zhang, Qi; Zhang, Yin; Duan, Huilin; He, X. T.

    2016-12-01

    Hydrodynamic properties and structure of strong shock waves in classical dense helium are simulated using non-equilibrium molecular dynamics methods. The shock speed in the simulation reaches 100 km/s and the Mach number is over 250, which are close to the parameters of shock waves in the implosion process of inertial confinement fusion. The simulations show that the high-Mach-number shock waves in dense media have notable differences from weak shock waves or those in dilute gases. These results will provide useful information on the implosion process, especially the structure of strong shock wave front, which remains an open question in hydrodynamic simulations.

  14. ALMA high spatial resolution observations of the dense molecular region of NGC 6302

    Science.gov (United States)

    Santander-García, M.; Bujarrabal, V.; Alcolea, J.; Castro-Carrizo, A.; Sánchez Contreras, C.; Quintana-Lacaci, G.; Corradi, R. L. M.; Neri, R.

    2017-01-01

    Context. The mechanism behind the shaping of bipolar planetary nebulae is still poorly understood. It is becoming increasingly clear that the main agents must operate at their innermost regions, where a significant equatorial density enhancement should be present and related to the collimation of light and jet launching from the central star preferentially towards the polar directions. Most of the material in this equatorial condensation must be lost during the asymptotic giant branch as stellar wind and later released from the surface of dust grains to the gas phase in molecular form. Accurately tracing the molecule-rich regions of these objects can give valuable insight into the ejection mechanisms themselves. Aims: We investigate the physical conditions, structure and velocity field of the dense molecular region of the planetary nebula NGC 6302 by means of ALMA band 7 interferometric maps. Methods: The high spatial resolution of the 12CO and 13CO J = 3-2 ALMA data allows for an analysis of the geometry of the ejecta in unprecedented detail. We built a spatio-kinematical model of the molecular region with the software SHAPE and performed detailed non-LTE calculations of excitation and radiative transfer with the shapemol plug-in. Results: We find that the molecular region consists of a massive ring out of which a system of fragments of lobe walls emerge and enclose the base of the lobes visible in the optical. The general properties of this region are in agreement with previous works, although the much greater spatial resolution of the data allows for a very detailed description. We confirm that the mass of the molecular region is 0.1 M⊙. Additionally, we report a previously undetected component at the nebular equator, an inner, younger ring inclined 60° with respect to the main ring, showing a characteristic radius of 7.5 × 1016 cm, a mass of 2.7 × 10-3M⊙, and a counterpart in optical images of the nebula. This inner ring has the same kinematical age as

  15. Molecular and atomic line surveys of galaxies I: the dense, star-forming phase as a beacon

    CERN Document Server

    Geach, James E

    2012-01-01

    We predict the space density of molecular gas reservoirs in the Universe, and place a lower limit on the number counts of carbon monoxide (CO), hydrogen cyanide (HCN) molecular and [CII] atomic emission lines in blind redshift surveys in the submillimeter-centimeter spectral regime. Our model uses: (a) recently available HCN Spectral Line Energy Distributions (SLEDs) of local Luminous Infrared Galaxies (LIRGs, L_IR>10^11 L_sun), (b) a value for epsilon=SFR/M_dense(H_2) provided by new developments in the study of star formation feedback on the interstellar medium and (c) a model for the evolution of the infrared luminosity density. Minimal 'emergent' CO SLEDs from the dense gas reservoirs expected in all star-forming systems in the Universe are then computed from the HCN SLEDs since warm, HCN-bright gas will necessarily be CO-bright, with the dense star-forming gas phase setting an obvious minimum to the total molecular gas mass of any star-forming galaxy. We include [CII] as the most important of the far-inf...

  16. Extended First-Principles Molecular Dynamics Method From Cold Materials to Hot Dense Plasmas

    CERN Document Server

    Zhang, Shen; Kang, Wei; Zhang, Ping; He, Xian-Tu

    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 elec- tronic structures. This gives an edge to the extended method in the calculation of the lowering of ionization potential, X-ray absorption/emission spectra, opacity, and high-Z dense plasmas, which are of particular interest to astrophysics, inertial confinement fusion engineering, and laboratory astrophysics.

  17. Dense molecular cloud cores as a source of micrometer-sized grains in galaxies

    CERN Document Server

    Hirashita, Hiroyuki; Nozawa, Takaya; Li, Zhi-Yun; Liu, Ming-Chang

    2014-01-01

    Coreshine in dense molecular cloud cores (dense cores) is interpreted as evidence for micrometer-sized grains (referred to as very large grains, VLGs). VLGs may have a significant influence on the total dust amount and the extinction curve. We estimate the total abundance of VLGs in the Galaxy, assuming that dense cores are the site of VLG formation. We find that the VLG abundance relative to the total dust mass is roughly $\\phi_\\mathrm{VLG}\\sim 0.01(1-\\epsilon )/\\epsilon (\\tau_\\mathrm{SF}/5\\times 10^9~\\mathrm{yr})^{-1} (f_\\mathrm{VLG}/0.5)(t_\\mathrm{shat}/10^8~\\mathrm{yr})$, where $\\epsilon$ is the star formation efficiency in dense cores, $\\tau_\\mathrm{SF}$ the timescale of gas consumption by star formation, $f_\\mathrm{VLG}$ the fraction of dust mass eventually coagulated into VLGs in dense cores, and $t_\\mathrm{shat}$ the lifetime of VLGs (determined by shattering). Adopting their typical values for the Galaxy, we obtain $\\phi_\\mathrm{VLG}\\sim 0.02$--0.09. This abundance is well below the value detected in...

  18. Quantum molecular dynamics simulations of transport properties in liquid and dense-plasma plutonium

    Science.gov (United States)

    Kress, J. D.; Cohen, James S.; Kilcrease, D. P.; Horner, D. A.; Collins, L. A.

    2011-02-01

    We have calculated the viscosity and self-diffusion coefficients of plutonium in the liquid phase using quantum molecular dynamics (QMD) and in the dense-plasma phase using orbital-free molecular dynamics (OFMD), as well as in the intermediate warm dense matter regime with both methods. Our liquid metal results for viscosity are about 40% lower than measured experimentally, whereas a previous calculation using an empirical interatomic potential (modified embedded-atom method) obtained results 3-4 times larger than the experiment. The QMD and OFMD results agree well at the intermediate temperatures. The calculations in the dense-plasma regime for temperatures from 50 to 5000 eV and densities about 1-5 times ambient are compared with the one-component plasma (OCP) model, using effective charges given by the average-atom code inferno. The inferno-OCP model results agree with the OFMD to within about a factor of 2, except for the viscosity at temperatures less than about 100 eV, where the disagreement is greater. A Stokes-Einstein relationship of the viscosities and diffusion coefficients is found to hold fairly well separately in both the liquid and dense-plasma regimes.

  19. Quantum molecular dynamics simulations of transport properties in liquid and dense-plasma plutonium.

    Science.gov (United States)

    Kress, J D; Cohen, James S; Kilcrease, D P; Horner, D A; Collins, L A

    2011-02-01

    We have calculated the viscosity and self-diffusion coefficients of plutonium in the liquid phase using quantum molecular dynamics (QMD) and in the dense-plasma phase using orbital-free molecular dynamics (OFMD), as well as in the intermediate warm dense matter regime with both methods. Our liquid metal results for viscosity are about 40% lower than measured experimentally, whereas a previous calculation using an empirical interatomic potential (modified embedded-atom method) obtained results 3-4 times larger than the experiment. The QMD and OFMD results agree well at the intermediate temperatures. The calculations in the dense-plasma regime for temperatures from 50 to 5000 eV and densities about 1-5 times ambient are compared with the one-component plasma (OCP) model, using effective charges given by the average-atom code INFERNO. The INFERNO-OCP model results agree with the OFMD to within about a factor of 2, except for the viscosity at temperatures less than about 100 eV, where the disagreement is greater. A Stokes-Einstein relationship of the viscosities and diffusion coefficients is found to hold fairly well separately in both the liquid and dense-plasma regimes.

  20. 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

  1. Dense Molecular Gas and H2O Maser Emission in Galaxies

    Indian Academy of Sciences (India)

    F. Huang; J. S. Zhang; R. M. Li; H. K. Li

    2014-09-01

    Extragalactic H2O masers have been found in dense gas circumstance in off-nuclear star formation regions or within parsecs of Active Galactic Nuclei (AGNs). HCN molecular (one of the best dense gas tracers) Emission has been detected in more than 60 galaxies. For HCN-detected galaxy sample, the relation of maser and gas emission was investigated here to identify physical observable properties that differentiate maser and non-maser galaxies. Our analysis results show that there is no significant difference on the infrared and gas emission between maser galaxies and galaxies without maser detection. For maser host HCN-galaxies, maser luminosity is found to be correlated to CO luminosity (a proxy of the total molecular gas) and HCN luminosity, i.e., kilomasers (H2O < 10⊙) with low maser luminosity having low gas emission luminosity, with respect to megamasers (H2O > 10⊙). For normalized maser and HCN luminosity (for removing distance effect), the correlation is still apparent. However, for normalized maser and CO luminosity, the correlation disappeared completely. Thus one proposition that the amount of dense molecular gas should be a good tracer of H2O maser emission can be made.

  2. 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

  3. LCA of selective waste collection systems in dense urban areas.

    Science.gov (United States)

    Iriarte, Alfredo; Gabarrell, Xavier; Rieradevall, Joan

    2009-02-01

    This paper presents research concerning the environmental analysis of the selective collection management of municipal solid waste. The main goal of this study is to quantify and to compare, by means of Life Cycle Assessment (LCA), the potential environmental impacts of three selective collection systems modelled on densely populated urban areas. These systems are: the mobile pneumatic, the multi-container and the door-to-door. Impact assessment method based on CML 2 baseline 2000 is applied to the different systems. The study separates and analyzes the collection systems in substages: two urban substages and one inter-city substage. At the urban level, the multi-container system has the least environmental impact of all systems. The mobile pneumatic system has greater environmental impacts in terms of global warming, fresh water aquatic ecotoxicity, terrestrial ecotoxicity, acidification and eutrophication. In this system, the pipes and the pneumatic transport have the greatest impacts. The door-to-door system has a greatest environmental impact in terms of abiotic depletion, ozone layer depletion and human toxicity. An overall evaluation of the three substages, with a sensitivity analysis, indicates that the mobile pneumatic system at an inter-city distance of 20 km shows the greatest environmental impacts and the greatest energy demand. Inter-city transport is key; the results show that from an inter-city distance of 11 km onwards, this becomes the substage which most contributes to global warming impact and energy demand, in all the systems.

  4. Compression behavior and structure of dense helium at high temperatures by molecular dynamics simulation

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    In this work,the isotherm and energy distribution at T=304 K of dense helium are studied by molecular dynamic (MD) simulations with exp-6 potential r*=2.9673 ? (the position of the well minimum) and ε/kB=10.8 K (ε is the well-depth and kB is the Boltzmann constant) given by Peter et al.,and different values of stiffness parameter α.The optimized value of α=12.7 is deduced that can describe the atomic interactions for dense helium satisfactorily.This optimized α in exp-6 potential is used to conduct MD simulations of two isotherms of dense helium at T=300 K and T=298K.The calculations are in good agreement with the experimental.We further employed this method to investigate the equation-of-state and structure of dense helium at higher temperatures and found that when the density remained 1.6 g/cm3,the second peak of the radial distribution function would disappear in the temperature range from 2000 to 3040 K,demonstrating that a solid-liquid transition or decrystallization had occurred.

  5. Compression behavior and structure of dense helium at high temperatures by molecular dynamics simulation

    Institute of Scientific and Technical Information of China (English)

    蔡灵仓; 陈其峰; 经福谦; 陈栋泉

    2000-01-01

    In this work, the isotherm and energy distribution at 7= 304 K of dense helium are studied by molecular dynamic (MD) simulations with exp-6 potential r* = 2.967 3 ε(the position of the well minimum) and ε/kb = 10.8 K (e is the well-depth and kB is the Boltzmann constant) given by Peter et al., and different values of stiffness parameter a. The optimized value of a = 12.7 is deduced that can de-scribe the atomic interactions for dense helium satisfactorily. This optimized a in exp-6 potential is used to conduct MD simulations of two isotherms of dense helium at T= 300 K and T= 298 K. The calcula-tions are in good agreement with the experimental. We further employed this method to investigate the equation-of-state and structure of dense helium at higher temperatures and found that when the density remained l .6 g/cm3, the second peak of the radial distribution function would disappear in the tempera-ture range from 2 000 to 3 040 K, demonstrating that a solid-liquid transition or decrystallization had o

  6. Kinetic equation for strongly interacting dense Fermi systems

    CERN Document Server

    Lipavsky, P; Spicka, V

    2001-01-01

    We review the non-relativistic Green's-function approach to the kinetic equations for Fermi liquids far from equilibrium. The emphasis is on the consistent treatment of the off-shell motion between collisions and on the non-instant and non-local picture of binary collisions. The resulting kinetic equation is of the Boltzmann type, and it represents an interpolation between the theory of transport in metals and the theory of moderately dense gases. The free motion of particles is renormalised by various mean field and mass corrections in the spirit of Landau's quasiparticles in metals. The collisions are non-local in the spirit of Enskog's theory of non-ideal gases. The collisions are moreover non-instant, a feature which is absent in the theory of gases, but which is shown to be important for dense Fermi systems. In spite of its formal complexity, the presented theory has a simple implementation within the Monte-Carlo simulation schemes. Applications in nuclear physics are given for heavy-ion reactions and th...

  7. Dense gas in the Galactic central molecular zone is warm and heated by turbulence

    CERN Document Server

    Ginsburg, Adam; Ao, Yiping; Riquelme, Denise; Kauffmann, Jens; Pillai, Thushara; Mills, Elisabeth A C; Requena-Torres, Miguel A; Immer, Katharina; Testi, Leonardo; Ott, Juergen; Bally, John; Battersby, Cara; Darling, Jeremy; Aalto, Susanne; Stanke, Thomas; Kendrew, Sarah; Kruijssen, J M Diederik; Longmore, Steven; Dale, James; Guesten, Rolf; Menten, Karl M

    2016-01-01

    The Galactic center is the closest region in which we can study star formation under extreme physical conditions like those in high-redshift galaxies. We measure the temperature of the dense gas in the central molecular zone (CMZ) and examine what drives it. We mapped the inner 300 pc of the CMZ in the temperature-sensitive J = 3-2 para-formaldehyde (p-H$_2$CO) transitions. We used the $3_{2,1} - 2_{2,0} / 3_{0,3} - 2_{0,2}$ line ratio to determine the gas temperature in $n \\sim 10^4 - 10^5 $cm$^{-3}$ gas. We have produced temperature maps and cubes with 30" and 1 km/s resolution and published all data in FITS form. Dense gas temperatures in the Galactic center range from ~60 K to > 100 K in selected regions. The highest gas temperatures T_G > 100 K are observed around the Sgr B2 cores, in the extended Sgr B2 cloud, the 20 km/s and 50 km/s clouds, and in "The Brick" (G0.253+0.016). We infer an upper limit on the cosmic ray ionization rate ${\\zeta}_{CR} < 10^{-14}$ 1/s. The dense molecular gas temperature o...

  8. Variations in the Star Formation Efficiency of the Dense Molecular Gas across the Disks of Star-forming Galaxies

    NARCIS (Netherlands)

    Usero, Antonio; Leroy, Adam K.; Walter, Fabian; Schruba, Andreas; García-Burillo, Santiago; Sandstrom, Karin; Bigiel, Frank; Brinks, Elias; Kramer, Carsten; Rosolowsky, Erik; Schuster, Karl-Friedrich; de Blok, W. J. G.

    2015-01-01

    We present a new survey of HCN(1-0) emission, a tracer of dense molecular gas, focused on the little-explored regime of normal star-forming galaxy disks. Combining HCN, CO, and infrared (IR) emission, we investigate the role of dense gas in star formation, finding systematic variations in both the a

  9. 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

  10. 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...

  11. Path Integral Monte Carlo and Density Functional Molecular Dynamics Simulations of Warm Dense Matter

    Science.gov (United States)

    Militzer, Burkhard; Driver, Kevin

    2011-10-01

    We analyze the applicability of two first-principles simulation techniques, path integral Monte Carlo (PIMC) and density functional molecular dynamics (DFT-MD), to study the regime of warm dense matter. We discuss the advantages as well as the limitations of each method and propose directions for future development. Results for dense, liquid helium, where both methods have been applied, demonstrate the range of each method's applicability. Comparison of the equations of state from simulations with analytical theories and free energy models show that DFT is useful for temperatures below 100000 K and then PIMC provides accurate results for all higher temperatures. We characterize the structure of the liquid in terms of pair correlation functions and study the closure of the band gap with increasing density and temperature. Finally, we discuss simulations of heavier elements and demonstrate the reliability are both methods in such cases with preliminary results.

  12. Theory for Indirect Conduction in Dense, Gas-Solid Systems

    Science.gov (United States)

    Lattanzi, Aaron; Hrenya, Christine

    2016-11-01

    Heat transfer in dense gas-solid systems is dominated by conduction, and critical to the operation of rotary-kilns, catalytic cracking, and heat exchangers with solid particles as the heat transfer fluid. In particular, the indirect conduction occurring between two bodies separated by a thin layer of fluid can significantly impact the heat transfer within gas-solid systems. Current state-of-the-art models for indirect conduction assume that particles are surrounded by a static "fluid lens" and that one-dimensional conduction occurs through the fluid lens when the lens overlaps another body. However, attempts to evaluate the effect of surface roughness and fluid lens thickness (theoretical inputs) on indirect conduction have been restricted to static, single-particle cases. By contrast, here we quantify these effects for dynamic, multi-particle systems. This analysis is compared to outputs from computational fluid dynamics and discrete element method (CFD-DEM) simulations of heat transfer in a packed bed and flow down a heated ramp. Analytical predictions for model sensitivity are found to be in agreement with simulation results and differ greatly from the static, single-particle analysis. Namely, indirect conduction in static systems is found to be most sensitive to surface roughness, while dynamic systems are sensitive to the fluid lens thickness.

  13. Effects of Atomistic Domain Size on Hybrid Lattice Boltzmann-Molecular Dynamics Simulations of Dense Fluids

    Science.gov (United States)

    Dupuis, A.; Koumoutsakos, P.

    We present a convergence study for a hybrid Lattice Boltzmann-Molecular Dynamics model for the simulation of dense liquids. Time and length scales are decoupled by using an iterative Schwarz domain decomposition algorithm. The velocity field from the atomistic domain is introduced as forcing terms to the Lattice Boltzmann model of the continuum while the mean field of the continuum imposes mean field conditions for the atomistic domain. In the present paper we investigate the effect of varying the size of the atomistic subdomain in simulations of two dimensional flows of liquid argon past carbon nanotubes and assess the efficiency of the method.

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

    Science.gov (United States)

    Li, Zhi-Guo; Cheng, Yan; Chen, Qi-Feng; Chen, Xiang-Rong

    2016-05-01

    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/cm3 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.

  15. Condition for the formation of micron-sized dust grains in dense molecular cloud cores

    CERN Document Server

    Hirashita, Hiroyuki

    2013-01-01

    We investigate the condition for the formation of micron-sized grains in dense cores of molecular clouds. This is motivated by the detection of the mid-infrared emission from deep inside a number of dense cores, the so-called `coreshine,' which is thought to come from scattering by micron-sized grains. Based on numerical calculations of coagulation starting from the typical grain size distribution in the diffuse interstellar medium, we obtain a conservative lower limit to the time $t$ to form micron-sized grains: $t/t_\\mathrm{ff}>3 (5/S) (n_\\mathrm{H}/10^5 \\mathrm{cm}^{-3})^{-1/4}$ (where $t_\\mathrm{ff}$ is the free-fall time at hydrogen number density $n_\\mathrm{H}$ in the core, and $S$ the enhancement factor to the grain-grain collision cross-section to account for non-compact aggregates). At the typical core density $n_\\mathrm{H}=10^5 \\mathrm{cm}^{-3}$, it takes at least a few free-fall times to form the micron-sized grains responsible for coreshine. The implication is that those dense cores observed in co...

  16. 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

  17. Dense Molecular Gas Tracers in the Outflow of the Starburst Galaxy NGC 253

    Science.gov (United States)

    Walter, Fabian; Bolatto, Alberto D.; Leroy, Adam K.; Veilleux, Sylvain; Warren, Steven R.; Hodge, Jacqueline; Levy, Rebecca C.; Meier, David S.; Ostriker, Eve C.; Ott, Jürgen; Rosolowsky, Erik; Scoville, Nick; Weiss, Axel; Zschaechner, Laura; Zwaan, Martin

    2017-02-01

    We present a detailed study of a molecular outflow feature in the nearby starburst galaxy NGC 253 using ALMA. We find that this feature is clearly associated with the edge of NGC 253's prominent ionized outflow, has a projected length of ∼300 pc, with a width of ∼50 pc, and a velocity dispersion of ∼40 km s‑1, which is consistent with an ejection from the disk about 1 Myr ago. The kinematics of the molecular gas in this feature can be interpreted (albeit not uniquely) as accelerating at a rate of 1 km s‑1 pc‑1. In this scenario, the gas is approaching an escape velocity at the last measured point. Strikingly, bright tracers of dense molecular gas (HCN, CN, HCO+, CS) are also detected in the molecular outflow: we measure an HCN(1–0)/CO(1–0) line ratio of ∼ 1/10 in the outflow, similar to that in the central starburst region of NGC 253 and other starburst galaxies. By contrast, the HCN/CO line ratio in the NGC 253 disk is significantly lower (∼ 1/30), similar to other nearby galaxy disks. This strongly suggests that the streamer gas originates from the starburst, and that its physical state does not change significantly over timescales of ∼1 Myr during its entrainment in the outflow. Simple calculations indicate that radiation pressure is not the main mechanism for driving the outflow. The presence of such dense material in molecular outflows needs to be accounted for in simulations of galactic outflows.

  18. 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.

  19. The Dense Gas Fraction in the Central Molecular Zone in the Milky Way

    Science.gov (United States)

    Vargas-Salazar, Irene; Battersby, Cara; Walker, Daniel; Zhang, Qizhou; CMZoom

    2017-01-01

    The Central Molecular Zone (CMZ), a large reservoir of dense molecular gas occupying the central 500pc of the Milky Way, is an extreme star-formation environment where the validity of star formation prescriptions can be tested. The star formation rate (SFR) in the CMZ is about an order of magnitude lower than predicted by the currently accepted prescriptions. An international team lead by PIs Battersby and Keto conducted a survey from 2013-2016 called CMZoom using the Submillimeter Array (SMA) to characterize star formation within resolved molecular clouds in this extreme region. One of the main goals of this survey is to further quantify and understand the low SFR found in this region of the Galaxy. Here, we use the CASA software package to run synthetic observations of hydrodynamical simulations of molecular clouds and vary the observation parameters in such a way that we explore the real parameter space that was probed during the survey. The purpose of this is to investigate how the different observational parameters affect the resultant data. Afterwards, we estimate the “dense gas fraction” (DGF) found in regions across the CMZ. This estimate was found by using the interferometric flux from SMA and the single-dish flux from the Bolocam Galactic Plane Survey. We analyzed the effects that different locations of the CMZ had on these approximate DGF. With these simulations and DGF estimates, we are able to generate improved methods to analyze the data from this survey that will help understand star formation in an extreme environment.The SAO REU program is funded in part by the National Science Foundation REU and Department of Defense ASSURE programs under NSF Grant no.1262851, and by the Smithsonian Institution.

  20. Laser cooling of dense atomic gases by collisional redistribution of radiation and spectroscopy of molecular dimers in a dense buffer gas environment

    CERN Document Server

    Saß, Anne; Christopoulos, Stavros; Knicker, Katharina; Moroshkin, Peter; Weitz, Martin

    2014-01-01

    We study laser cooling of atomic gases by collisional redistribution of fluorescence. In a high pressure buffer gas regime, frequent collisions perturb the energy levels of alkali atoms, which allows for the absorption of a far red detuned irradiated laser beam. Subsequent spontaneous decay occurs close to the unperturbed resonance frequency, leading to a cooling of the dense gas mixture by redistribution of fluorescence. Thermal deflection spectroscopy indicates large relative temperature changes down to and even below room temperature starting from an initial cell temperature near 700 K. We are currently performing a detailed analysis of the temperature distribution in the cell. As we expect this cooling technique to work also for molecular-noble gas mixtures, we also present initial spectroscopic experiments on alkali-dimers in a dense buffer gas surrounding.

  1. Variations in the Star Formation Efficiency of the Dense Molecular Gas across the Disks of Star-Forming Galaxies

    CERN Document Server

    Usero, Antonio; Walter, Fabian; Schruba, Andreas; García-Burillo, Santiago; Sandstrom, Karin; Bigiel, Frank; Brinks, Elias; Kramer, Carsten; Rosolowsky, Erik; Schuster, Karl-Friedrich; de Blok, W J G

    2015-01-01

    We present a new survey of HCN(1-0) emission, a tracer of dense molecular gas, focused on the little-explored regime of normal star-forming galaxy disks. Combining HCN, CO, and infrared (IR) emission, we investigate the role of dense gas in Star Formation (SF), finding systematic variations in both the apparent dense gas fraction and the apparent SF efficiency (SFE) of dense gas. The latter may be unexpected, given the popularity of gas density threshold models to explain SF scaling relations. We used the IRAM 30-m telescope to observe HCN(1-0) across 29 nearby disk galaxies whose CO(2-1) emission has previously been mapped by the HERACLES survey. Because our observations span a range of galactocentric radii, we are able to investigate the properties of the dense gas as a function of local conditions. We focus on how the IR/CO, HCN/CO, and IR/HCN ratios (observational cognates of the SFE, dense gas fraction, and dense gas SFE) depend on the stellar surface density and the molecular/atomic ratio. The HCN/CO ra...

  2. Equations of state and transport properties of warm dense beryllium: a quantum molecular dynamics study.

    Science.gov (United States)

    Wang, Cong; Long, Yao; Tian, Ming-Feng; He, Xian-Tu; Zhang, Ping

    2013-04-01

    We have calculated the equations of state, the viscosity and self-diffusion coefficients, and electronic transport coefficients of beryllium in the warm dense regime for densities from 4.0 to 6.0 g/cm(3) and temperatures from 1.0 to 10.0 eV by using quantum molecular dynamics simulations. The principal Hugoniot curve is in agreement with underground nuclear explosive and high-power laser experimental results up to ~20 Mbar. The calculated viscosity and self-diffusion coefficients are compared with the one-component plasma model, using effective charges given by the average-atom model. The Stokes-Einstein relationship, which connects viscosity and self-diffusion coefficients, is found to hold fairly well in the strong coupling regime. The Lorenz number, which is the ratio between thermal and electrical conductivities, is computed via Kubo-Greenwood formula and compared to the well-known Wiedemann-Franz law in the warm dense region.

  3. Orbital-free molecular dynamics simulations of transport properties in dense-plasma uranium

    Science.gov (United States)

    Kress, J. D.; Cohen, James S.; Kilcrease, D. P.; Horner, D. A.; Collins, L. A.

    2011-09-01

    We have calculated the self-diffusion coefficients and shear viscosity of dense-plasma uranium using orbital-free molecular dynamics (OFMD) at the Thomas-Fermi-Dirac level. The transport properties of uranium in this regime have not previously been investigated experimentally or theoretically. The OFMD calculations were performed for temperatures from 50 to 5000 eV and densities from ambient to 10 times compressed. The results are compared with the one-component-plasma (OCP) model, using effective charges given by the average-atom code INFERNO and by the regularization procedure from the OFMD method. The latter generally showed better agreement with the OFMD for viscosity and the former for diffusion. A Stokes-Einstein relationship of the OFMD viscosities and diffusion coefficients is found to hold fairly well with a constant of 0.075 ± 0.10, while the OCP/INFERNO model yields 0.13 ± 0.10.

  4. Quantum molecular dynamics simulations of equation of state of warm dense ethane

    Science.gov (United States)

    Li, Chuan-Ying; Wang, Cong; Li, Yong-Sheng; Li, Da-Fang; Li, Zi; Zhang, Ping

    2016-09-01

    The equation of state of warm dense ethane is obtained using quantum molecular dynamics simulations based on finite-temperature density functional theory for densities from 0.1 g / cm 3 to 3.1 g / cm 3 and temperatures from 0.1 eV to 5.17 eV. The calculated pressure and internal energy are fitted with cubic polynomials in terms of density and temperature. Specific density-temperature-pressure tracks such as the principal and double shock Hugoniot curves along with release isentropes are predicted which are fundamental for the analysis and interpretation of high-pressure experiments. The principal and double shock Hugoniot curves are in agreement with the experimental data from the Sandia Z-Machine [Magyar et al., Phys. Rev. B 91, 134109 (2015)].

  5. Molecular line emission in NGC1068 imaged with ALMA. I An AGN-driven outflow in the dense molecular gas

    CERN Document Server

    Garcia-Burillo, S; Usero, A; Aalto, S; Krips, M; Viti, S; Alonso-Herrero, A; Hunt, L K; Schinnerer, E; Baker, A J; Casasola, F Boone V; Colina, L; Costagliola, F; Eckart, A; Fuente, A; Henkel, C; Labiano, A; Martin, S; Marquez, I; Muller, S; Planesas, P; Almeida, C Ramos; Spaans, M; Tacconi, L J; van der Werf, P P

    2014-01-01

    We investigate the fueling and the feedback of star formation and nuclear activity in NGC1068, a nearby (D=14Mpc) Seyfert 2 barred galaxy, by analyzing the distribution and kinematics of the molecular gas in the disk. We have used ALMA to map the emission of a set of dense molecular gas tracers (CO(3-2), CO(6-5), HCN(4-3), HCO+(4-3) and CS(7-6)) and their underlying continuum emission in the central r ~ 2kpc of NGC1068 with spatial resolutions ~ 0.3"-0.5" (~ 20-35pc). Molecular line and dust continuum emissions are detected from a r ~ 200pc off-centered circumnuclear disk (CND), from the 2.6kpc-diameter bar region, and from the r ~ 1.3kpc starburst (SB) ring. Most of the emission in HCO+, HCN and CS stems from the CND. Molecular line ratios show dramatic order-of-magnitude changes inside the CND that are correlated with the UV/X-ray illumination by the AGN, betraying ongoing feedback. The gas kinematics from r ~ 50pc out to r ~ 400pc reveal a massive (M_mol ~ 2.7 (+0.9, -1.2) x 10^7 Msun) outflow in all molec...

  6. On the Ubiquity of Molecular Anions in the Dense Interstellar Medium

    Science.gov (United States)

    Cordiner, M. A.; Buckle, J. V.; Wirstroem, E. S.; Olofsson, A. O. H.; Charnley, S. B.

    2013-01-01

    Results are presented from a survey for molecular anions in seven nearby Galactic star-forming cores and molecular clouds. The hydrocarbon anion C6H(-) is detected in all seven target sources, including four sources where no anions have been previously detected: L1172, L1389, L1495B, and TMC-1C. The C6H(-) /C6H column density ratio is approx. > 1.0% in every source, with a mean value of 3.0% (and standard deviation 0.92%). Combined with previous detections, our results show that anions are ubiquitous in dense clouds wherever C6H is present. The C6H(-)/C6H ratio is found to show a positive correlation with molecular hydrogen number density, and with the apparent age of the cloud.We also report the first detection of C4H(-) in TMC-1 (at 4.8 sigma confidence), and derive an anion-to-neutral ratio C4H(-) /C4H = (1.2 +/- 0.4)×10(exp -5)(= 0.0012% +/- 0.0004%). Such a low value compared with C6H(-) highlights the need for a revised radiative electron attachment rate for C4H. Chemical model calculations show that the observed C4H(-) could be produced as a result of reactions of oxygen atoms with C5H(-) and C6H(-).

  7. Excitatory and Inhibitory Neurons in the Hippocampus Exhibit Molecularly Distinct Large Dense Core Vesicles

    Directory of Open Access Journals (Sweden)

    Jose Jorge Ramirez-Franco

    2016-08-01

    Full Text Available Hippocampal interneurons comprise a diverse family of inhibitory neurons which function is critical for fine information processing. Along with gamma-aminobutyric acid (GABA, interneurons secrete a myriad of neuroactive substances via secretory vesicles which molecular composition and regulatory mechanisms remain unknown. In this study, we have carried out an immunohistofluorescence analysis to describe the molecular content of vesicles in distinct populations of hippocampal neurons. Our results indicate that phogrin, an integral protein of secretory vesicles in neuroendocrine cells, is highly enriched in parvalbumin-positive interneurons. Consistently, immunoelectron microscopy revealed phogrin staining in axon terminals of symmetrical synapses establishing inhibitory contacts with cell bodies of CA1 pyramidal neurons. Furthermore, phogrin is highly expressed in CA3 and dentate gyrus interneurons which are both positive for PV and neuropeptide Y. Surprisingly, chromogranin B a canonical large dense core vesicle marker, is excluded from inhibitory cells in the hippocampus but highly expressed in excitatory CA3 pyramidal neurons and dentate gyrus granule cells. Our results provide the first evidence of phogrin expression in hippocampal interneurons and suggest the existence of molecularly distinct populations of secretory vesicles in different types of inhibitory neurons.

  8. Molecular line emission in NGC 1068 imaged with ALMA. II. The chemistry of the dense molecular gas

    Science.gov (United States)

    Viti, S.; García-Burillo, S.; Fuente, A.; Hunt, L. K.; Usero, A.; Henkel, C.; Eckart, A.; Martin, S.; Spaans, M.; Muller, S.; Combes, F.; Krips, M.; Schinnerer, E.; Casasola, V.; Costagliola, F.; Marquez, I.; Planesas, P.; van der Werf, P. P.; Aalto, S.; Baker, A. J.; Boone, F.; Tacconi, L. J.

    2014-10-01

    Aims: We present a detailed analysis of Atacama Large Millimeter/submillimeter Array (ALMA) Bands 7 and 9 data of CO, HCO+, HCN, and CS, augmented with Plateau de Bure Interferometer (PdBI) data of the ~200 pc circumnuclear disc (CND) and the ~1.3 kpc starburst ring (SB ring) of NGC 1068, a nearby (D = 14 Mpc) Seyfert 2 barred galaxy. We aim to determine the physical characteristics of the dense gas present in the CND, and to establish whether the different line intensity ratios we find within the CND, as well as between the CND and the SB ring, are due to excitation effects (gas density and temperature differences) or to a different chemistry. Methods: We estimate the column densities of each species in local thermodynamic equilibrium (LTE). We then compute large one-dimensional, non-LTE radiative transfer grids (using RADEX) by using only the CO transitions first, and then all the available molecules to constrain the densities, temperatures, and column densities within the CND. We finally present a preliminary set of chemical models to determine the origin of the gas. Results: We find that, in general, the gas in the CND is very dense (>105 cm-3) and hot (T> 150 K), with differences especially in the temperature across the CND. The AGN position has the lowest CO/HCO+, CO/HCN, and CO/CS column density ratios. The RADEX analyses seem to indicate that there is chemical differentiation across the CND. We also find differences between the chemistry of the SB ring and some regions of the CND; the SB ring is also much colder and less dense than the CND. Chemical modelling does not succeed in reproducing all the molecular ratios with one model per region, suggesting the presence of multi-gas phase components. Conclusions: The LTE, RADEX, and chemical analyses all indicate that more than one gas-phase component is necessary to uniquely fit all the available molecular ratios within the CND. A higher number of molecular transitions at the ALMA resolution is necessary to

  9. Low-temperature phases of dense hydrogen and deuterium by first-principles path-integral molecular dynamics

    Science.gov (United States)

    Torrent, Marc; Geneste, Gregory

    2012-02-01

    The low-temperature phases of dense hydrogen and deuterium have been investigated using first-principles path-integral molecular dynamics, a technique that we have recently implemented in the ABINIT code and that allows to account for the quantum fluctuations of atomic nuclei. A massively parallelized scheme is applied to produce trajectories of several tens of thousands steps using a 64-atom supercell and a Trotter number of 64. The so-called phases I, II and III are studied and compared to the structures proposed in the literature. The quantum fluctuations produce configurational disorder and are shown to systematically enhance the symmetry of the system: a continuous gain of symmetry in the angular density of probability of the molecules is found from classical particles to quantum D2 and finally to quantum H2. Particular emphasis is made on the ``broken-symmetry'' phase (phase II).

  10. Restricted Path-Integral Molecular Dynamics for Simulating the Correlated Electron Plasma in Warm Dense Matter

    Science.gov (United States)

    Kapila, Vivek; Deymier, Pierre; Runge, Keith

    2011-10-01

    Several areas of study including heavy ion beam, large scale laser, and high pressure or Thomson scattering studies necessitate a fundamental understanding of warm dense matter (WDM) i.e. matter at high temperature and high density. The WDM regime, however, lacks any adequate highly developed class of simulation methods. Recent progress to address this deficit has been the development of orbital-free Density Functional Theory (ofDFT). However, scant benchmark information is available on temperature and pressure dependence of simple but realistic models in WDM regime. The present work aims to fill this critical gap using the restricted path-integral molecular dynamics (rPIMD) method. Within the discrete path integral representation, electrons are described as harmonic necklaces. Quantum exchange takes the form of cross linking between electron necklaces. The fermion sign problem is addressed by restricting the density matrix to positive values. The molecular dynamics algorithm is employed to sample phase space. Here, we focus on the behavior of strongly correlated electron plasmas under WDM conditions. We compute the kinetic and potential energies and compare them to those obtained with the ofDFT method. Several areas of study including heavy ion beam, large scale laser, and high pressure or Thomson scattering studies necessitate a fundamental understanding of warm dense matter (WDM) i.e. matter at high temperature and high density. The WDM regime, however, lacks any adequate highly developed class of simulation methods. Recent progress to address this deficit has been the development of orbital-free Density Functional Theory (ofDFT). However, scant benchmark information is available on temperature and pressure dependence of simple but realistic models in WDM regime. The present work aims to fill this critical gap using the restricted path-integral molecular dynamics (rPIMD) method. Within the discrete path integral representation, electrons are described as

  11. Dense Gas in Molecular Cores Associated with Planck Galactic Cold Clumps

    Science.gov (United States)

    Yuan, Jinghua; Wu, Yuefang; Liu, Tie; Zhang, Tianwei; Zeng Li, Jin; Liu, Hong-Li; Meng, Fanyi; Chen, Ping; Hu, Runjie; Wang, Ke

    2016-03-01

    We present the first survey of dense gas toward Planck Galactic Cold Clumps (PGCCs). Observations in the J = 1-0 transitions of HCO+ 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+ and 158 in HCN. Spectra of the J = 1-0 transitions from 12CO, 13CO, and C18O 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+, 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 C18O 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+ are positively correlated with those of HCN, suggesting that these two species are well coupled and chemically connected. The detected abundances of both HCO+ 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.

  12. ON THE UBIQUITY OF MOLECULAR ANIONS IN THE DENSE INTERSTELLAR MEDIUM

    Energy Technology Data Exchange (ETDEWEB)

    Cordiner, M. A.; Wirstroem, E. S.; Charnley, S. B. [Astrochemistry Laboratory and The Goddard Center for Astrobiology, NASA Goddard Space Flight Center, Code 691, 8800 Greenbelt Road, Greenbelt, MD 20771 (United States); Buckle, J. V. [Cavendish Astrophysics Group and Kavli Institute for Cosmology, Institute of Astronomy, University of Cambridge, Madingley Road, Cambridge CB3 0HE (United Kingdom); Olofsson, A. O. H., E-mail: martin.cordiner@nasa.gov [Department of Earth and Space Sciences, Chalmers University of Technology, Onsala Space Observatory, SE-439 92 Onsala (Sweden)

    2013-06-10

    Results are presented from a survey for molecular anions in seven nearby Galactic star-forming cores and molecular clouds. The hydrocarbon anion C{sub 6}H{sup -} is detected in all seven target sources, including four sources where no anions have been previously detected: L1172, L1389, L1495B, and TMC-1C. The C{sub 6}H{sup -}/C{sub 6}H column density ratio is {approx}> 1.0% in every source, with a mean value of 3.0% (and standard deviation 0.92%). Combined with previous detections, our results show that anions are ubiquitous in dense clouds wherever C{sub 6}H is present. The C{sub 6}H{sup -}/C{sub 6}H ratio is found to show a positive correlation with molecular hydrogen number density, and with the apparent age of the cloud. We also report the first detection of C{sub 4}H{sup -} in TMC-1 (at 4.8{sigma} confidence), and derive an anion-to-neutral ratio C{sub 4}H{sup -}/C{sub 4}H =(1.2 {+-} 0.4) Multiplication-Sign 10{sup -5}(= 0.0012% {+-} 0.0004%). Such a low value compared with C{sub 6}H{sup -} highlights the need for a revised radiative electron attachment rate for C{sub 4}H. Chemical model calculations show that the observed C{sub 4}H{sup -} could be produced as a result of reactions of oxygen atoms with C{sub 5}H{sup -} and C{sub 6}H{sup -}.

  13. Detection of HCN, HCO+ and HNC in the Mrk231 molecular outflow - Dense molecular gas in the AGN wind

    CERN Document Server

    Aalto, S; Muller, S; Winters, J M; van der Werf, P; Henkel, C; Costagliola, F; Neri, R

    2011-01-01

    We detect luminous emission from HCN, HCO+ and HNC 1--0 in the QSO ULIRG Mrk~231 with the IRAM Plateau de Bure Interferometer at 1."55 by 1."28 resolution. All three lines show broad line wings - which are particularly prominent for HCN. Velocities are found to be similar (750 km/s) to those found for CO 1-0. This is the first time bright HCN, HCO+ and HNC emission has been detected in a large-scale galactic outflow. We find that both the blue- and red-shifted line wings are spatially extended by at least 0."75 (700 pc) in a north-south direction. The line wings are brighter (relative to the line center intensity) in HCN than in CO 1-0 and line ratios suggest that the molecular outflow consists of dense (n>10E4 cmE-3) and clumpy gas with a high HCN abundance X(HCN)>10E-8. These properties are consistent with the molecular gas being compressed and fragmented by shocks in the outflow. Alternatively, HCN is instead pumped by mid-IR continuum, but we propose that this effect is not strong for the spatially extend...

  14. Variation in dust properties in a dense filament of the Taurus molecular complex (L1506)

    CERN Document Server

    Ysard, Nathalie; Ristorcelli, Isabelle; Juvela, Mika; Pagani, Laurent; Konyves, Vera; Spencer, Locke; White, Glenn; Zavagno, Annie

    2013-01-01

    We observed the L1506 filament, which is located in the Taurus molecular complex, with the Herschel PACS and SPIRE instruments. Our aim is to prove the variation in grain properties along the entire length of the filament. In particular, we want to determine above which gas density this variation arises and what changes in the grain optical properties/size distribution are required. We use the 3D radiative transfer code CRT, coupled to the dust emission and extinction code DustEM, to model the emission and extinction of the dense filament. We test a range of optical properties and size distributions for the grains: dust of the diffuse interstellar medium (interstellar PAHs and amorphous carbons and silicates) and both compact and fluffy aggregates. We find that the grain opacity has to increase across the filament to fit simultaneously the near-IR extinction and Herschel emission profiles of L1506. We interpret this change to be a consequence of the coagulation of dust grains to form fluffy aggregates. Grains...

  15. Dense Molecular Gas around AGN: HCN/CO in NGC3227

    CERN Document Server

    Davies, R; Sternberg, A

    2011-01-01

    There is now convincing evidence that the intensity of HCN molecular line emission is enhanced around active galactic nuclei. In this paper we examine the specific case of the Seyfert galaxy NGC3227, for which there are subarcsecond resolution data for the HCN (1-0) 88 GHz and CO (2-1) 230 GHz rotational lines, enabling us to spatially separate a circumnuclear ring at a radius of 140pc and an inner nuclear region within 40pc of the AGN. The HCN(1-0)/CO(2-1) flux ratio differs by more than an order of magnitude between these two regions. We carry out large velocity gradient (LVG) computations to determine the range of parameters (gas temperature and density, HCN/CO abundance ratio, column densities and velocity gradients) that yield physically plausible solutions for the observed flux ratio in the central 100pc. The observed HCN/CO intensity ratio in the nucleus is consistent with very optically thick thermalized emission in very dense (>=10^5cm^{-3}) gas, in which case the HCN/CO abundance ratio there is unco...

  16. Path integral Monte Carlo and density functional molecular dynamics simulations of hot, dense helium

    Science.gov (United States)

    Militzer, B.

    2009-04-01

    Two first-principles simulation techniques, path integral Monte Carlo (PIMC) and density functional molecular dynamics (DFT-MD), are applied to study hot, dense helium in the density-temperature range of 0.387-5.35gcm-3 and 500K-1.28×108K . One coherent equation of state is derived by combining DFT-MD data at lower temperatures with PIMC results at higher temperatures. Good agreement between both techniques is found in an intermediate-temperature range. For the highest temperatures, the PIMC results converge to the Debye-Hückel limiting law. In order to derive the entropy, a thermodynamically consistent free-energy fit is used that reproduces the internal energies and pressure derived from the first-principles simulations. The equation of state is presented in the form of a table as well as a fit and is compared with different free-energy models. Pair-correlation functions and the electronic density of states are discussed. Shock Hugoniot curves are compared with recent laser shock-wave experiments.

  17. Dense gas in molecular cores associated with Planck Galactic cold clumps

    CERN Document Server

    Yuan, Jinghua; Liu, Tie; Zhang, Tianwei; Li, Jin Zeng; Liu, Hong-Li; Meng, Fanyi; Chen, Ping; Hu, Runjie; Wang, Ke

    2016-01-01

    We present the first survey of dense gas towards Planck Galactic Cold Clumps (PGCCs). Observations in the J=1-0 transitions of HCO+ and HCN towards 621 molecular cores associated with PGCCs were performed using the Purple Mountain Observatory 13.7-m telescope. Among them, 250 sources have detection, including 230 cores detected in HCO+ and 158 in HCN. Spectra of the J=1-0 transitions from CO, 13CO, and C18O 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 well consistence among central velocities of CO, HCO+, and HCN spectra, suggests that the CO-selected Planck cores are more quiescent compared to classical star-forming regions. The small difference between line widths of C18O and HCN indicates that the inner regions of CO-selected Planck cores are not more turbulent than the exterior. The velocity-integrated intensities and abundances of HCO+ are p...

  18. A massive molecular outflow in the dense dust core AGAL G337.916-00.477

    CERN Document Server

    Torii, Kazufumi; Hasegawa, Keisuke; Ohama, Akio; Yamamoto, Hiroaki; Tachihara, Kengo; Tokuda, Kazuki; Onishi, Toshikazu; Hattori, Yasuki; Ishihara, Daisuke; Kaneda, Hidehiro; Fukui, Yasuo

    2016-01-01

    The massive molecular outflows erupting from the high-mass young stellar objects provide important clues to understand the mechanism of the high-mass star formation. Based on new CO J=3-2 and J=1-0 observations with ASTE and Mopra, we discovered a new and very young massive bipolar outflow associated with the dense dust core AGAL G337.916-00.477 (AGAL337.9-S), located at 3.2kpc. The outflow is very compact less than 1,pc and is not fully resolved in the angular resolutions of ASTE and Mopra. The maximum velocities of the outflow lobes are as high as 30-40km/s. The total source luminosity for AGAL337.9-S was estimated to be ~10^5 Lo. Compared with the other massive outflows, we concluded that the AGAL337.9-S outflow is certainly one of the most massive and youngest high-mass young stellar objects ever known in the Milky Way. The short dynamical timescale ~10^4yrs of the outflow and mid-infrared-faint spectral energy distribution of AGAL337.9-S support for its young age. We also found that another dust core AGA...

  19. A Massive Molecular Outflow in the Dense Dust Core AGAL G337.916-00.477

    Science.gov (United States)

    Torii, Kazufumi; Hattori, Yusuke; Hasegawa, Keisuke; Ohama, Akio; Yamamoto, Hiroaki; Tachihara, Kengo; Tokuda, Kazuki; Onishi, Toshikazu; Hattori, Yasuki; Ishihara, Daisuke; Kaneda, Hidehiro; Fukui, Yasuo

    2017-05-01

    Massive molecular outflows erupting from high-mass young stellar objects (YSOs) provide important clues to understanding the mechanism of high-mass star formation. Based on new CO J = 3-2 and J = 1-0 observations using the Atacama Submillimeter Telescope Experiment (ASTE) and Mopra telescope facilities, we discovered a massive bipolar outflow associated with the dense dust core AGAL G337.916-00.477 (AGAL337.9-S), located 3.48 kpc from the Sun. The outflow lobes have extensions of less than 1 pc—and thus were not fully resolved in the angular resolutions of ASTE and Mopra—and masses of ˜50 M ⊙. The maximum velocities of the outflow lobes are as high as 36-40 {km} {{{s}}}-1. Our analysis of the infrared and submillimeter data indicates that AGAL337.9-S is in an early evolutionary stage of high-mass star formation, having the total far-infrared luminosity of ˜ 5× {10}4 {L}⊙ . We also found that another dust core, AGAL G337.922-00.456 (AGAL337.9-N), located 2‧ north of AGAL337.9-S, is a high-mass YSO in an earlier evolutionary stage than AGAL337.9-S, as it is less bright in the mid-infrared than AGAL337.9-S.

  20. Quantum molecular dynamics study of expanded beryllium: evolution from warm dense matter to atomic fluid.

    Science.gov (United States)

    Li, Dafang; Liu, Haitao; Zeng, Siliang; Wang, Cong; Wu, Zeqing; Zhang, Ping; Yan, Jun

    2014-07-31

    By performing quantum molecular dynamics (QMD) simulations, we investigate the equation of states, electrical and optical properties of the expanded beryllium at densities two to one-hundred lower than the normal solid density, and temperatures ranging from 5000 to 30000 K. With decreasing the density of Be, the optical response evolves from the one characteristic of a simple metal to the one of an atomic fluid. By fitting the optical conductivity spectra with the Drude-Smith model, it is found that the conducting electrons become localized at lower densities. In addition, the negative derivative of the electrical resistivity on temperature at density about eight lower than the normal solid density demonstrates that the metal to nonmetal transition takes place in the expanded Be. To interpret this transition, the electronic density of states is analyzed systematically. Furthermore, a direct comparison of the Rosseland opacity obtained by using QMD and the standard opacity code demonstrates that QMD provides a powerful tool to validate plasma models used in atomic physics approaches in the warm dense matter regime.

  1. Dense molecular gas toward W49A: A template for extragalactic starbursts?

    CERN Document Server

    Roberts, Helen; Fuller, Gary; Plume, René; Bayet, Estelle

    2010-01-01

    The HCN, HCO+, and HNC molecules are commonly used as tracers of dense star-forming gas in external galaxies, but such observations are spatially unresolved. Reliably inferring the properties of galactic nuclei and disks requires detailed studies of sources whose structure is spatially resolved. We compare the spatial distributions and abundance ratios of HCN, HCO+, and HNC in W49A, the most massive and luminous star-forming region in the Galactic disk, based on maps of a 2' (6.6 pc) field at 14" (0.83 pc) resolution of the J=4-3 transitions of HCN, H13CN, HC15N, HCO+, H13CO+, HC18O+ and HNC. The kinematics of the molecular gas in W49A appears complex, with a mixture of infall and outflow motions. Both the line profiles and comparison of the main and rarer species show that the main species are optically thick. Two 'clumps' of infalling gas appear to be at ~40 K, compared to ~100 K at the source centre, and may be ~10x denser than the rest of the outer cloud. Chemical modelling suggests that the HCN/HNC ratio...

  2. Charge of interstellar dust in dense molecular clouds: Effect of cosmic rays

    CERN Document Server

    Ivlev, Alexei; Galli, Daniele; Caselli, Paola

    2015-01-01

    The local cosmic-ray (CR) spectra are calculated for typical characteristic regions of a cold dense molecular cloud, to investigate two so far neglected mechanisms of dust charging: collection of suprathermal CR electrons and protons by grains, and photoelectric emission from grains due to the UV radiation generated by CRs. The two mechanisms add to the conventional charging by ambient plasma, produced in the cloud by CRs. We show that the CR-induced photoemission can dramatically modify the charge distribution function for submicron grains. We demonstrate the importance of the obtained results for dust coagulation: While the charging by ambient plasma alone leads to a strong Coulomb repulsion between grains and inhibits their further coagulation, the combination with the photoemission provides optimum conditions for the growth of large dust aggregates in a certain region of the cloud, corresponding to the densities $n(\\mathrm{H_2})$ between $\\sim10^4$ cm$^{-3}$ and $\\sim10^6$ cm$^{-3}$. The charging effect o...

  3. Dense gas without star formation: The kpc-sized molecular disk in 3C326 N

    CERN Document Server

    Nesvadba, Nicole; Lehnert, Matt; Guillard, Pierre; Salome, Philippe

    2011-01-01

    We report the discovery of a 3 kpc disk of few 10^9 Ms of dense, warm H_2 in the nearby radio galaxy 3C326 N, which shows no signs of on-going or recent star formation and falls a factor 60 below the Schmidt-Kennicutt law. VLT/SINFONI imaging spectroscopy shows broad (FWHM \\sim 500 km/s) ro-vibrational H_2 lines across all of the disk, with irregular profiles and line ratios consistent with shocks. The ratio of turbulent and gravitational energy suggests that the gas is highly turbulent and not gravitationally bound. In absence of the driving by the jet, short turbulent dissipation times suggest the gas should collapse rapidly and form stars, at odds with the recent star-formation history. Motivated by hydrodynamic models of rapid H_2 formation boosted by turbulent compression, we propose that the molecules formed from diffuse atomic gas in the turbulent jet cocoon. Since the gas is not self-gravitating, it cannot form molecular clouds or stars while the jet is active, and is likely to disperse and become ato...

  4. 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....

  5. 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.

  6. 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.

  7. 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

  8. A 100-parsec elliptical and twisted ring of cold and dense molecular clouds revealed by Herschel around the Galactic Center

    CERN Document Server

    Molinari, S; Noriega-Crespo, A; Compiègne, M; Bernard, J P; Paradis, D; Martin, P; Testi, L; Barlow, M; Moore, T; Plume, R; Swinyard, B; Zavagno, A; Calzoletti, L; Di Giorgio, A M; Elia, D; Faustini, F; Natoli, P; Pestalozzi, M; Pezzuto, S; Piacentini, F; Polenta, G; Polychroni, D; Schisano, E; Traficante, A; Veneziani, M; Battersby, C; Burton, M; Carey, S; Fukui, Y; Li, J Z; Lord, S D; Morgan, L; Motte, F; Schuller, F; Stringfellow, G S; Tan, J C; Thompson, M A; Ward-Thompson, D; White, G; Umana, G

    2011-01-01

    Thermal images of cold dust in the Central Molecular Zone of the Milky Way, obtained with the far-infrared cameras on-board the Herschel satellite, reveal a 3x10^7 solar masses ring of dense and cold clouds orbiting the Galactic Center. Using a simple toy-model, an elliptical shape having semi-major axes of 100 and 60 parsecs is deduced. The major axis of this 100-pc ring is inclined by about 40 degrees with respect to the plane-of-the-sky and is oriented perpendicular to the major axes of the Galactic Bar. The 100-pc ring appears to trace the system of stable x_2 orbits predicted for the barred Galactic potential. Sgr A* is displaced with respect to the geometrical center of symmetry of the ring. The ring is twisted and its morphology suggests a flattening-ratio of 2 for the Galactic potential, which is in good agreement with the bulge flattening ratio derived from the 2MASS data.

  9. Heterogeneous Atomistic-Continuum Methods for Dense Fluid Systems

    Science.gov (United States)

    Hadjiconstantinou, Nicolas; Patera, Anthony

    1997-08-01

    We present new results obtained using the formulation and numerical solution procedure for heterogeneous atomistic--continuum representations of fluid flows presented in [1]. The ingredients are, from the atomistic side, non-equilibrium molecular dynamics, and from the continuum side, finite element solution; the matching is provided by a classical procedure, the Schwarz alternating method with overlapping subdomains. The technique is applied to the flow of two immiscible fluids in a microscale channel. The problem "presents" a particular modelling challenge because of the stress singularity at the moving contact line which is usually relieved through ad hoc methods, the most popular of which is the assumption of slip close to the contact line. The Heterogeneous method properly addresses the problem by treating the region near the contact line with molecular dynamics. References 1. Hadjiconstantinou N., Patera, A.T., Proceedings of the Sixth International Conference on Discrete Models for Fluid Mechanics, To appear as a special edition of the International Journal of Modern Physics C.

  10. The Galactic Center Molecular Cloud Survey. II. A Lack of Dense Gas & Cloud Evolution along Galactic Center Orbits

    CERN Document Server

    Kauffmann, Jens; Zhang, Qizhou; Menten, Karl M; Goldsmith, Paul F; Lu, Xing; Guzmán, Andrés E; Schmiedeke, Anika

    2016-01-01

    We present the first systematic study of the density structure of clouds found in a complete sample covering all major molecular clouds in the Central Molecular Zone (CMZ; inner $\\sim{}200~\\rm{}pc$) of the Milky Way. This is made possible by using data from the Galactic Center Molecular Cloud Survey (GCMS), the first study resolving all major molecular clouds in the CMZ at interferometer angular resolution. We find that many CMZ molecular clouds have unusually shallow density gradients compared to regions elsewhere in the Milky Way. This is possibly a consequence of weak gravitational binding of the clouds. The resulting relative absence of dense gas on spatial scales $\\sim{}0.1~\\rm{}pc$ is probably one of the reasons why star formation (SF) in dense gas of the CMZ is suppressed by a factor $\\sim{}10$, compared to solar neighborhood clouds. Another factor suppressing star formation are the high SF density thresholds that likely result from the observed gas kinematics. Further, it is possible but not certain t...

  11. The Dense Filamentary Giant Molecular Cloud G23.0-0.4: Birthplace of Ongoing Massive Star Formation

    CERN Document Server

    Su, Yang; Shao, Xiangjun; Yang, Ji

    2015-01-01

    We present observations of 1.5 square degree maps of the 12CO, 13CO, and C18O (J=1-0) emission toward the complex region of the supernova remnant (SNR) W41 and SNR G22.7-0.2. A massive (~5E5Msun), large (~84x15 pc), and dense (~10E3 cm^-3) giant molecular cloud (GMC), G23.0-0.4 with VLSR~77 km/s, is found to be adjacent to the two SNRs. The GMC displays a filamentary structure approximately along the Galactic plane. The filamentary structure of the dense molecular gas, traced by C18O (J=1-0) emission, is also coincident well with the distribution of the dust-continuum emission in the direction. Two dense massive MC clumps, two 6.7 GHz methanol masers, and one HII/SNR complex, associated with the 77 km/s GMC G23.0-0.4, are aligned along the filamentary structure, indicating the star forming activity within the GMC. These sources have periodic projected spacing of 0.18-0.26degree along the giant filament, which is consistent well with the theoretical predictions of 0.22degree. It indicates that the turbulence s...

  12. Interspecies stress in momentum equations for dense binary particulate systems.

    Science.gov (United States)

    Zhang, D Z; Ma, X; Rauenzahn, R M

    2006-07-28

    For two-species particulate systems, ensemble averaged continuity and momentum equations for each species are derived based on the Liouville equation of the system. The ensemble average used is species specific. It is found that the interaction between species results in not only the interspecies force but also a stress in the momentum equations. In the limit that particles of one of the species can be considered as a continuum, the existence of the interspecies stress enables us to reduce the derived equations to the familiar form for dispersed two-phase flows.

  13. 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

  14. Launching of Microwaves into a Dense Plasma in Open Confinement Systems

    Energy Technology Data Exchange (ETDEWEB)

    Timofeev, A. V. [Russian Research Centre Kurchatov Institute (Russian Federation)

    2001-02-15

    A study is made of the propagation of microwave beams in a plasma and their passage through the critical surface. It is shown that, in order for microwaves to penetrate deeply into a dense plasma, it is necessary to launch them through a magnetic mirror at a slight angle to the device axis. The characteristic features of ray trajectories are analyzed both ahead of and behind the critical surface. In a dense plasma behind the critical surface, microwaves tend to run out of the axial region toward the plasma periphery. This tendency may be unfavorable for heating plasmas whose radial density profiles are strongly peaked about the system axis. The problems under analysis are particularly important for assessing the prospects for ECR heating of dense plasmas in open confinement systems.

  15. Glass and percolation transitions in dense attractive micellar system

    Science.gov (United States)

    Mallamace, F.; Beneduci, R.; Gambadauro, P.; Lombardo, D.; Chen, S. H.

    2001-12-01

    In this work, we study a copolymer-micellar system characterized by clustering processes due to a short-range attractive interaction. This originates a percolation process and a new type of kinetic glass transition. We have studied these intriguing dynamical situations by means of an extensive set of light scattering and viscoelasticity experiments. Obtained data, in both the phenomena, are accounted for by considering in a proper way fractal clustering processes and the related scaling concepts. Near the percolation line the main role in the system structure and dynamics is played by the cluster's partial screening of hydrodynamic interaction, that behaves, on approaching the percolation threshold, dramatic effects on the rheological properties and on the density decay relaxations. The ergodic-nonergodic transition line (glass transition) is studied in terms of the intermediate scattering functions (ISF) in the frame of the mode coupling theory. The measured ISF gives evidence of a logarithmic decay on the density fluctuation followed by a power law behavior. This latter phenomenon is the signature of a high-order glass transition of the A3 type (cusp-like singularity).

  16. Molecular Dynamics Simulation of Strong Shock Waves Propagating in Dense Deuterium With the Effect of Excited Electrons

    CERN Document Server

    Liu, Hao; Kang, Wei; Zhang, Ping; Duan, Huiling; He, X T

    2016-01-01

    We present a molecular dynamics simulation of shock waves propagating in dense deuterium with the electron force field method [J. T. Su and W. A. Goddard, Phys. Rev. Lett. 99, 185003 (2007)], which explicitly takes the excitation of electrons into consideration. Non-equilibrium features associated with the excitation of electrons are systematically investigated. We show that chemical bonds in D$_2$ molecules lead to a more complicated shock wave structure near the shock front, compared with the results of classical molecular dynamics simulation. Charge separation can bring about accumulation of net charges on the large scale, instead of the formation of a localized dipole layer, which might cause extra energy for the shock wave to propagate. In addition, the simulations also display that molecular dissociation at the shock front is the major factor corresponding to the "bump" structure in the principal Hugoniot. These results could help to build a more realistic picture of shock wave propagation in fuel mater...

  17. Photostability of gas- and solid-phase biomolecules within dense molecular clouds due to soft X-rays

    CERN Document Server

    Pilling, S; Nascimento, E M do; Marinho, R R T; Boechat-Roberty, H M; de Coutinho, L H; de Souza, G G B; de Castilho, R B; Cavasso-Filho, R L; Lago, A F; de Brito, A N

    2010-01-01

    An experimental photochemistry study involving gas- and solid-phase amino acids (glycine, DL-valine, DL-proline) and nucleobases (adenine and uracil) under soft X-rays was performed. The aim was to test the molecular stabilities of essential biomolecules against ionizing photon fields inside dense molecular clouds and protostellar disks analogs. In these environments, the main energy sources are the cosmic rays and soft X-rays. The measurements were taken at the Brazilian Synchrotron Light Laboratory (LNLS), employing 150 eV photons. In-situ sample analysis was performed by Time-of-flight mass spectrometer (TOF-MS) and Fourier transform infrared (FTIR) spectrometer, for gas- and solid- phase analysis, respectively. The half-life of solid phase amino acids, assumed to be present at grain mantles, is at least 3E5 years and 3E8 years inside dense molecular clouds and protoplanetary disks, respectively. We estimate that for gas-phase compounds these values increase one order of magnitude since the dissociation cr...

  18. Dense Molecular Gas Excitation at High Redshift: Detection of HCO+(J=4-3) Emission in the Cloverleaf Quasar

    CERN Document Server

    Riechers, Dominik A; Carilli, Christopher L; Cox, Pierre; Weiss, Axel; Bertoldi, Frank; Menten, Karl M

    2010-01-01

    We report the detection of HCO+(J=4-3) emission in the Cloverleaf Quasar at z=2.56, using the IRAM Plateau de Bure Interferometer. HCO+ emission is a star formation indicator similar to HCN, tracing dense molecular hydrogen gas (n(H2) ~= 10^5 cm^-3) within star-forming molecular clouds. We derive a lensing-corrected HCO+(J=4-3) line luminosity of L'(HCO+(4-3)) = (1.6+/-0.3) x 10^9 (mu_L/11)^-1 K km/s pc^2, which corresponds to only 48% of the HCO+(J=1=0) luminosity, and <~4% of the CO(J=3-2) luminosity. The HCO+ excitation thus is clearly subthermal in the J=4-3 transition. Modeling of the HCO+ line radiative transfer suggests that the HCO+ emission emerges from a region with physical properties comparable to that exhibiting the CO line emission, but 2x higher gas density. This suggests that both HCO+ and CO lines trace the warm, dense molecular gas where star formation actively takes place. The HCO+ lines have only ~2/3 the width of the CO lines, which may suggest that the densest gas is more spatially co...

  19. Controllability of Non-densely Defined Neutral Functional Differential Systems in Abstract Space

    Institute of Scientific and Technical Information of China (English)

    Xianlong FU; Xingbo LIU

    2007-01-01

    In this paper, by means of Sadovskii fixed point theorem, the authors establish a result concerning the controllability for a class of abstract neutral functional differential systems where the linear part is non-densely defined and satisfies the Hille-Yosida condition.As an application, an example is provided to illustrate the obtained result.

  20. 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...

  1. H2O Southern Galactic Plane Survey (HOPS): Paper III - properties of dense molecular gas across the inner Milky Way

    Science.gov (United States)

    Longmore, S. N.; Walsh, A. J.; Purcell, C. R.; Burke, D. J.; Henshaw, J.; Walker, D.; Urquhart, J.; Barnes, A. T.; Whiting, M.; Burton, M. G.; Breen, S. L.; Britton, T.; Brooks, K. J.; Cunningham, M. R.; Green, J. A.; Harvey-Smith, L.; Hindson, L.; Hoare, M. G.; Indermuehle, B.; Jones, P. A.; Lo, N.; Lowe, V.; Moore, T. J. T.; Thompson, M. A.; Voronkov, M. A.

    2017-09-01

    The H2O Southern Galactic Plane Survey (HOPS) has mapped 100 deg2 of the Galactic plane for water masers and thermal molecular line emission using the 22 m Mopra telescope. We describe the automated spectral-line fitting pipelines used to determine the properties of emission detected in HOPS data cubes, and use these to derive the physical and kinematic properties of gas in the survey. A combination of the angular resolution, sensitivity, velocity resolution and high critical density of lines targeted make the HOPS data cubes ideally suited to finding precursor clouds to the most massive and dense stellar clusters in the Galaxy. We compile a list of the most massive HOPS ammonia regions and investigate whether any may be young massive cluster progenitor gas clouds. HOPS is also ideally suited to trace the flows of dense gas in the Galactic Centre. We find the kinematic structure of gas within the inner 500 pc of the Galaxy is consistent with recent predictions for the dynamical evolution of gas flows in the centre of the Milky Way. We confirm a recent finding that the dense gas in the inner 100 pc has an oscillatory kinematic structure with characteristic length-scale of 20 pc, and also identify similar oscillatory kinematic structure in the gas at radii larger than 100 pc. Finally, we make all of the above fits and the remaining HOPS data cubes across the 100 deg2 of the survey available to the community.

  2. Study of the dense molecular gas surrounding the "Extended Green Object" G35.03+0.35

    CERN Document Server

    Paron, S; Petriella, A; Rubio, M; Giacani, E; Dubner, G

    2011-01-01

    We present the results of a new study of the molecular gas associated with the "extended green object" (EGO) G35.03+0.35. This object, very likely a massive young stellar object, is embedded in a molecular cloud at the border of an HII region. The observations were performed with the Atacama Submillimeter Telescope Experiment (ASTE) in the 12CO and 13CO J=3-2, HCO+ J=4-3, and CS J=7-6 lines with an angular resolution about 22". From the 12CO J=3-2 line we discovered outflowing activity of the massive young stellar object. We obtained a total mass and kinetic energy for the outflows of 30 M_sun and 3000 M_sun (km/s)^2 (6 x 10^{46} ergs), respectively. We discovered a HCO+ and CS clump towards the EGO G35.03+0.35. The detection of these molecular species supports the presence of molecular outflows and a dense molecular envelope with temperatures and densities above 40 K and 6 x 10^{6} cm^{-3}, respectively. Using public near- and mid-IR, and sub-mm data we investigated the spectral energy distribution confirmin...

  3. An origin of arc structures deeply embedded in dense molecular cloud cores

    CERN Document Server

    Matsumoto, Tomoaki; Tokuda, Kazuki; Inutsuka, Shu-ichiro

    2015-01-01

    We investigated the formation of arc-like structures in the infalling envelope around protostars, motivated by the recent ALMA observations of the high-density molecular cloud core, MC27/L1527F. We performed self-gravitational hydrodynamical numerical simulations with an adaptive mesh refinement code. A filamentary cloud with a 0.1~pc width fragments into cloud cores because of perturbations due to weak turbulence. The cloud core undergoes gravitational collapse to form multiple protostars, and gravitational torque from the orbiting protostars produces arc structures extending up to a 1000~AU scale. As well as on a spatial extent, the velocity ranges of the arc structures, $\\sim0.5\\,\\mathrm{km\\,s}^{-1}$, are in agreement with the ALMA observations. We also found that circumstellar disks are often misaligned in triple system. The misalignment is caused by the tidal interaction between the protostars when they undergo close encounters because of a highly eccentric orbit of the tight binary pair.

  4. 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.

  5. 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.

  6. Two Mass Distributions in the L 1641 Molecular Clouds: The Herschel connection of Dense Cores and Filaments in Orion A

    CERN Document Server

    Polychroni, D; Elia, D; Roy, A; Molinari, S; Martin, P; Andre, Ph; Turrini, D; Rygl, K L J; Benedettini, M; Busquet, G; di Giorgio, A M; Pestalozzi, M; Pezzuto, S; Arzoumanian, D; Bontemps, S; Di Francesco, J; Hennemann, M; Hill, T; Konyves, V; Menshchikov, A; Motte, F; Nguyen-Luong, Q; Peretto, N; Schneider, N; White, G

    2013-01-01

    We present the Herschel Gould Belt 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 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 Solar masses and drives the shape of the CMF at higher masses, which we fit with a power law of the form d$N$/dlog$M \\propto M^{-1.4\\pm0.4}$. The mass distribution of the sources off the filaments, on the other hand, peaks at 0.8 Solar masses and leads to a flattening of the CMF at masses lower than ~4 Solar masses. We postulate that this difference between the mass distributi...

  7. Molecular interpretation of nonclassical gas dynamics of dense vapors under the van der Waals model

    NARCIS (Netherlands)

    Colonna, P.; Guardone, A.

    2006-01-01

    The van der Waals polytropic gas model is used to investigate the role of attractive and repulsive intermolecular forces and the influence of molecular complexity on the possible nonclassical gas dynamic behavior of vapors near the liquid-vapor saturation curve. The decrease of the sound speed upon

  8. Molecular interpretation of nonclassical gas dynamics of dense vapors under the van der Waals model

    NARCIS (Netherlands)

    Colonna, P.; Guardone, A.

    2006-01-01

    The van der Waals polytropic gas model is used to investigate the role of attractive and repulsive intermolecular forces and the influence of molecular complexity on the possible nonclassical gas dynamic behavior of vapors near the liquid-vapor saturation curve. The decrease of the sound speed upon

  9. Molecular Emission in Dense Massive Clumps from the Star-Forming Regions S231-S235

    CERN Document Server

    Ladeyschikov, D A; Tsivilev, A P; Sobolev, A M

    2016-01-01

    The article deals with observations of star-forming regions S231-S235 in 'quasi-thermal' lines of ammonia (NH$_3$), cyanoacetylene (HC$_3$N) and maser lines of methanol (CH$_3$OH) and water vapor (H$_2$O). S231-S235 regions is situated in the giant molecular cloud G174+2.5. We selected all massive molecular clumps in G174+2.5 using archive CO data. For the each clump we determined mass, size and CO column density. After that we performed observations of these clumps. We report about first detections of NH$_3$ and HC$_3$N lines toward the molecular clumps WB89 673 and WB89 668. This means that high-density gas is present there. Physical parameters of molecular gas in the clumps were estimated using the data on ammonia emission. We found that the gas temperature and the hydrogen number density are in the ranges 16-30 K and 2.8-7.2$\\times10^3$ cm$^{-3}$, respectively. The shock-tracing line of CH$_3$OH molecule at 36.2 GHz is newly detected toward WB89 673.

  10. Molecular dynamics simulation of strong shock waves propagating in dense deuterium, taking into consideration effects of excited electrons

    Science.gov (United States)

    Liu, Hao; Zhang, Yin; Kang, Wei; Zhang, Ping; Duan, Huiling; He, X. T.

    2017-02-01

    We present a molecular dynamics simulation of shock waves propagating in dense deuterium with the electron force field method [J. T. Su and W. A. Goddard, Phys. Rev. Lett. 99, 185003 (2007), 10.1103/PhysRevLett.99.185003], which explicitly takes the excitation of electrons into consideration. Nonequilibrium features associated with the excitation of electrons are systematically investigated. We show that chemical bonds in D2 molecules lead to a more complicated shock wave structure near the shock front, compared with the results of classical molecular dynamics simulation. Charge separation can bring about accumulation of net charges on large scales, instead of the formation of a localized dipole layer, which might cause extra energy for the shock wave to propagate. In addition, the simulations also display that molecular dissociation at the shock front is the major factor that accounts for the "bump" structure in the principal Hugoniot. These results could help to build a more realistic picture of shock wave propagation in fuel materials commonly used in the inertial confinement fusion.

  11. Molecular dynamics simulation of strong shock waves propagating in dense deuterium, taking into consideration effects of excited electrons.

    Science.gov (United States)

    Liu, Hao; Zhang, Yin; Kang, Wei; Zhang, Ping; Duan, Huiling; He, X T

    2017-02-01

    We present a molecular dynamics simulation of shock waves propagating in dense deuterium with the electron force field method [J. T. Su and W. A. Goddard, Phys. Rev. Lett. 99, 185003 (2007)PRLTAO0031-900710.1103/PhysRevLett.99.185003], which explicitly takes the excitation of electrons into consideration. Nonequilibrium features associated with the excitation of electrons are systematically investigated. We show that chemical bonds in D_{2} molecules lead to a more complicated shock wave structure near the shock front, compared with the results of classical molecular dynamics simulation. Charge separation can bring about accumulation of net charges on large scales, instead of the formation of a localized dipole layer, which might cause extra energy for the shock wave to propagate. In addition, the simulations also display that molecular dissociation at the shock front is the major factor that accounts for the "bump" structure in the principal Hugoniot. These results could help to build a more realistic picture of shock wave propagation in fuel materials commonly used in the inertial confinement fusion.

  12. Molecular line emission in NGC1068 imaged with ALMA: II. The chemistry of the dense molecular gas

    CERN Document Server

    Viti, S; Fuente, A; Hunt, L K; Usero, A; Henkel, C; Eckart, A; Martin, S; Spaans, M; Muller, S; Combes, F; Krips, M; Schinnerer, E; Casasola, V; Costagliola, F; Marquez, I; Planesas, P; van der Werf, P P; Aalto, S; Baker, A J; Boone, F; Tacconi, L J

    2014-01-01

    We present a detailed analysis of ALMA Bands 7 and 9 data of CO, HCO+, HCN and CS, augmented with Plateau de Bure Interferometer (PdBI) data of the ~ 200 pc circumnuclear disk (CND) and the ~ 1.3 kpc starburst ring (SB ring) of NGC~1068, a nearby (D = 14 Mpc) Seyfert 2 barred galaxy. We aim at determining the physical characteristics of the dense gas present in the CND and whether the different line intensity ratios we find within the CND as well as between the CND and the SB ring are due to excitation effects (gas density and temperature differences) or to a different chemistry. We estimate the column densities of each species in Local Thermodynamic Equilibrium (LTE). We then compute large one-dimensional non-LTE radiative transfer grids (using RADEX) by using first only the CO transitions, and then all the available molecules in order to constrain the densities, temperatures and column densities within the CND. We finally present a preliminary set of chemical models to determine the origin of the gas. We fi...

  13. 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%.

  14. 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%.

  15. Self Configurable Intelligent Distributed Antenna System for Resource Management in Multilayered Dense-nets

    DEFF Research Database (Denmark)

    Kumar, Ambuj; Mihovska, Albena Dimitrova; Prasad, Ramjee

    2016-01-01

    to their respective Base Stations (BS). Moreover, in earlier generations of MCC, antennas were deemed collocated with their respective BSs. Later, the concepts like Distributed Antenna Systems (DAS) and Cloud RAN (C-RAN) made it possible to place these antennas distant from their respective BSs. However, being mapped...... with their respective base stations, spectrum pooling and management at antenna end is not efficient. The situation worsens in Heterogeneous and Dense-net conditions in an Area of Interest (AoI). In this paper, we propose a DAS based intelligent architecture referred to as Self Configurable Intelligent Distributed...... Antenna System (SCIDAS) that can simultaneously accommodate multilayer communication environment over a common BS....

  16. Design and Realization of Uniform Fiber Bragg Grating Used in Dense Wavelength Division Multiplexing Systems

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Relation of optical properties in a uniform fiber Bragg grating(FBG) with its grating parameters and the laser beam engraving conditions is analyzed. The principle and method for designing the uniform FBG used in dense wavelength division multiplexing(DWDM) system is given. By adopting the double exposure technique, with a uniform phase mask and Gaussian laser beam, the uniform FBG used in DWDM system is designed and engraved, whose bandwidth of the main reflection band is about 0.4nm and 0.7nm at -5dB and -25dB respectively.

  17. Molecular line emission in NGC 1068 imaged with ALMA : I. An AGN-driven outflow in the dense molecular gas

    NARCIS (Netherlands)

    García-Burillo, S.; Combes, F.; Usero, A.; Aalto, S.; Krips, M.; Viti, S.; Alonso-Herrero, A.; Hunt, L. K.; Schinnerer, E.; Baker, A. J.; Boone, F.; Casasola, V.; Colina, L.; Costagliola, F.; Eckart, A.; Fuente, A.; Henkel, C.; Labiano, A.; Martín, S.; Márquez, I.; Muller, S.; Planesas, P.; Ramos Almeida, C.; Spaans, M.; Tacconi, L. J.; van der Werf, P. P.

    2014-01-01

    Aims: We investigate the fueling and the feedback of star formation and nuclear activity in NGC 1068, a nearby (D = 14 Mpc) Seyfert 2 barred galaxy, by analyzing the distribution and kinematics of the molecular gas in the disk. We aim to understand if and how gas accretion can self-regulate. Methods

  18. Molecular line emission in NGC 1068 imaged with ALMA. I. An AGN-driven outflow in the dense molecular gas

    NARCIS (Netherlands)

    García-Burillo, S.; Combes, F.; Usero, A.; Aalto, S.; Krips, M.; Viti, S.; Alonso-Herrero, A.; Hunt, L. K.; Schinnerer, E.; Baker, A. J.; Boone, F.; Casasola, V.; Colina, L.; Costagliola, F.; Eckart, A.; Fuente, A.; Henkel, C.; Labiano, A.; Martín, S.; Márquez, I.; Muller, S.; Planesas, P.; Ramos Almeida, C.; Spaans, M.; Tacconi, L. J.; van der Werf, P. P.

    2014-01-01

    Aims: We investigate the fueling and the feedback of star formation and nuclear activity in NGC 1068, a nearby (D = 14 Mpc) Seyfert 2 barred galaxy, by analyzing the distribution and kinematics of the molecular gas in the disk. We aim to understand if and how gas accretion can self-regulate. Methods

  19. A dense molecular cloud in the OMC-1/OMC-2 region

    Science.gov (United States)

    Kutner, M. L.; Evans, N. J., II; Tucker, K. D.

    1976-01-01

    H2CO emission at 2 mm is seen over a region 30 arcmin in extent which includes OMC-1 and OMC-2. The mass of this cloud, estimated from H2CO and CO observations, is about 7000 solar masses. The velocity pattern is one of rotation, with evidence for fragmentation into two or three distinct condensations. A sharp boundary to the molecular cloud is observed at the edge of the H II region in NGC 1977. It appears likely that NGC 1977 is a condensation at the northern end of the cloud, complementary to the Orion Nebula at the southern end.

  20. A dense molecular cloud in the OMC-1/OMC-2 region

    Science.gov (United States)

    Kutner, M. L.; Evans, N. J., II; Tucker, K. D.

    1976-01-01

    H2CO emission at 2 mm is seen over a region 30 arcmin in extent which includes OMC-1 and OMC-2. The mass of this cloud, estimated from H2CO and CO observations, is about 7000 solar masses. The velocity pattern is one of rotation, with evidence for fragmentation into two or three distinct condensations. A sharp boundary to the molecular cloud is observed at the edge of the H II region in NGC 1977. It appears likely that NGC 1977 is a condensation at the northern end of the cloud, complementary to the Orion Nebula at the southern end.

  1. Multi-line spectral imaging of dense cores in the Lupus molecular cloud

    CERN Document Server

    Benedettini, Milena; Burton, Micheal G; Viti, Serena; Molinari, Sergio; Caselli, Paola; Testi, Leonardo

    2011-01-01

    The molecular clouds Lupus 1, 3 and 4 were mapped with the Mopra telescope at 3 and 12 mm. Emission lines from high density molecular tracers were detected, i.e. NH$_3$ (1,1), NH$_3$ (2,2), N$_2$H$^+$ (1-0), HC$_3$N (3-2), HC$_3$N (10-9), CS (2-1), CH$_3$OH (2$_0-1_0$)A$^+$ and CH$_3$OH (2$_{-1}-1_{-1}$)E. Velocity gradients of more than 1 km s$^{-1}$ are present in Lupus 1 and 3 and multiple gas components are present in these clouds along some lines of sight. Lupus 1 is the cloud richest in high density cores, 8 cores were detected in it, 5 cores were detected in Lupus 3 and only 2 in Lupus 4. The intensity of the three species HC$_3$N, NH$_3$ and N$_2$H$^+$ changes significantly in the various cores: cores that are brighter in HC$_3$N are fainter or undetected in NH$_3$ and N$_2$H$^+$ and vice versa. We found that the column density ratios HC$_3$N/N$_2$H$^+$ and HC$_3$N/NH$_3$ change by one order of magnitude between the cores, indicating that also the chemical abundance of these species is different. The ...

  2. HCO mapping of the Horsehead: tracing the illuminated dense molecular cloud surfaces

    Science.gov (United States)

    Gerin, M.; Goicoechea, J. R.; Pety, J.; Hily-Blant, P.

    2009-02-01

    Context: Far-UV photons (FUV) strongly affect the physical and chemical state of molecular gas in the vicinity of young massive stars. Aims: Finding molecular tracers of the presence of FUV radiation fields in the millimeter wavelength domain is desirable because IR diagnostics (for instance PAHs) are not easily accessible along high extinction line-of-sights. Furthermore, gas phase diagnostics provide information on the velocity fields. Methods: We have obtained maps of the HCO and H13CO+ ground state lines towards the Horsehead edge at 5'' angular resolution with a combination of Plateau de Bure Interferometer (PdBI) and the IRAM-30 m telescope observations. These maps have been complemented with IRAM-30 m observations of several excited transitions at two different positions. Results: Bright formyl radical emission delineates the illuminated edge of the nebula, with a faint emission remaining towards the shielded molecular core. Viewed from the illuminated star, the HCO emission almost coincides with the PAH and CCH emission. HCO reaches a similar abundance to HCO+ in the photon dissociation region (PDR), ≃1-2×10-9 with respect to H2. To our knowledge, this is the highest HCO abundance ever measured. Pure gas-phase chemistry models fail to reproduce the observed HCO abundance by ~2 orders of magnitude, except if reactions of atomic oxygen with carbon radicals abundant in the PDR (i.e., CH2) play a significant role in the HCO formation. Alternatively, HCO could be produced in the PDR by non-thermal processes such as photo-processing of ice mantles and subsequent photo-desorption of either HCO or H2CO, and further gas phase photodissociation. Conclusions: The measured HCO/H13CO+ abundance ratio is large towards the PDR (≃50), and much lower toward the gas shielded from FUV radiation (≲1). We propose that high HCO abundances (≳10-10) together with large HCO/H13CO+ abundance ratios (≳1) are sensitive diagnostics of the presence of active photochemistry

  3. Simulation of the Correlated Electron Plasma in the Warm Dense Matter Regime by Restricted Path-Integral Molecular Dynamics

    Science.gov (United States)

    Kapila, Vivek; Deymier, Pierre; Runge, Keith

    2012-02-01

    Warm dense matter (WDM) can be characterized by electron temperatures of a few eV and densities an order of magnitude or more beyond ambient. This regime currently lacks any adequate highly developed class of simulation methods. Recent developments in orbital-free Density Functional Theory (ofDFT) aim to provide such a simulation method, however, little benchmark information is available on temperature and pressure dependence of simple but realistic models in WDM regime. The present work aims to fill this critical gap using the restricted path-integral molecular dynamics (rPIMD) method. Within the discrete path integral representation, electrons are described as harmonic necklaces, while, quantum exchange takes the form of cross linking between electron necklaces. The fermion sign problem is addressed by restricting the density matrix to positive values and a molecular dynamics algorithm is employed to sample phase space. Here, we focus on the behavior of strongly correlated electron plasmas under WDM conditions. We compute the kinetic and potential energies and compare them to those obtained with the ofDFT method.

  4. Deeply Embedded Protostellar Population in the Central Molecular Zone Suggested by H$_2$O Masers and Dense Cores

    CERN Document Server

    Lu, Xing; Kauffmann, Jens; Pillai, Thushara; Longmore, Steven N; Kruijssen, J M Diederik; Battersby, Cara

    2016-01-01

    The Central Molecular Zone (CMZ), usually referring to the inner 500 pc of the Galaxy, contains a dozen of massive ($\\sim10^5$ $M_\\odot$) molecular clouds. Are these clouds going to actively form stars like Sgr B2? How are they affected by the extreme physical conditions in the CMZ, such as strong turbulence? Here we present a first step towards answering these questions. Using high-sensitivity, high angular resolution radio and (sub)millimeter observations, we studied deeply embedded star formation in six massive clouds in the CMZ, including the 20 and 50 km s$^{-1}$ clouds, Sgr B1 off (as known as dust ridge clouds e/f), Sgr C, Sgr D, and G0.253-0.016. The VLA water maser observations suggest a population of deeply embedded protostellar candidates, many of which are new detections. The SMA 1.3 mm continuum observations reveal peaks in dust emission associated with the masers, suggesting the existence of dense cores. While our findings confirm that clouds such as G0.253-0.016 lack internal compact substructu...

  5. Solution of dense systems of linear equations in electromagnetic scattering calculations

    Energy Technology Data Exchange (ETDEWEB)

    Rahola, J. [Center for Scientific Computing, Espoo (Finland)

    1994-12-31

    The discrete-dipole approximation (DDA) is a method for calculating the scattering of light by an irregular particle. The DDA has been used for example in calculations of optical properties of cosmic dust. In this method the particle is approximated by interacting electromagnetic dipoles. Computationally the DDA method includes the solution of large dense systems of linear equations where the coefficient matrix is complex symmetric. In the author`s work, the linear systems of equations are solved by various iterative methods such as the conjugate gradient method applied to the normal equations and QMR. The linear systems have rather low condition numbers due to which many iterative methods perform quite well even without any preconditioning. Some possible preconditioning strategies are discussed. Finally, some fast special methods for computing the matrix-vector product in the iterative methods are considered. In some cases, the matrix-vector product can be computed with the fast Fourier transform, which enables the author to solve dense linear systems of hundreds of thousands of unknowns.

  6. 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.

  7. The Bolocam Galactic Plane Survey. XIII. Physical Properties and Mass Functions of Dense Molecular Cloud Structures

    CERN Document Server

    Ellsworth-Bowers, Timothy P; Riley, Allyssa; Rosolowsky, Erik; Ginsburg, Adam; Evans, Neal J; Bally, John; Battersby, Cara; Shirley, Yancy L; Merello, Manuel

    2015-01-01

    We use the distance probability density function (DPDF) formalism of Ellsworth-Bowers et al. (2013, 2015) to derive physical properties for the collection of 1,710 Bolocam Galactic Plane Survey (BGPS) version 2 sources with well-constrained distance estimates. To account for Malmquist bias, we estimate that the present sample of BGPS sources is 90% complete above 400 $M_\\odot$ and 50% complete above 70 $M_\\odot$. The mass distributions for the entire sample and astrophysically motivated subsets are generally fitted well by a lognormal function, with approximately power-law distributions at high mass. Power-law behavior emerges more clearly when the sample population is narrowed in heliocentric distance (power-law index $\\alpha = 2.0\\pm0.1$ for sources nearer than 6.5 kpc and $\\alpha = 1.9\\pm0.1$ for objects between 2 kpc and 10 kpc). The high-mass power-law indices are generally $1.85 \\leq \\alpha \\leq 2.05$ for various subsamples of sources, intermediate between that of giant molecular clouds and the stellar ...

  8. A Search for Small-Scale Clumpiness in Dense Cores of Molecular Clouds

    CERN Document Server

    Pirogov, L E; 10.1134/S1063772908120020

    2009-01-01

    We have analyzed HCN(1-0) and CS(2-1) line profiles obtained with high signal-to-noise ratios toward distinct positions in three selected objects in order to search for small-scale structure in molecular cloud cores associated with regions of high-mass star formation. In some cases, ripples were detected in the line profiles, which could be due to the presence of a large number of unresolved small clumps in the telescope beam. The number of clumps for regions with linear scales of ~0.2-0.5 pc is determined using an analytical model and detailed calculations for a clumpy cloud model; this number varies in the range: ~2 10^4-3 10^5, depending on the source. The clump densities range from ~3 10^5-10^6 cm^{-3}, and the sizes and volume filling factors of the clumps are ~(1-3) 10^{-3} pc and ~0.03-0.12. The clumps are surrounded by inter-clump gas with densities not lower than ~(2-7) 10^4 cm^{-3}. The internal thermal energy of the gas in the model clumps is much higher than their gravitational energy. Their mean ...

  9. Lock-and-key dimerization in dense Brownian systems of hard annular sector particles

    Science.gov (United States)

    Hodson, Wade D.; Mason, Thomas G.

    2016-08-01

    We develop a translational-rotational cage model that describes the behavior of dense two-dimensional (2D) Brownian systems of hard annular sector particles (ASPs), resembling C shapes. At high particle densities, pairs of ASPs can form mutually interdigitating lock-and-key dimers. This cage model considers either one or two mobile central ASPs which can translate and rotate within a static cage of surrounding ASPs that mimics the system's average local structure and density. By comparing with recent measurements made on dispersions of microscale lithographic ASPs [P. Y. Wang and T. G. Mason, J. Am. Chem. Soc. 137, 15308 (2015), 10.1021/jacs.5b10549], we show that mobile two-particle predictions of the probability of dimerization Pdimer, equilibrium constant K , and 2D osmotic pressure Π2 D as a function of the particle area fraction ϕA correspond closely to these experiments. By contrast, predictions based on only a single mobile particle do not agree well with either the two-particle predictions or the experimental data. Thus, we show that collective entropy can play an essential role in the behavior of dense Brownian systems composed of nontrivial hard shapes, such as ASPs.

  10. Lock-and-key dimerization in dense Brownian systems of hard annular sector particles.

    Science.gov (United States)

    Hodson, Wade D; Mason, Thomas G

    2016-08-01

    We develop a translational-rotational cage model that describes the behavior of dense two-dimensional (2D) Brownian systems of hard annular sector particles (ASPs), resembling C shapes. At high particle densities, pairs of ASPs can form mutually interdigitating lock-and-key dimers. This cage model considers either one or two mobile central ASPs which can translate and rotate within a static cage of surrounding ASPs that mimics the system's average local structure and density. By comparing with recent measurements made on dispersions of microscale lithographic ASPs [P. Y. Wang and T. G. Mason, J. Am. Chem. Soc. 137, 15308 (2015)JACSAT0002-786310.1021/jacs.5b10549], we show that mobile two-particle predictions of the probability of dimerization P_{dimer}, equilibrium constant K, and 2D osmotic pressure Π_{2D} as a function of the particle area fraction ϕ_{A} correspond closely to these experiments. By contrast, predictions based on only a single mobile particle do not agree well with either the two-particle predictions or the experimental data. Thus, we show that collective entropy can play an essential role in the behavior of dense Brownian systems composed of nontrivial hard shapes, such as ASPs.

  11. 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.

  12. The path to achieving molecular dispersion in an extremely dense reactive mixture

    Science.gov (United States)

    Patel, Jigneshkumar; Xiang, Zou; Hsu, Shaw; Schoch, Andrew

    2015-03-01

    In any multicomponent reactive system, a uniform and continuous dispersion of reactants is necessary to achieve a complete reaction. In this study, we have examined the role of one additional component to disperse two seemingly unlikely reactants, including a highly crystalline hexamethylenetetramine (hexa) and strongly hydrogen bonded phenol formaldehyde resin. By combining information from NMR, infrared spectroscopy and differential scanning calorimetry, we were able to decipher the role of specific intermolecular interactions in order for this additional component to dissolve the highly crystalline hexa and to plasticize the phenol formaldehyde resin in this crosslinking reaction. It is clear that the presence of the third component increased the segmental mobility, disrupted the hydrogen bonded matrix, and freed the hydroxyl units, which further increased the solubility of hexa. Both the endothermic and exothermic transitions are accounted for in the calorimetric data obtained. For the first time, it is possible to understand the miscibility behavior of this multicomponent system. By designing the additional component to form a hydrogen bond with one or more N of the highly symmetric hexamethylenetetramine, it is then possible to obtain the effective molar ratio of each component needed to complete the crosslinking reaction efficiently. The understanding of this system is applicable to a broad range of reactive systems.

  13. 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.

  14. The BLAST Survey of the Vela Molecular Cloud: Physical Properties of the Dense Cores in Vela-D

    CERN Document Server

    Olmi, Luca; Angles-Alcazar, Daniel; Bock, James J; Chapin, Edward L; De Luca, Massimo; Devlin, Mark J; Dicker, Simon; Elia, Davide; Fazio, Giovanni G; Giannini, Teresa; Griffin, Matthew; Gundersen, Joshua O; Halpern, Mark; Hargrave, Peter C; Hughes, David H; Klein, Jeff; Lorenzetti, Dario; Marengo, Massimo; Marsden, Gaelen; Martin, Peter G; Massi, Fabrizio; Mauskopf, Philip; Netterfield, Calvin B; Patanchon, Guillaume; Rex, Marie; Salama, Alberto; Scott, Douglas; Semisch, Christopher; Smith, Howard A; Strafella, Francesco; Thomas, Nicholas; Truch, Matthew D P; Tucker, Carole; Tucker, Gregory S; Viero, Marco P; Wiebe, Donald V

    2009-01-01

    The Balloon-borne Large-Aperture Submillimeter Telescope (BLAST) carried out a 250, 350 and 500 micron 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 square degrees, 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 beta = 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 proto-stellar 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 proto-stellar cores, and we find that there appe...

  15. Conceptual Design of an Ultra-Dense Phase Injector and Feed System

    Energy Technology Data Exchange (ETDEWEB)

    Ken Sprouse; Fred Widman; Alan Darby

    2006-03-30

    Pratt & Whitney Rocketdyne (PWR) has developed an innovative gasifier concept that uses rocket engine technology to significantly improve gasifier performance, life, and cost compared to current state-of-the-art systems. One key feature of the PWR concept is the use of an ultra-dense phase feed system to provide dry coal to the multi-element injector. This report describes the design of an ultra-dense phase multi-element injector and feed system for use on PWR gasifiers operating at pressures to 1,000 psia. For the design of this injector and feed system, the pulverized coal's Bingham fluid yield stress is approximately 11 Pascals (Pa) with a coefficient of rigidity of 10 centipoise (cp). These values are typical of earlier experimental testing conducted with dried pulverized coal below 18 wt% moisture -- see, e.g., Sprouse and Schuman (1983, 1986). Each individual injector element is designed for a coal flow rate between 3 and 4 tons/hr (0.76 to 1.0 kg/sec) at full flow conditions. Hence, a small 400 to 500 tons/day (4.2 to 5.25 kg/sec) gasifier will require a 6-element injector, a 1,500 tons/day (15.7 kg/sec) gasifier will require an 18-element injector and a 3,000 tons/day (31.5 kg/sec) gasifier will require a 36-element injector. These injectors and feed systems are capable of 'turn-down' below 50% of full-flow operation.

  16. Multichannel Adaptive Polarization Mode Dispersion Compensation with One Compensator in Dense Wavelength Division Multiplexing Transmission Systems

    Institute of Scientific and Technical Information of China (English)

    ZHANG Qi; CHEN Ming-hua; ZHANG Ji-yu; XIE Shi-zhong

    2007-01-01

    A simple two-section polarization mode dispersion(PMD) compensator is proposed for multichannel PMD compensation, which can compensate two or even more channels simultaneously. Because of the statistical characteristics and the frequency-dependence of PMD, for current single mode fiber with moderate PMD, the probability that all channels are severely degraded at the same time is extremely small, which makes it possible to compensate a dense wavelength division multiplexing(DWDM) transmission system with moderate PMD using this compensator. It is shown that the outage probability of a 40×43Gb/s DWDM transmission system using this compensator is decreased significantly from 3.6×10-3 to 3.6×10-5.

  17. 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 viny

  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. GPU-Enabled Particle-Particle Particle-Tree Scheme for Simulating Dense Stellar Cluster System

    CERN Document Server

    Iwasawa, Masaki; Makino, Junichiro

    2015-01-01

    We describe the implementation and performance of the ${\\rm P^3T}$ (Particle-Particle Particle-Tree) scheme for simulating dense stellar systems. In ${\\rm P^3T}$, the force experienced by a particle is split into short-range and long-range contributions. Short-range forces are evaluated by direct summation and integrated with the fourth order Hermite predictor-corrector method with the block timesteps. For long-range forces, we use a combination of the Barnes-Hut tree code and the leapfrog integrator. The tree part of our simulation environment is accelerated using graphical processing units (GPU), whereas the direct summation is carried out on the host CPU. Our code gives excellent performance and accuracy for star cluster simulations with a large number of particles even when the core size of the star cluster is small.

  20. 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.

  1. PdBI U/LIRG Survey (PULS): Dense molecular gas in Arp 220 and NGC 6240

    Science.gov (United States)

    Sliwa, Kazimierz; Downes, Dennis

    2017-07-01

    Aims: We present new IRAM Plateau de Bure Interferometer observations of Arp 220 in HCN, HCO+, HN13C J = 1 - 0, C2H N = 1 - 0, SiO J = 2 - 1, HNCO Jk,k' = 50,4 - 40,4, CH3CN(6-5), CS J = 2 - 1 and 5-4 and 13CO J = 1 - 0 and 2-1 and of NGC 6240 in HCN, HCO+J = 1 - 0 and C2H N = 1 - 0. In addition, we present Atacama Large Millimeter/submill-meter Array science verification observations of Arp 220 in CS J = 4 - 3 and CH3CN(10-9). Various lines are used to analyse the physical conditions of the molecular gas including the [12CO]/[13CO] and [12CO]/[C18O] abundance ratios. These observations will be made available to the public. Methods: We create brightness temperature line ratio maps to present the different physical conditions across Arp 220 and NGC 6240. In addition, we use the radiative transfer code RADEX and a Monte Carlo Markov chain likelihood code to model the 12CO, 13CO and C18O lines of Arp 220 at 2'' ( 700 pc) scales, where the 12CO and C18O measurements were obtained from literature. Results: Line ratios of optically thick lines such as 12CO show smoothly varying ratios while the line ratios of optically thin lines such as 13CO show a east-west gradient across Arp 220. The HCN/HCO+ line ratio differs between Arp 220 and NGC 6240, where Arp 220 has line ratios above 2 and NGC 6240 below 1. The radiative transfer analysis solution is consistent with a warm ( 40 K), moderately dense ( 103.4 cm-3) molecular gas component averaged over the two nuclei. We find [12CO]/[13CO] and [12CO]/[C18O] abundance ratios of 90 for both. The abundance enhancement of C18O can be explained by stellar nucleosynthesis enrichment of the interstellar medium.

  2. Energy Dissipation in Molecular Systems

    CERN Document Server

    Tramer, André; Lahmani, Fran oise

    2005-01-01

    Energy Dissipation in Molecular Systems analyzes experimental data on the redistribution and dissipation of energy injected into molecular systems by radiation or charged particles. These processes, competing with such practically important relaxation channels as chemical reaction or stimulated emission (laser action), are the primary focus in this monograph. Among other topics, the book treats vibrational redistribution and electronic relaxation in isolated molecules and the effects of inter-molecular interactions (collisions, complex formation, solvent effects) on the relaxation paths. Primary photo-chemical processes (such as isomerization, proton or hydrogen-atom transfer, electron transfer and ionization) are also treated as particular cases of vibrational or electronic relaxation. Only a basic knowledge of quantum mechanics and spectroscopy is assumed and calculations are kept to a strict minimum, making the book more accessible to students.

  3. Performance optimization of dense-array concentrator photovoltaic system considering effects of circumsolar radiation and slope error.

    Science.gov (United States)

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

    2015-07-27

    This paper presents an approach to optimize the electrical performance of dense-array concentrator photovoltaic system comprised of non-imaging dish concentrator by considering the circumsolar radiation and slope error effects. Based on the simulated flux distribution, a systematic methodology to optimize the layout configuration of solar cells interconnection circuit in dense array concentrator photovoltaic module has been proposed by minimizing the current mismatch caused by non-uniformity of concentrated sunlight. An optimized layout of interconnection solar cells circuit with minimum electrical power loss of 6.5% can be achieved by minimizing the effects of both circumsolar radiation and slope error.

  4. Resonance effects on the dynamics of dense granular beds: achieving optimal energy transfer in vibrated granular systems

    NARCIS (Netherlands)

    Windows-Yule, C.R.K.; Rosato, A.D.; Thornton, A.R.; Parker, D.J.

    2015-01-01

    Using a combination of experimental techniques and discrete particle method simulations, we investigate the resonant behaviour of a dense, vibrated granular system. We demonstrate that a bed of particles driven by a vibrating plate may exhibit marked differences in its internal energy dependent on t

  5. Dense Breasts

    Science.gov (United States)

    ... also appear white on mammography, they can be hidden by or within dense breast tissue. Other imaging ... understanding of the possible charges you will incur. Web page review process: This Web page is reviewed ...

  6. Iterative solution of dense linear systems arising from the electrostatic integral equation in MEG

    Energy Technology Data Exchange (ETDEWEB)

    Rahola, Jussi [Simulintu Oy, Espoo (Finland); Tissari, Satu [CSC - Scientific Computing Ltd, Espoo (Finland)]. E-mail: satu.tissari@csc.fi

    2002-03-21

    We study the iterative solution of dense linear systems that arise from boundary element discretizations of the electrostatic integral equation in magnetoencephalography (MEG). We show that modern iterative methods can be used to decrease the total computation time by avoiding the time-consuming computation of the LU decomposition of the coefficient matrix. More importantly, the modern iterative methods make it possible to avoid the explicit formation of the coefficient matrix which is needed when a large number of unknowns are used. To study the convergence of iterative solvers we examine the eigenvalue distributions of the coefficient matrices. For the sphere we show how the eigenvalues of the integral operator are approximated by the eigenvalues of the coefficient matrix when the collocation and Galerkin methods are used as discretization methods. The collocation method approximates the eigenvalues of the integral operator directly. The Galerkin method produces a coefficient matrix that needs to be preconditioned in order to maintain optimal convergence speed. With the ILU(0) preconditioner iterative methods converge fast and independent of the number of discretization points for both the collocation and Galerkin approaches. The preconditioner has no significant effect on the total computational time. (author)

  7. 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

  8. 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

  9. Systems biology in molecular psychiatry.

    Science.gov (United States)

    Gebicke-Haerter, P J

    2008-09-01

    The last ten to fifteen years have seen a remarkable shift of research strategies from hypothesis-driven, reductionistic to data driven, hypothesis-free approaches. This tendency has become evident after completion of the sequencing of the human genome, when publications under the label systems biology have been skyrocketing. This shift marks a gradual revision of scientific understanding of biological systems. Whilst the former has been component-oriented, precluding elements that do not belong to the hypothesis, the latter try to extract information from the whole system in the first place. Only with this information at hand, data driven strategies develop hypotheses. Data driven strategies unearth the immense complexity of biological systems and, hence, necessitate computer-aided support. Mathematical tools derived from chaos theory appear to be applicable in biological systems, but require significant improvements. The combination of high throughput data collection with in silico modelling of molecular or higher order systems can markedly extend our understanding of onset and progression of diseases. Undoubtedly, systems thinking in brain research is the greatest challenge for the years to come.

  10. Equation of state of a dense plasma by orbital-free and quantum molecular dynamics: examination of two isothermal-isobaric mixing rules.

    Science.gov (United States)

    Danel, J-F; Kazandjian, L

    2015-01-01

    We test two isothermal-isobaric mixing rules, respectively based on excess-pressure and total-pressure equilibration, applied to the equation of state of a dense plasma. While the equation of state is generally known for pure species, that of arbitrary mixtures is not available so that the validation of accurate mixing rules, that implies resorting to first-principles simulations, is very useful. Here we consider the case of a plastic with composition C(2)H(3) and we implement two complementary ab initio approaches adapted to the dense plasma domain: quantum molecular dynamics, limited to low temperature by its computational cost, and orbital-free molecular dynamics, that can be implemented at high temperature. The temperature and density range considered is 1-10 eV and 0.6-10 g/cm(3) for quantum molecular dynamics, and 5-1000 eV and 1-10 g/cm(3) for orbital-free molecular dynamics. Simulations for the full C(2)H(3) mixture are the benchmark against which to assess the mixing rules, and both pressure and internal energy are compared. We find that the mixing rule based on excess-pressure equilibration is overall more accurate than that based on total-pressure equilibration; except for quantum molecular dynamics and a thermodynamic domain characterized by very low or negative excess pressures, it gives pressures which are generally within statistical error or within 1% of the exact ones. Besides, its superiority is amplified in the calculation of a principal Hugoniot.

  11. High pressure studies on the ferromagnetic dense Kondo systems CeRh3B2 and UCu2Ge2

    Science.gov (United States)

    Cornelius, A. L.; Schilling, J. S.; Endstra, T.; Mydosh, J. A.

    1994-07-01

    The dependence of the Curie temperature of the anomalous ferromagnets UCu2Ge2 and CeRh3B2 on hydrostatic pressure to 11 GPa is determined using a diamond-anvil cell loaded with dense helium as pressure medium. A sensitive primary/secondary coil system allows the detection of the ferromagnetic transition in the ac susceptibility for tiny samples with less than 1 μ mass. The Curie temperatures of the above two compounds, Tc≊110 K and 118 K, both increase initially under pressure but pass through maxima at 8 GPa and 2 GPa, respectively, before falling rapidly at higher pressures. We take this as evidence that both compounds behave as dense Kondo system, where Tc depends on the exchange coupling J according to a magnetic phase diagram originally proposed by Doniach.

  12. Role of arches in the generation of shear bands in a dense 3D granular system under shear

    Energy Technology Data Exchange (ETDEWEB)

    Sigaud, L [Instituto de Fisica, Universidade Federal do Rio de Janeiro, P.O. 68528, 21941-972 Rio de Janeiro, RJ (Brazil); Bordignon, A L; Lopes, H; Lewiner, T; Tavares, G [Departamento de Matematica, PontifIcia Universidade Catolica do Rio de Janeiro, C.P. 38071, 22452 970 Rio de Janeiro (Brazil); Morgado, W A M, E-mail: lucas@if.ufrj.b [Departamento de Fisica, PontifIcia Universidade Catolica do Rio de Janeiro and National Institute of Science and Technology for Complex Systems, C.P. 38071, 22452-970 Rio de Janeiro (Brazil)

    2010-09-01

    A model for propagation of arches on cubic lattices, to simulate the internal mobility of grains in a dense granular system under shear is proposed. In this model, the role of the arches in granular transportation presents a non-linear dependence on the local values of the stress components that can be modeled geometrically. In particular, we study a modified Couette flow and were able to reproduce qualitatively the experimental results found in the literature.

  13. 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.

  14. Diffusion and partitioning of macromolecules in casein microgels: evidence for size-dependent attractive interactions in a dense protein system.

    Science.gov (United States)

    Peixoto, Paulo D S; Bouchoux, Antoine; Huet, Sébastien; Madec, Marie-Noëlle; Thomas, Daniel; Floury, Juliane; Gésan-Guiziou, Geneviève

    2015-02-10

    Understanding the mechanisms that determine the diffusion and interaction of macromolecules (such as proteins and polysaccharides) that disperse through dense media is an important fundamental issue in the development of innovative technological and medical applications. In the current work, the partitioning and diffusion of macromolecules of different sizes (from 4 to 10 nm in diameter) and shapes (linear or spherical) within dispersions of casein micelles (a protein microgel) is studied. The coefficients for diffusion and partition are measured using FRAP (fluorescence recovery after photobleaching) and analyzed with respect to the structural characteristics of the microgel determined by the use of TEM (transmission electron microscopy) tomography. The results show that the casein microgel displays a nonspecific attractive interaction for all macromolecules studied. When the macromolecular probes are spherical, this affinity is clearly size-dependent, with stronger attraction for the larger probes. The current data show that electrostatic effects cannot account for such an attraction. Rather, nonspecific hydration molecular forces appear to explain these results. These findings show how weak nonspecific forces affect the diffusion and partitioning of proteins and polysaccharides in a dense protein environment. These results could be useful to better understand the mechanisms of diffusion and partitioning in other media such as cells and tissues. Furthermore, there arises the possibility of using the casein micelle as a size-selective molecular device.

  15. 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.)

  16. 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.

  17. Periodic domain boundary ordering in a dense molecular adlayer: Sub-saturation carbon monoxide on Pd(111)

    Science.gov (United States)

    Xu, Pan; Liu, Shizhong; Hong, Sung-Young; Liu, Ping; White, Michael G.; Camillone, Nicholas

    2017-04-01

    We describe a previously unreported ordered phase of carbon monoxide adsorbed on the (111) facet of single crystal palladium at near-saturation coverage. The adlayer superstructure is identified from low energy electron diffraction to be c(16×2) with respect to the underlying Pd(111) surface net. The ideal coverage is determined to be 0.6875 ML, approximately 92% of the 0.75-ML saturation coverage. Density functional theory calculations support a model for the molecular packing characterized by strips of locally-saturated (2×2) regions, with the CO bound near high-symmetry surface sites, separated by antiphase domain boundaries. The structure exists in a narrow coverage range and is prepared by heating the saturated adlayer to desorb a small fraction of the CO. Comparison of the c(16×2) domain-boundary structure with structural motifs at lower coverages suggests that between 0.6 and 0.6875 ML the adlayer order may be more strongly influenced by interadsorbate repulsion than by adsorption-site-specific interactions. The system is an example of the structural complexity that results from the compromise between adsorbate-substrate and adsorbate-adsorbate interactions.

  18. Molecular Spectroscopy of Living Systems

    Science.gov (United States)

    Cheng, Ji-Xin

    2016-06-01

    Molecular spectroscopy has been a powerful tool in the study of molecules in gas phase, condensed phase, and at interfaces. The transition from in vitro spectroscopy to spectroscopic imaging of living systems is opening new opportunities to reveal cellular machinery and to enable molecule-based diagnosis (Science 2015, 350: 1054). Such a transition involves more than a simple combination of spectrometry and microscopy. In this presentation, I will discuss the most recent efforts that have pushed the physical limits of spectroscopic imaging in terms of spectral acquisition speed, detection sensitivity, spatial resolution and imaging depth. I will further highlight significant applications in functional analysis of single cells and in label-free detection of diseases.

  19. Structure of dense molecular gas in TMC 1 from observations of three transitions of HC3N

    Science.gov (United States)

    Schloerb, F. P.; Snell, R. L.; Young, J. S.

    1983-01-01

    The Taurus dark cloud complex is a collection of many individual clouds scattered across approximately 50 pc. Within one of these, Heiles Cloud 2, is the dense condensation TMC 1. TMC 1 is one of the few sources in which some of the long carbon chain molecules are found. The present investigation is concerned with a mapping of the density structure in a narrow ridge of the TMC 1 structure. It is shown that the HC3N emission from the J = 5 to 4, J = 9 to 8, and J = 12 to 11 transitions is well matched by a narrow ridge of material at a single density of 50,000-100,000 per cu cm. There is evidence that the HC3N fractional abundance is variable along the ridge. Evidence is also found for the presence of subcondensations within this ridge from maps at individual velocities.

  20. Reactions of small molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Wittig, C. [Univ. of Southern California, Los Angeles, CA (United States)

    1993-12-01

    This DOE program remains focused on small molecular systems relevant to combustion. Though a number of experimental approaches and machines are available for this research, the authors` activities are centered around the high-n Rydberg time-of-flight (HRTOF) apparatus in this laboratory. One student and one postdoc carry out experiments with this machine and also engage in small intra-group collaborations involving shared equipment. This past year was more productive than the previous two, due to the uninterrupted operation of the HRTOF apparatus. Results were obtained with CH{sub 3}OH, CH{sub 3}SH, Rg-HX complexes, HCOOH, and their deuterated analogs where appropriate. One paper is in print, three have been accepted for publication, and one is under review. Many preliminary results that augur well for the future were obtained with other systems such as HNO{sub 3}, HBr-HI complexes, toluene, etc. Highlights from the past year are presented below that display some of the features of this program.

  1. Dense Molecular Gas in the First Galactic Quadrant: A New Distance Estimation Technique and the Molecular Cloud Clump Mass Function, Physical Properties, and Galactic Distribution from the Bolocam Galactic Plane Survey

    Science.gov (United States)

    Glenn, Jason; Ellsworth-Bowers, Timothy; Bolocam Galactic Plane Survey

    2015-01-01

    Large submillimeter and millimeter Galactic dust continuum surveys of the Milky Way, such as the Bolocam Galactic Plane Survey (BGPS), Hi-GAL, ATLAS-GAL, and JCMT-JPS cumulatively have discovered 105 cores, clumps, and other structures in Galactic molecular clouds. Robust distance measurements to these structures are needed to enable the large range of quantitative astrophysics that these surveys promise, such as physical properties of clumps, the clump mass function, and the three-dimensional distribution of dense gas and star formation in the Milky Way. We have developed a technique for deriving distances to continuum-identified molecular cloud clumps employing kinematic distances and a suite of distance estimators for breaking kinematic distance ambiguities. Application to the BGPS has yielded 3,700 distance probability density functions (DPDFs) and 1,800 well-constrained distances (typical σdist ≈ 0.5 kpc). These have been used to determine sizes and masses of molecular cloud clumps, derive the clump mass function, and map the three-dimensional distribution of dense gas in the first Galactic quadrant. Among the interesting results are a mass function intermediate between molecular clouds and the stellar initial mass function and inter-arm star formation. Next, we plan to apply the technique to Hi-GAL, which covers the entire Galactic plane and whose submilllimeter maps provide for temperature and bolometric luminosity measurements of cloud structures.

  2. The Bolocam Galactic Plane Survey. XII. Distance Catalog Expansion Using Kinematic Isolation of Dense Molecular Cloud Structures With 13CO(1-0)

    CERN Document Server

    Ellsworth-Bowers, Timothy P; Glenn, Jason; Ginsburg, Adam; Evans, Neal J; Battersby, Cara; Shirley, Yancy L; Svoboda, Brian

    2014-01-01

    We present an expanded distance catalog for 1,710 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+(3-2), NH3(1,1)) used to derive line-of-sight velocities for kinematic distances, we utilize the Galactic Ring Survey 13CO(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 13CO data, along with a reference region to subtract enveloping diffuse emission, to produce a line profile of 13CO matched to the BGPS source. For objects with a HCO+(3-2) velocity, \\approx 95% of the new 13CO(1-0) velocities agree with that of the dense gas. A new prior DPDF for kinematic distance ambiguity (KDA) resolution, based on a validated f...

  3. Equation of state of warm dense deuterium and its isotopes from density-functional theory molecular dynamics.

    Science.gov (United States)

    Danel, J-F; Kazandjian, L; Piron, R

    2016-04-01

    Of the two approaches of density-functional theory molecular dynamics, quantum molecular dynamics is limited at high temperature by computational cost whereas orbital-free molecular dynamics, based on an approximation of the kinetic electronic free energy, can be implemented in this domain. In the case of deuterium, it is shown how orbital-free molecular dynamics can be regarded as the limit of quantum molecular dynamics at high temperature for the calculation of the equation of state. To this end, accurate quantum molecular dynamics calculations are performed up to 20 eV at mass densities as low as 0.5g/cm^{3} and up to 10 eV at mass densities as low as 0.2g/cm^{3}. As a result, the limitation in temperature so far attributed to quantum molecular dynamics is overcome and an approach combining quantum and orbital-free molecular dynamics is used to construct an equation of state of deuterium. The thermodynamic domain addressed is that of the fluid phase above 1 eV and 0.2g/cm^{3}. Both pressure and internal energy are calculated as functions of temperature and mass density, and various exchange-correlation contributions are compared. The generalized gradient approximation of the exchange-correlation functional, corrected to approximately include the influence of temperature, is retained and the results obtained are compared to other approaches and to experimental shock data; in parts of the thermodynamic domain addressed, these results significantly differ from those obtained in other first-principles investigations which themselves disagree. The equations of state of hydrogen and tritium above 1 eV and above, respectively, 0.1g/cm^{3} and 0.3g/cm^{3}, can be simply obtained by mass density scaling from the results found for deuterium. This ab initio approach allows one to consistently cover a very large domain of temperature on the domain of mass density outlined above.

  4. The influence of PRF on BER performance of THSS UWB radio system with PPM in dense multipath fading environments

    Institute of Scientific and Technical Information of China (English)

    Jia Lin; Zhang Zhongzhao

    2005-01-01

    The influence of pulse repetition frequency(PRF) on performance of wireless digital time hopping spread spectrum(THSS) ultrawide bandwidth(UWB) radio systems with PPM in dense multipath fading environments is firstly investigated. The receiver used in this UWB system is a hybrid selection/maximal-ratio combining(H-S/MRC) diversity receiver in which L strongest multipath components out of N multipath diversity branches are selected and combined using maximal-ratio combining. The exact expressions for the bit error rate(BER) of this UWB system are firstly derived by using the virtual branch technique in term of PRF, the number of multipath components selected and combined L,and multipath spread of the channel and then this BER performance is evaluated. With the computer simulation for impulses having different pulse shapes, numerical results show that PRF, as well as pulse shape and the number of multipath diversity branches selected and combined L, has much effect on the BER performance of this UWB system in dense multipath fading environments. As PRF increases, the BER performance of this UWB system is much degraded under the conditions of fixed L and pulse shape.

  5. Impact of polarization mode dispersion and nonlinear effect on 40 Gbit/s dense wavelength division multiplexing system

    Institute of Scientific and Technical Information of China (English)

    SUN Xue-ming; ZHANG Hui-jian; ZUO Meng; GU Wan-yi; XU Da-xiong

    2006-01-01

    Dense wavelength division multiplexing (DWDM) system is the ultimate selection as an optical communication system because of its high speeds and capacities.However,the fiber nonlinear effects and polarization mode dispersion severely limit the performance of the system when signal propagates at 40 Gbit/s in a single channel.The coupled nonlinear Schr(o)dinger equations of a single channel in DWDM,which are all considered factors of group velocity dispersion (GVD),self phase modulation (SPM),cross phase modulation (XPM),four wave mixing (FWM) and polarization mode dispersion (PMD),are derived,while their number results are obtained with extended split-step Fourier method.Finally,to analyze the impacts of the fiber nonlinear effects and PMD on the optical communication system,the simulated results of an 8x40 Gbit/s DWDM system are discussed under different conditions respectively.

  6. MALATANG: MApping the dense moLecular gAs in the sTrongest stAr-formiNg Galaxies

    Science.gov (United States)

    Gao, Yu; Zhang, Zhiyu; Greve, Thomas; MALATANG Team

    2017-01-01

    The MALATANG Large Program is a 390 hr campaign, using the heterodyne array HARP on the JCMT to map theHCN and HCO+ J = 4 - 3 line emission in 23 of the nearest IR-brightest galaxies beyond the Local Group. Theobservations will reach a sensitivity of 0.3 K km/s (~ 4.5 x 10^6 Msun) at linear resolutions of 0.2-2.8kpc. It is thefirst survey to systematically map the distribution of dense molecular gas out to large galactocentric distances in a statisticallysignificant sample of nearby galaxies. MALATANG will bridge the gap, in terms of physical scale and luminosity,between extragalactic (i.e., galaxy-integrated) and Galactic (i.e., single molecular clouds) observations. A primarygoal of the survey is to delineate for the first time the distributed dense gas star-formation relations, as traced by theHCN and HCO+ J = 4-3, on scales of ~1kpc across our targets. Exploring the behaviour of these star-formationrelations in low surface density regions found in the disks as well as in the nuclear regions where surface densitiesare high, will shed new light on whether such environments are host to fundamentally different star-formation modes.The MALATANG data products of resolved HCN and HCO+ J = 4-3 maps of 23 IR-bright local galaxies, will beof great value to the extragalactic community and, in and of themselves, carry significant legacy value. At the moment,about 50% (~195hrs) of the 390hrs of time allocated to MALATANG has been observed. We here show somevery preliminary results as well after introducing our project.

  7. The Atlas3D Project -- XI. Dense molecular gas properties of CO-luminous early-type galaxies

    CERN Document Server

    Crocker, Alison; Bureau, Martin; Young, Lisa M; Davis, Timothy A; Bayet, Estelle; Alatalo, Katherine; Blitz, Leo; Bois, Maxime; Bournaud, Frédéric; Cappellari, Michele; Davies, Roger L; de Zeeuw, P T; Duc, Pierre-Alain; Emsellem, Eric; Khochfar, Sadegh; Krajnovic, Davor; Kuntschner, Harald; Lablanche, Pierre-Yves; McDermid, Rchard M; Morganti, Raffaella; Naab, Thorsten; Oosterloo, Tom; Sarzi, Marc; Scott, Nicholas; Serra, Paolo; Weijmans, Anne-Marie

    2011-01-01

    Surveying eighteen 12CO-bright galaxies from the ATLAS3D early-type galaxy sample with the Institut de Radio Astronomie Millim\\'etrique (IRAM) 30m telescope, we detect 13CO(1-0) and 13CO(2-1) in all eighteen galaxies, HCN(1-0) in 12/18 and HCO+(1-0) in 10/18. We find that the line ratios 12CO(1-0)/13CO(1-0) and 12CO(1-0)/HCN(1-0) are clearly correlated with several galaxy properties: total stellar mass, luminosity-weighted mean stellar age, molecular to atomic gas ratio, dust temperature and dust morphology. We suggest that these correlations are primarily governed by the optical depth in the 12CO lines; interacting, accreting and/or starbursting early-type galaxies have more optically thin molecular gas while those with settled dust and gas discs host optically thick molecular gas. The ranges of the integrated line intensity ratios generally overlap with those of spirals, although we note some outliers in the 12CO(1- 0)/13CO(1-0), 12CO(2-1)/13CO(2-1) and HCN/HCO+(1-0) ratios. In particular, three galaxies ar...

  8. Dense gas and exciting sources of the molecular outflow in the AFGL 437 star-forming region

    CERN Document Server

    Manjarrez, G; de Gregorio-Monsalvo, I

    2011-01-01

    We present Very Large Array (VLA) high resolution observations of the NH3(1,1) and NH3(2,2) molecular transitions towards the high mass star forming region AFGL 437. Our aim was to investigate if the poorly collimated CO molecular outflow previously detected in the region is the result of a projection effect, with no intrinsic bipolarity, as suggested by Gomez et al. We complemented our observations with radio continuum archived data from the VLA at 2 and 3.6 cm, and with unpublished public data at 450 {\\mu}m taken with Submillimetre Common-User Bolometer Array at the James Clerk Maxwell Telescope. Ammonia emission was found mainly in three clumps located at the south and east of the position of the compact infrared cluster of AFGL 437, where the CO outflow seemed to have its origin. One of the NH3(1,1) clumps coincides with the maximum of NH3(2,2) and with a local peak of emission at 450 {\\mu}m. A near infrared source (s11) is also found at that position. Our continuum map at 2 cm shows extended elongated em...

  9. Unitary equivalence and decompositions of finite systems of closed densely defined operators in Hilbert spaces

    CERN Document Server

    Niemiec, Piotr

    2011-01-01

    An \\textit{ideal} of $N$-tuples of operators is a class invariant with respect to unitary equivalence which contains direct sums of arbitrary collections of its members as well as their (reduced) parts. New decomposition theorems (with respect to ideals) for $N$-tuples of closed densely defined linear operators acting in a common (arbitrary) Hilbert space are presented. Algebraic and order (with respect to containment) properties of the class $CDD_N$ of all unitary equivalence classes of such $N$-tuples are established and certain ideals in $CDD_N$ are distinguished. It is proved that infinite operations in $CDD_N$ may be reconstructed from the direct sum operation of a pair. \\textit{Prime decomposition} in $CDD_N$ is proposed and its (in a sense) uniqueness is established. The issue of classification of ideals in $CDD_N$ (up to isomorphism) is discussed. A model for $CDD_N$ is described and its concrete realization is presented. A new partial order of $N$-tuples of operators is introduced and its fundamental...

  10. Infall/Expansion Velocities in the Low-mass Dense Cores L492, L694-2, and L1521F: Dependence on Position and Molecular Tracer

    Science.gov (United States)

    Keown, Jared; Schnee, Scott; Bourke, Tyler L.; Di Francesco, James; Friesen, Rachel; Caselli, Paola; Myers, Philip; Williger, Gerard; Tafalla, Mario

    2016-12-01

    Although surveys of infall motions in dense cores have been carried out for years, few surveys have focused on mapping infall across cores using multiple spectral-line observations. To fill this gap, we present IRAM 30 m telescope maps of N2H+(1-0), DCO+(2-1), DCO+(3-2), and HCO+(3-2) emission toward two prestellar cores (L492 and L694-2) and one protostellar core (L1521F). We find that the measured infall velocity varies with position across each core and choice of molecular line, likely as a result of radial variations in core chemistry and dynamics. Line-of-sight infall speeds estimated from DCO+(2-1) line profiles can decrease by 40-50 m s-1 when observing at a radial offset ≥slant 0.04 pc from the core's dust continuum emission peak. Median infall speeds calculated from all observed positions across a core can also vary by as much as 65 m s-1, depending on the transition. These results show that while single-pointing, single-transition surveys of core infall velocities may be good indicators of whether a core is either contracting or expanding, the magnitude of the velocities they measure are significantly impacted by the choice of molecular line, proximity to the core center, and core evolutionary state.

  11. 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.

  12. Dynamic modeling of a solar receiver/thermal energy storage system based on a compartmented dense gas fluidized bed

    Science.gov (United States)

    Solimene, Roberto; Chirone, Roberto; Chirone, Riccardo; Salatino, Piero

    2017-06-01

    Fluidized beds may be considered a promising option to collection and storage of thermal energy of solar radiation in Concentrated Solar Power (CSP) systems thanks to their excellent thermal properties in terms of bed-to-wall heat transfer coefficient and thermal diffusivity and to the possibility to operate at much higher temperature. A novel concept of solar receiver for combined heat and power (CHP) generation consisting of a compartmented dense gas fluidized bed has been proposed to effectively accomplish three complementary tasks: collection of incident solar radiation, heat transfer to the working fluid of the thermodynamic cycle and thermal energy storage. A dynamical model of the system laid the basis for optimizing collection of incident radiative power, heat transfer to the steam cycle, storage of energy as sensible heat of bed solids providing the ground for the basic design of a 700kWth demonstration CSP plant.

  13. Dense molecular cocoons in the massive protocluster W3 IRS5: a test case for models of massive star formation

    CERN Document Server

    Wang, K -S; Hogerheijde, M R; van der Tak, F F S; Benz, A O; Megeath, S T; Wilson, T L

    2013-01-01

    [Context] Two competing models describe the formation of massive stars in objects like the Orion Trapezium. In the turbulent core accretion model, the resulting stellar masses are directly related to the mass distribution of the cloud condensations. In the competitive accretion model, the gravitational potential of the protocluster captures gas from the surrounding cloud for which the individual cluster members compete. [Aims] With high resolution submillimeter observations of the structure, kinematics, and chemistry of the proto-Trapezium cluster W3 IRS5, we aim to determine which mode of star formation dominates. [Methods] We present 354 GHz Submillimeter Array observations at resolutions of 1"-3" (1800-5400 AU) of W3 IRS5. ...... [Results] The observations show five emission peaks (SMM1-5). SMM1 and SMM2 contain massive embedded stars (~20 Msun); SMM3-5 are starless or contain low-mass stars (= 10^7 cm^-3, but the core masses are small, 0.2-0.6 Msun. The detected molecular emission reveals four different c...

  14. Molecular assembly in natural and engineered systems

    CERN Document Server

    Howorka, Stefan

    2011-01-01

    This volume explores some of the most exciting recent advances in basic research on molecular assembly in natural and engineered systems and how this knowledge is leading to advances in the various fields.* This series provides a forum for discussion of new discoveries, approaches, and ideas * Contributions from leading scholars and industry experts * Reference guide for researchers involved in molecular biology and related fields

  15. Very Dense High Speed 3u VPX Memory and Processing Space Systems Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Today, memory and payload processing systems for space applications are typically designed for a specific application for a specific mission. Many of these systems...

  16. 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.

  17. Orthogonal photoswitching in a multifunctional molecular system

    NARCIS (Netherlands)

    Lerch, Michael M.; Hansen, Mickel J.; Velema, Willem A.; Szymanski, Wiktor; Feringa, Ben L.

    2016-01-01

    The wavelength-selective, reversible photocontrol over various molecular processes in parallel remains an unsolved challenge. Overlapping ultraviolet-visible spectra of frequently employed photoswitches have prevented the development of orthogonally responsive systems, analogous to those that rely o

  18. High immersive three-dimensional tabletop display system with high dense light field reconstruction

    Science.gov (United States)

    Zheng, Mengqing; Yu, Xunbo; Xie, Songlin; Sang, Xinzhu; Yu, Chongxiu

    2014-11-01

    Three-dimensional (3D) tabletop display is a kind of display with wide range of potential applications. An auto-stereoscopic 3D tabletop display system is designed to provide the observers with high level of immersive perception. To improve the freedom of viewing position, the eye tracking system and a set of active partially pixelated masks are utilized. To improve the display quality, large number of images is prepared to generate the stereo pair. The light intensity distribution and crosstalk of parallax images are measured respectively to evaluate the rationality of the auto-stereoscopic system. In the experiment, the high immersive auto-stereoscopic tabletop display system is demonstrated, together with the system architectures including hardware and software. Experimental results illustrate the effectiveness of the high immersive auto-stereoscopic tabletop display system.

  19. Infall/Expansion Velocities in the Low-Mass Dense Cores L492, L694-2, and L1521F: Dependence on Position and Molecular Tracer

    CERN Document Server

    Keown, Jared; Bourke, Tyler L; Di Francesco, James; Friesen, Rachel; Caselli, Paola; Myers, Philip; Williger, Gerard; Tafalla, Mario

    2016-01-01

    Although surveys of infall motions in dense cores have been carried out for years, few surveys have focused on mapping infall across cores using multiple spectral line observations. To fill this gap, we present IRAM 30-m Telescope maps of N2H+(1-0), DCO+(2-1), DCO+(3-2), and HCO+(3-2) emission towards two prestellar cores (L492 and L694-2) and one protostellar core (L1521F). We find that the measured infall velocity varies with position across each core and choice of molecular line, likely as a result of radial variations in core chemistry and dynamics. Line-of-sight infall speeds estimated from DCO+(2-1) line profiles can decrease by 40-50 m/s when observing at a radial offset >= 0.04 pc from the core's dust continuum emission peak. Median infall speeds calculated from all observed positions across a core can also vary by as much as 65 m/s depending on the transition. These results show that while single-pointing, single-transition surveys of core infall velocities may be good indicators of whether a core is...

  20. 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.

  1. Assessment of Energy and Economic Effectiveness of Photovoltaic Systems Operating in a Dense Urban Context

    Directory of Open Access Journals (Sweden)

    Maurizio Cellura

    2013-06-01

    Full Text Available A methodology that permits testing the level of integration of the photovoltaic technology in urban areas is presented. The percentage of coverage of the electricity demand of grid-connected photovoltaic systems installed on the roofs of buildings were investigated in a district of the city of Palermo (Sicily. After classifying roofs according to their shape, orientation and pitch by means of satellite images provided by Google Earth, the ratio of the productivity of the PV systems and the consumption of electricity of the households was analysed. The results of the energy assessment have been screened considering the economic feasibility of grid-connected photovoltaic systems: the energy produced by the PV systems whose economic analysis showed disadvantageous values of NPV or IRR was rejected. As a result, it can be concluded that the size of the PV system that may be installed corresponding to the number of floors, and the consequent production of electricity, does not recover the costs for installation and maintenance of the system.

  2. Characterizing Molecular Interactions in Chemical Systems.

    Science.gov (United States)

    Günther, David; Boto, Roberto A; Contreras-Garcia, Juila; Piquemal, Jean-Philip; Tierny, Julien

    2014-12-01

    Interactions between atoms have a major influence on the chemical properties of molecular systems. While covalent interactions impose the structural integrity of molecules, noncovalent interactions govern more subtle phenomena such as protein folding, bonding or self assembly. The understanding of these types of interactions is necessary for the interpretation of many biological processes and chemical design tasks. While traditionally the electron density is analyzed to interpret the quantum chemistry of a molecular system, noncovalent interactions are characterized by low electron densities and only slight variations of them--challenging their extraction and characterization. Recently, the signed electron density and the reduced gradient, two scalar fields derived from the electron density, have drawn much attention in quantum chemistry since they enable a qualitative visualization of these interactions even in complex molecular systems and experimental measurements. In this work, we present the first combinatorial algorithm for the automated extraction and characterization of covalent and noncovalent interactions in molecular systems. The proposed algorithm is based on a joint topological analysis of the signed electron density and the reduced gradient. Combining the connectivity information of the critical points of these two scalar fields enables to visualize, enumerate, classify and investigate molecular interactions in a robust manner. Experiments on a variety of molecular systems, from simple dimers to proteins or DNA, demonstrate the ability of our technique to robustly extract these interactions and to reveal their structural relations to the atoms and bonds forming the molecules. For simple systems, our analysis corroborates the observations made by the chemists while it provides new visual and quantitative insights on chemical interactions for larger molecular systems.

  3. Applying Virtual Realitzy to Molecular Graphics System

    Institute of Scientific and Technical Information of China (English)

    ChangNoYoon; MyungHwanChi; 等

    1996-01-01

    Mlecular graphics can be thought of as a window to the computer through which the chemist expresses ideas for computational evaluation and receives results in an understandable form.Furthermore,with beautiful graphic images it can give out the realistic molecular model like a real thing in real world.Molecule has various properties including volume,electronic,van der waals forces,etc.These properties are very important to understand the molecular world.So if the virtual reality tools are used,then the imaginary world can be studied intuitively by touching and feeling a tremendous amount of data.Computational chemistry generates such amount of molecular property data through supercomputing with molecular simulation experiment.One of the objects to investigate the molecular world is to understand the intermolecular interaction such as drug-receptor interaction.Another thing is to measure the geometrical data in molecular architecture.Virtual reality system provides the easiest way to meet these objects.This kind of simple system changes a numerical data set,which is very difficults to deal with,into a visible and understandable data set.Recently two functions of such a system were improved to get an insight into biomolecular interaction.The first one is a real time force generation during navigation in macromolecular environment.An cylindrical arrow shows the magnitude and direction of molecular force.The second one is to see a molecular vibration such as a concerted motion of the binding site in protein molecule.So one can understand th molecular shape change for drugreceptor docking procedure.But some problems which are difficult to solve still remain.

  4. Investigation of proper modeling of very dense granular flows in the recirculation system of CFBs

    Institute of Scientific and Technical Information of China (English)

    Aristeidis Nikolopoulos; Nikos Nikolopoulos; Nikos Varveris; Sotirios Karellas; Panagiotis Grammelis; Emmanuel Kakaras

    2012-01-01

    The aim of this paper is the development of new models and/or the improvement of existing numerical models,used for simulating granular flow in CFB (circulating fluidized bed) recirculation systems.Most recent models follow the TFM (two-fluid model) methodology,but they cannot effectively simulate the inter-particle friction forces in the recirculation system,because the respective stress tensor does not incorporate compressibility of flow due to change of effective particle density.As a consequence,the induced normal and shear stresses are not modeled appropriately during the flow of the granular phase in the CFB recirculation system.The failure of conventional models,such as that of von Mises/Coulomb,is mainly caused by false approximation of the yield criterion which is not applicable to the CFB recirculation system.The present work adopts an alternative yield function,used for the first time in TFM Eulerian modeling.The proposed model is based on the Pitman-Schaeffer-Gray-Stiles yield criterion.Both the temporal deformation of the solid granular phase and the repose angle that the granular phase forms are more accurately simulated by this model.The numerical results of the proposed model agree well with experimental data,implying that frictional forces are efficiently simulated by the new model.

  5. 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.

  6. 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.

  7. Modeling interchannel four-wave mixing for 8-Ary modulated dense wavelength division multiplexing systems over dispersion map

    Science.gov (United States)

    Du, Jianxin; Shen, Ninghang; Xu, Yue

    2016-08-01

    Semianalytic models are developed to deterministically calculate the variances of degenerate and nondegenerate four-wave mixing (FWM) noises for dispersion-managed dense wavelength division multiplexing (DWDM) systems with 8-Ary modulations [i.e., 8-level amplitude- and differential phase-shift keying (8APSK) and constant-amplitude optical differential 8-level phase-shift keying (D8PSK)]. The semianalytic models include various important propagation effects for exact numerical results. A 5.28-Tb/s (40-Gs/s/ch) 100-GHz-spaced 33-channel DWDM system with a dispersion map is then numerically analyzed by using the newly derived semianalytic models. It is numerically validated that FWM impacts coming from 8APSK pump channels are more severe than those coming from D8PSK ones, where pump channels denote the channels whose energies are transferred to a probe channel through the FWM process. The numerical results show that although FWM tolerance of a central channel with 8APSK is worse than that with D8PSK, a central channel with 8APSK is still superior to that with D8PSK when some linear noises and FWM noise are simultaneously taken into account for our given system conditions, which is mainly attributed to a relatively larger minimum Euclidean distance for the 8APSK constellation than the D8PSK one.

  8. The Dense Plasma Focus Opportunities in Detection of Hidden Objects by Using Nanosecond Impulse Neutron Inspection System (NINIS)

    Science.gov (United States)

    Gribkov, V.; Dubrovsky, A.; Karpiński, L.; Miklaszewski, R.; Paduch, M.; Scholz, M.; StrzyŻewski, P.; Tomaszewski, K.

    2006-12-01

    Dense Plasma Focus device is proposed for use as a neutron source to generate very powerful pulses of neutrons in the nanosecond (ns) range of its duration. Our devices PF-6, recently put into operation at the Institute of Plasma Physics and Laser Microfusion, Warsaw, Poland, and PF-10 belonging to the Institute for Theoretical and Experimental Physics, Moscow, Russia, have energy storages in its capacitor banks 7.4 kJ and 13 kJ as a maximum. Operated with the DPF chambers of a special design they have a current maximum up to ˜760 kA with a quarter period of the discharge equal to 1 microsecond. They generate circa 109 of 2.5-MeV neutrons in one pulse of ≅ 10-ns duration when working with deuterium, what permit to expect 1011 14-MeV neutrons at their operation with DT-mixture. This feature gives a principal possibility to create a "single-shot detection system" for interrogation of hidden objects. It means that all necessary information will be received during a single bright pulse of neutrons having duration in a nanosecond range by means of the time-of-flight technique with a short flight base. It might be a base for the creation of the Nanosecond Impulse Neutron Inspection System (NINIS). These characteristics of the neutron source open a number of opportunities while interrogation time in this case would now depend only on the data-processing system.

  9. 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.

  10. Effects of AMM on the EoS of Magnetized Dense Systems

    CERN Document Server

    Paret, D Manreza; Ferrer, E J; de la Incera, V

    2014-01-01

    We investigate the effects of the anomalous magnetic moment (AMM) in the EoS of a fermion system in the presence of a magnetic field. In the region of strong magnetic fields ($B>m^2$) the AMM is found from the one-loop fermion self-energy. In contrast to the weak-field AMM found by Schwinger, in the strong magnetic field case, the AMM depends on the Landau level (LL) and decreases with it. The effects of the AMM in the EoS at intermediate-to-large fields can be found introducing the one-loop, LL-dependent AMM in the effective Lagrangian that is then used to find the thermodynamic potential of the system. We compare the plots of the parallel and perpendicular pressures versus the magnetic field in the strong field region considering the LL-dependent AMM, the Schwinger AMM, and no AMM at all. The results clearly show a separation between the physical magnitudes found using the Schwinger AMM and the LL-dependent AMM. This is an indication of the inconsistency of considering the Schwinger AMM beyond the weak fiel...

  11. Gravitational conundrum? Dynamical mass segregation versus disruption of binary stars in dense stellar systems

    CERN Document Server

    de Grijs, Richard; Zheng, Yong; Deng, Licai; Hu, Yi; Kouwenhoven, M B N; Wicker, James E

    2013-01-01

    Upon their formation, dynamically cool (collapsing) star clusters will, within only a few million years, achieve stellar mass segregation for stars down to a few solar masses, simply because of gravitational two-body encounters. Since binary systems are, on average, more massive than single stars, one would expect them to also rapidly mass segregate dynamically. Contrary to these expectations and based on high-resolution Hubble Space Telescope observations, we show that the compact, 15-30 Myr-old Large Magellanic Cloud cluster NGC 1818 exhibits tantalizing hints at the >= 2 sigma level of significance (> 3 sigma if we assume a power-law secondary-to-primary mass-ratio distribution) of an increasing fraction of F-star binary systems (with combined masses of 1.3-1.6 Msun) with increasing distance from the cluster center, specifically between the inner 10 to 20" (approximately equivalent to the cluster's core and half-mass radii) and the outer 60 to 80". If confirmed, this will offer support of the theoretically...

  12. Barcode System for Genetic Identification of Soybean [Glycine max (L.) Merrill] Cultivars Using InDel Markers Specific to Dense Variation Blocks.

    Science.gov (United States)

    Sohn, Hwang-Bae; Kim, Su-Jeong; Hwang, Tae-Young; Park, Hyang-Mi; Lee, Yu-Young; Markkandan, Kesavan; Lee, Dongwoo; Lee, Sunghoon; Hong, Su-Young; Song, Yun-Ho; Koo, Bon-Cheol; Kim, Yul-Ho

    2017-01-01

    For genetic identification of soybean [Glycine max (L.) Merrill] cultivars, insertions/deletions (InDel) markers have been preferred currently because they are easy to use, co-dominant and relatively abundant. Despite their biological importance, the investigation of InDels with proven quality and reproducibility has been limited. In this study, we described soybean barcode system approach based on InDel makers, each of which is specific to a dense variation block (dVB) with non-random recombination due to many variations. Firstly, 2,274 VBs were mined by analyzing whole genome data in six soybean cultivars (Backun, Sinpaldal 2, Shingi, Daepoong, Hwangkeum, and Williams 82) for transferability to dVB-specific InDel markers. Secondly, 73,327 putative InDels in the dVB regions were identified for the development of soybean barcode system. Among them, 202 dVB-specific InDels from all soybean cultivars were selected by gel electrophoresis, which were converted as 2D barcode types according to comparing amplicon polymorphisms in the five cultivars to the reference cultivar. Finally, the polymorphism of the markers were assessed in 147 soybean cultivars, and the soybean barcode system that allows a clear distinction among soybean cultivars is also detailed. In addition, the changing of the dVBs in a chromosomal level can be quickly identified due to investigation of the reshuffling pattern of the soybean cultivars with 27 maker sets. Especially, a backcross-inbred offspring, "Singang" and a recurrent parent, "Sowon" were identified by using the 27 InDel markers. These results indicate that the soybean barcode system enables not only the minimal use of molecular markers but also comparing the data from different sources due to no need of exploiting allele binning in new varieties.

  13. 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 degrees

    CERN Document Server

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

    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 square degrees. We present spectroscopic observations using the Heinrich Hertz Submillimeter Telescope of the dense gas tracers, HCO+ and N2H+ 3-2, for all 6194 sources in the Bolocam Galactic Plane Survey v1.0.1 catalog between 7.5 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 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 NH3 observations. These intensity correlations are driven by the sensitivity of the 3-2 transitions to excitation conditions rathe...

  14. 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.

  15. Theory for the dynamics of dense systems of athermal self-propelled particles

    Science.gov (United States)

    Szamel, Grzegorz

    2016-01-01

    We present a derivation of a recently proposed theory for the time dependence of density fluctuations in stationary states of strongly interacting, athermal, self-propelled particles. The derivation consists of two steps. First, we start from the equation of motion for the joint distribution of particles' positions and self-propulsions and we integrate out the self-propulsions. In this way we derive an approximate, many-particle evolution equation for the probability distribution of the particles' positions. Second, we use this evolution equation to describe the time dependence of steady-state density correlations. We derive a memory function representation of the density correlation function and then we use a factorization approximation to obtain an approximate expression for the memory function. In the final equation of motion for the density correlation function the nonequilibrium character of the active system manifests itself through the presence of a new steady-state correlation function that quantifies spatial correlations of the velocities of the particles. This correlation function enters into the frequency term, and thus it describes the dependence of the short-time dynamics on the properties of the self-propulsions. More importantly, the correlation function of particles' velocities enters into the vertex of the memory function and through the vertex it modifies the long-time glassy dynamics.

  16. An LMT/AzTEC 1.1 mm Survey of Dense Cores in the Monoceros R2 Giant Molecular Cloud

    Science.gov (United States)

    Sokol, Alyssa D.; Gutermuth, Robert A.; Wilson, Grant; Offner, Stella; Heyer, Mark H.; Pokhrel, Riwaj; Gomez-Ruiz, Arturo; Luna, Abraham

    2017-01-01

    We present a census of dense gas cores in the MonR2 Giant Molecular Cloud with observations from the AzTEC instrument on the Large Millimeter Telescope (LMT) at λ = 1.1 mm. We detect 270 cores total, 84 with protostars, and 186 starless. AzTEC’s excellent 8‧‧resolution allows for the identification of discrete 1.1 mm sources about 0.05 × 0.05 pc in size in this distant (830 pc) cloud. After performing total flux and half-power area corrections for under-detected low S/N cores, we find that the cores have a median mass ˜ 2.8 M⊙ and a median deconvolved FWHM size ˜ 0.09 pc. 58% of the cores (154) lie above the Bonnor-Ebert mass versus size stability line for cores with T˜12K, suggesting they are unstable to further collapse. Bonnor-Ebert, Plummer-like, and Gaussian models are fit to 1-D and 2-D core radial column density profiles, with Plummer-like performing the best fit of the three models. We present a correlation between local core mass density and column density of gas (as traced by Herschel) characterized by a steep power-law that flattens above Σgas ~ 62 M⊙pc-2 (4.15 AV )smoothing over parsec scales. This core-gas correlation’s resemblance to the star-gas correlation for YSOs in Gutermuth et al. (2011) yields an approximate Mstar ˜ 0.4Mcore and indicates that stellar clustering is likely set by core clustering. Finally we derive an estimated global core formation efficiency that increases with increasing Herschel column density and asymptotically approaches CFE ˜ 0.4 for AV > 15.

  17. 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.

  18. 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)

  19. 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...

  20. Photocatalytic and biocidal activities of novel coating systems of mesoporous and dense TiO₂-anatase containing silver nanoparticles.

    Science.gov (United States)

    Roldán, María V; de Oña, Paula; Castro, Yolanda; Durán, Alicia; Faccendini, Pablo; Lagier, Claudia; Grau, Roberto; Pellegri, Nora S

    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 SiO2 followed by a layer of mesoporous or dense TiO2-anatase, and doping with silver nanoparticles (Ag NPs). The coatings were synthesized via a sol-gel technique by combining colloidal Ag NPs with TiO2 and SiO2 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-SiO2/TiO2 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 TiO2 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 TiO2, 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(+) ion release. Overall, the results included in this article show that the architecture of the

  1. Thermophysical properties of warm dense hydrogen

    CERN Document Server

    Holst, Bastian; Desjarlais, Michael P

    2007-01-01

    We study the thermophysical properties of warm dense hydrogen using quantum molecular dynamics simulations. New results are presented for the pair distribution functions, the equation of state, the Hugoniot curve, and the reflectivity. We compare with available experimental data and predictions of the chemical picture. Especially, we discuss the nonmetal-to-metal transition which occurs at about 40 GPa in the dense fluid.

  2. Relaxation time in disordered molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Rocha, Rodrigo P. [Departamento de Física, Universidade Federal de Santa Catarina, 88040-900 Florianópolis-SC (Brazil); Freire, José A., E-mail: jfreire@fisica.ufpr.br [Departamento de Física, Universidade Federal do Paraná, 81531-990 Curitiba-PR (Brazil)

    2015-05-28

    Relaxation time is the typical time it takes for a closed physical system to attain thermal equilibrium. The equilibrium is brought about by the action of a thermal reservoir inducing changes in the system micro-states. The relaxation time is intuitively expected to increase with system disorder. We derive a simple analytical expression for this dependence in the context of electronic equilibration in an amorphous molecular system model. We find that the disorder dramatically enhances the relaxation time but does not affect its independence of the nature of the initial state.

  3. 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.

  4. DNA-enabled integrated molecular systems for computation and sensing.

    Science.gov (United States)

    LaBoda, Craig; Duschl, Heather; Dwyer, Chris L

    2014-06-17

    CONSPECTUS: Nucleic acids have become powerful building blocks for creating supramolecular nanostructures with a variety of new and interesting behaviors. The predictable and guided folding of DNA, inspired by nature, allows designs to manipulate molecular-scale processes unlike any other material system. Thus, DNA can be co-opted for engineered and purposeful ends. This Account details a small portion of what can be engineered using DNA within the context of computer architectures and systems. Over a decade of work at the intersection of DNA nanotechnology and computer system design has shown several key elements and properties of how to harness the massive parallelism created by DNA self-assembly. This work is presented, naturally, from the bottom-up beginning with early work on strand sequence design for deterministic, finite DNA nanostructure synthesis. The key features of DNA nanostructures are explored, including how the use of small DNA motifs assembled in a hierarchical manner enables full-addressability of the final nanostructure, an important property for building dense and complicated systems. A full computer system also requires devices that are compatible with DNA self-assembly and cooperate at a higher level as circuits patterned over many, many replicated units. Described here is some work in this area investigating nanowire and nanoparticle devices, as well as chromophore-based circuits called resonance energy transfer (RET) logic. The former is an example of a new way to bring traditional silicon transistor technology to the nanoscale, which is increasingly problematic with current fabrication methods. RET logic, on the other hand, introduces a framework for optical computing at the molecular level. This Account also highlights several architectural system studies that demonstrate that even with low-level devices that are inferior to their silicon counterparts and a substrate that harbors abundant defects, self-assembled systems can still

  5. Dense topological spaces and dense continuity

    Science.gov (United States)

    Aldwoah, Khaled A.

    2013-09-01

    There are several attempts to generalize (or "widen") the concept of topological space. This paper uses equivalence relations to generalize the concept of topological space via the concept of equivalence relations. By the generalization, we can introduce from particular topology on a nonempty set X many new topologies, we call anyone of these new topologies a dense topology. In addition, we formulate some simple properties of dense topologies and study suitable generalizations of the concepts of limit points, closeness and continuity, as well as Jackson, Nörlund and Hahn dense topologies.

  6. Intelligent systems for the molecular biologist

    Energy Technology Data Exchange (ETDEWEB)

    Brutlag, D.L.

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. In this paper, one objective is to identify properties of DNA sequences that determine their function, by computer-aided statistical analysis and to accurately predict its function, given a new sequence. A related problem is to predict protein structure and function from the sequence.

  7. Optical antenna for photofunctional molecular systems.

    Science.gov (United States)

    Ikeda, Katsuyoshi; Uosaki, Kohei

    2012-02-06

    Optical antennas can enhance the efficiency of photon-molecule interactions. To design efficient antenna structures, it is essential to consider physicochemical aspects in addition to electromagnetic considerations. Specifically, chemical interactions between optical antennas and molecules have to be controlled to enhance the overall efficiency. For this purpose, sphere-plane nanostructures are suitable optical antennas for molecular-modified functional electrode systems when a well-defined electrode is utilized as a platform.

  8. Contemporary kinematics of the Ordos block, North China and its adjacent rift systems constrained by dense GPS observations

    Science.gov (United States)

    Zhao, Bin; Zhang, Caihong; Wang, Dongzhen; Huang, Yong; Tan, Kai; Du, Ruilin; Liu, Jingnan

    2017-03-01

    The detailed kinematic pattern of the Ordos block, North China and its surrounding rift systems remains uncertain, mainly due to the low signal-to-noise ratio of the Global Positioning System (GPS) velocity data and the lack of GPS stations in this region. In this study, we have obtained a new and dense velocity field by processing GPS data primarily collected from the Crustal Motion Observation Network of China and from other GPS networks between 1998 and 2014. The GPS velocities within the Ordos block can be interpreted as counterclockwise rotation of the block about the Euler pole with respect to the Eurasia plate. Velocity profiles across the graben-bounding faults show relatively rapid right-lateral strike-slip motion along the Yinchuan graben, with a rate of 0.8-2.6 mm/a from north to south. In addition, a right-lateral slip rate of 1.1-1.6 mm/a is estimated along the central segment of the Shanxi rift. However, strike-slip motion is not detected along the northern and southern margins of the Ordos block. Conversely, significant extension motion is detected across the northwestern corner of the block, with a value of 1.6 mm/a, and along the northern segment of the Shanxi rift, where an extensional rate of 1.3-1.7 mm/a is measured. Both the Daihai and Datong basins are experiencing crustal extension. On the southwestern margin of the block, deformation across the compressional zone of the Liupanshan range is subtle; however, the far-field shorting rate is as high as 3.0 mm/a, implying that this region is experiencing ongoing compression. The results reveal that present-day fault slip occurs mainly along the block bounding faults, with the exception of faults along the northern and southern margins of the block. These results provide new insights into the nature of tectonic deformation around the Ordos block, and are useful for assessing the seismic activity in this region.

  9. Conductive dense hydrogen

    Science.gov (United States)

    Eremets, M.; Troyan, I.

    2012-12-01

    Hydrogen at ambient pressures and low temperatures forms a molecular crystal which is expected to display metallic properties under megabar pressures. This metal is predicted to be superconducting with a very high critical temperature Tc of 200-400 K. The superconductor may potentially be recovered metastably at ambient pressures, and it may acquire a new quantum state as a metallic superfluid and a superconducting superfluid. Recent experiments performed at low temperatures T 220 GPa, new Raman modes arose, providing evidence for the transformation to a new opaque and electrically conductive phase IV. Above 260 GPa, in the next phase V, hydrogen reflected light well. Its resistance was nearly temperature-independent over a wide temperature range, down to 30 K, indicating that the hydrogen was metallic. Releasing the pressure induced the metallic phase to transform directly into molecular hydrogen with significant hysteresis at 200 GPa and 295 K. These data were published in our paper: M. I. Eremets and I. A. Troyan "Conductive dense hydrogen." Nature Materials 10: 927-931. We will present also new results on hydrogen: phase diagram with phases IV and V determined in P,T domain up to 300 GPa and 350 K. We will also discuss possible structures of phase IV based on our Raman and infrared measurements up to 300 GPa.

  10. Accounting for intra-molecular vibrational modes in open quantum system description of molecular systems.

    Science.gov (United States)

    Roden, Jan; Strunz, Walter T; Whaley, K Birgitta; Eisfeld, Alexander

    2012-11-28

    Electronic-vibrational dynamics in molecular systems that interact with an environment involve a large number of degrees of freedom and are therefore often described by means of open quantum system approaches. A popular approach is to include only the electronic degrees of freedom into the system part and to couple these to a non-Markovian bath of harmonic vibrational modes that is characterized by a spectral density. Since this bath represents both intra-molecular and external vibrations, it is important to understand how to construct a spectral density that accounts for intra-molecular vibrational modes that couple further to other modes. Here, we address this problem by explicitly incorporating an intra-molecular vibrational mode together with the electronic degrees of freedom into the system part and using the Fano theory for a resonance coupled to a continuum to derive an "effective" bath spectral density, which describes the contribution of intra-molecular modes. We compare this effective model for the intra-molecular mode with the method of pseudomodes, a widely used approach in simulation of non-Markovian dynamics. We clarify the difference between these two approaches and demonstrate that the respective resulting dynamics and optical spectra can be very different.

  11. Low-molecular-weight metabolite systems chemistry

    Directory of Open Access Journals (Sweden)

    Franz eHadacek

    2015-03-01

    Full Text Available Low-molecular-weight metabolites (LMWMs comprise primary or central and a plethora of intermediary or secondary metabolites, all of which are characterized by a molecular weight below 900 Dalton. The latter are especially prominent in sessile higher organisms, such as plants, corals, sponges and fungi, but are produced by all types of microbial organisms too. Common to all of these carbon molecules are oxygen, nitrogen and, to a lesser extent, sulfur, as heteroatoms. The latter can contribute as electron donators or acceptors to cellular redox chemistry and define the potential of the molecule to enter charge-transfer complexes. Furthermore, they allow LMWMs to serve as organic ligands in coordination complexes of various inorganic metals as central atoms. Especially the transition metals Fe, Cu and Mn can catalyze one electron reduction of molecular oxygen, which results in formation of free radical species and reactive follow-up reaction products. As antioxidants LMWMs can scavenge free radicals. Depending on the chemical environment, the same LMWMs can act as pro-oxidants by reducing molecular oxygen. The cellular regulation of redox homeostasis, a balance between oxidation and reduction, is still far from being understood. Charge-transfer and coordination complex formation with metals shapes LMWMs into gel-like matrices in the cytosol. The quasi-polymer structure is lost usually during the isolation procedure. In the gel state, LMWMs possess semiconductor properties. Also proteins and membranes are semiconductors. Together they can represent biotransistor components that can be part of a chemoelectrical signaling system that coordinates systems chemistry by initiating cell differentiation or tissue homeostasis, the activated and the resting cell state, when it is required. This concept is not new and dates back to Albert Szent-Györgyi.

  12. Warm dense crystallography

    Science.gov (United States)

    Valenza, Ryan A.; Seidler, Gerald T.

    2016-03-01

    The intense femtosecond-scale pulses from x-ray free electron lasers (XFELs) are able to create and interrogate interesting states of matter characterized by long-lived nonequilibrium semicore or core electron occupancies or by the heating of dense phases via the relaxation cascade initiated by the photoelectric effect. We address here the latter case of "warm dense matter" (WDM) and investigate the observable consequences of x-ray heating of the electronic degrees of freedom in crystalline systems. We report temperature-dependent density functional theory calculations for the x-ray diffraction from crystalline LiF, graphite, diamond, and Be. We find testable, strong signatures of condensed-phase effects that emphasize the importance of wide-angle scattering to study nonequilibrium states. These results also suggest that the reorganization of the valence electron density at eV-scale temperatures presents a confounding factor to achieving atomic resolution in macromolecular serial femtosecond crystallography (SFX) studies at XFELs, as performed under the "diffract before destroy" paradigm.

  13. Dense Axion Stars

    Science.gov (United States)

    Braaten, Eric; Mohapatra, Abhishek; Zhang, Hong

    2016-09-01

    If the dark matter particles are axions, gravity can cause them to coalesce into axion stars, which are stable gravitationally bound systems of axions. In the previously known solutions for axion stars, gravity and the attractive force between pairs of axions are balanced by the kinetic pressure. The mass of these dilute axion stars cannot exceed a critical mass, which is about 10-14M⊙ if the axion mass is 10-4 eV . We study axion stars using a simple approximation to the effective potential of the nonrelativistic effective field theory for axions. We find a new branch of dense axion stars in which gravity is balanced by the mean-field pressure of the axion Bose-Einstein condensate. The mass on this branch ranges from about 10-20M⊙ to about M⊙ . If a dilute axion star with the critical mass accretes additional axions and collapses, it could produce a bosenova, leaving a dense axion star as the remnant.

  14. 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.

  15. Molecular and Crystal Magnetic Engineering of Polymetallic Coupling System: From Magnetic Molecules to Molecular Magnets

    Institute of Scientific and Technical Information of China (English)

    程鹏; 廖代正

    2001-01-01

    One of the main challenges in the field of molecular materials is the design of molecular ferromagnets. General design strategy includes two steps, that is molecular magnetic engineering and crystal magnetic engineering. The first step is the synthesis of ferromagnetically coupled polymetallic systems.Tne second step is the assembly of polymetallic systems with muti-dimensional structure and exhibiting a ferromagnetic transition.This paper summarized the strategies of molecular design and crystal engineering allowed to obtain such systems and our efforts in the fields of molecular magnetism and molecular-based magnets.

  16. Advances in molecular genetic systems in malaria.

    Science.gov (United States)

    de Koning-Ward, Tania F; Gilson, Paul R; Crabb, Brendan S

    2015-06-01

    Robust tools for analysing gene function in Plasmodium parasites, which are the causative agents of malaria, are being developed at an accelerating rate. Two decades after genetic technologies for use in Plasmodium spp. were first described, a range of genetic tools are now available. These include conditional systems that can regulate gene expression at the genome, transcriptional or protein level, as well as more sophisticated tools for gene editing that use piggyBac transposases, integrases, zinc-finger nucleases or the CRISPR-Cas9 system. In this Review, we discuss the molecular genetic systems that are currently available for use in Plasmodium falciparum and Plasmodium berghei, and evaluate the advantages and limitations of these tools. We examine the insights that have been gained into the function of genes that are important during the blood stages of the parasites, which may help to guide the development and improvement of drug therapies and vaccines.

  17. 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 ...... specific nucleic acid probes are discussed and exemplified by studies of anaerobic granular sludge, biofilm and digester systems......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...... and malfunctions of anaerobic digesters occasionally experienced, leading to sub-optimal methane production and wastewater treatment. Using a variety of molecular techniques, we are able to determine which microorganisms are active, where they are active, and when they are active, but we still need to determine...

  18. Molecular Imaging System for Monitoring Tumor Angiogenesis

    Science.gov (United States)

    Aytac, Esra; Burcin Unlu, Mehmet

    2012-02-01

    In cancer, non-invasive imaging techniques that monitor molecular processes associated with the tumor angiogenesis could have a central role in the evaluation of novel antiangiogenic and proangiogenic therapies as well as early detection of the disease. Matrix metalloproteinases (MMP) can serve as specific biological targets for imaging of angiogenesis since expression of MMPs is required for angiogenesis and has been found to be upregulated in every type of human cancer and correlates with stage, invasive, metastatic properties and poor prognosis. However, for most cancers it is still unknown when, where and how MMPs are involved in the tumor angiogenesis [1]. Development of high-resolution, high sensitivity imaging techniques in parallel with the tumor models could prove invaluable for assessing the physical location and the time frame of MMP enzymatic acitivity. The goal of this study is to understand where, when and how MMPs are involved in the tumor angiogenesis. We will accomplish this goal by following two objectives: to develop a high sensitivity, high resolution molecular imaging system, to develop a virtual tumor simulator that can predict the physical location and the time frame of the MMP activity. In order to achieve our objectives, we will first develop a PAM system and develop a mathematical tumor model in which the quantitative data obtained from the PAM can be integrated. So, this work will develop a virtual tumor simulator and a molecular imaging system for monitoring tumor angiogenesis. 1.Kessenbrock, K., V. Plaks, and Z. Werb, MMP:regulators of the tumor microenvironment. Cell, 2010. 141(1)

  19. Microelectromechanical systems integrating molecular spin crossover actuators

    Science.gov (United States)

    Manrique-Juarez, Maria D.; Rat, Sylvain; Mathieu, Fabrice; Saya, Daisuke; Séguy, Isabelle; Leïchlé, Thierry; Nicu, Liviu; Salmon, Lionel; Molnár, Gábor; Bousseksou, Azzedine

    2016-08-01

    Silicon MEMS cantilevers coated with a 200 nm thin layer of the molecular spin crossover complex [Fe(H2B(pz)2)2(phen)] (H2B(pz)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 (Δfr = -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.

  20. Systems Pharmacology in Small Molecular Drug Discovery.

    Science.gov (United States)

    Zhou, Wei; Wang, Yonghua; Lu, Aiping; Zhang, Ge

    2016-02-18

    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.

  1. Systems Pharmacology in Small Molecular Drug Discovery

    Science.gov (United States)

    Zhou, Wei; Wang, Yonghua; Lu, Aiping; Zhang, Ge

    2016-01-01

    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. PMID:26901192

  2. 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.

  3. Molecular hydrogen absorption systems in SDSS

    CERN Document Server

    Balashev, S A; Ivanchik, A V; Varshalovich, D A; Petitjean, P; Noterdaeme, P

    2014-01-01

    We present a systematic search for molecular hydrogen absorption systems at high redshift in quasar spectra from the Sloan Digital Sky Survey (SDSS) II Data Release 7 and SDSS-III Data Release 9. We have selected candidates using a modified profile fitting technique taking into account that the Ly$\\alpha$ forest can effectively mimic H$_2$ absorption systems at the resolution of SDSS data. To estimate the confidence level of the detections, we use two methods: a Monte-Carlo sampling and an analysis of control samples. The analysis of control samples allows us to define regions of the spectral quality parameter space where H$_2$ absorption systems can be confidently identified. We find that H$_2$ absorption systems with column densities $\\log {\\rm N_{H_2}} > 19$ can be detected in only less than 3% of SDSS quasar spectra. We estimate the upper limit on the detection rate of saturated H$_2$ absorption systems ($\\log {\\rm N_{H_2}} > 19$) in Damped Ly-$\\alpha$ (DLA) systems to be about 7%. We provide a sample of ...

  4. 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.

  5. [Novel bioconversion systems using a yeast molecular display system].

    Science.gov (United States)

    Shibasaki, Seiji

    2010-11-01

    The budding yeast Saccharomyces cerevisiae has been used for the process of fermentation as well as for studies in biochemistry and molecular biology as a eukaryotic model cell or tool for the analysis of gene functions. Thus, yeast is essential in industries and researches. Yeast cells have a cell wall, which is one characteristic that helps distinguish yeast cells from other eukaryotic cells such as mammalian cells. We have developed a molecular display system using the protein of the yeast cell wall as an anchor for foreign proteins. Yeast cells have been designed for use in sensing and metal adsorption, and have been used in vaccines and for screening novel proteins. Currently, yeast is used not only as a tool for analyzing gene or protein function but also in molecular display technology. The phage display system, which is at the forefront of molecular display technologies, is a powerful tool for screening ligands bound to a target molecule and for analyzing protein-protein interactions; however, in some cases, eukaryotic proteins are not easily expressed by this system. On the other hand, yeast cells have the ability to express eukaryotic proteins and proliferate; thus, these cells display various proteins. Yeast cells are more appropriate for white biotechnology. In this review, displays of enzymes that are important in bioconversion, such as lipases and β-glucosidases, are going to be introduced.

  6. Dense with Sense

    Science.gov (United States)

    Aletras, Anthony H.; Ingkanisorn, W. Patricia; Mancini, Christine; Arai, Andrew E.

    2005-09-01

    Displacement encoding with stimulated echoes (DENSE) with a low encoding strength phase-cycled meta-DENSE readout and a two fold SENSE acceleration ( R = 2) is described. This combination reduces total breath-hold times for increased patient comfort during cardiac regional myocardial contractility studies. Images from phantoms, normal volunteers, and a patient are provided to demonstrate the SENSE-DENSE combination of methods. The overall breath-hold time is halved while preserving strain map quality.

  7. 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.

  8. 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.

  9. Quantum dense key distribution

    CERN Document Server

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

    2004-01-01

    This paper proposes a new 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 BB84 one. We hereinafter prove the security of this scheme against individual eavesdropping attacks, and we present preliminary experimental results, showing its feasibility.

  10. 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.

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

    Institute of Scientific and Technical Information of China (English)

    LI Jia-Hua; LIU Ji-Bing; LUO Jin-Ming; XIE Xiao-Tao

    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 dipoledipole (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.

  12. Control of density fluctuations in atomistic-continuum simulations of dense liquids

    DEFF Research Database (Denmark)

    Kotsalis, E.M.; Walther, Jens Honore; Koumoutsakos, P.

    2007-01-01

    We present a control algorithm to eliminate spurious density fluctuations associated with the coupling of atomistic and continuum descriptions for dense liquids. A Schwartz domain decomposition algorithm is employed to couple molecular dynamics for the simulation of the atomistic system with a co...

  13. 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...

  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. Method for dense packing discovery.

    Science.gov (United States)

    Kallus, Yoav; Elser, Veit; Gravel, Simon

    2010-11-01

    The problem of packing a system of particles as densely as possible is foundational in the field of discrete geometry and is a powerful model in the material and biological sciences. As packing problems retreat from the reach of solution by analytic constructions, the importance of an efficient numerical method for conducting de novo (from-scratch) searches for dense packings becomes crucial. In this paper, we use the divide and concur framework to develop a general search method for the solution of periodic constraint problems, and we apply it to the discovery of dense periodic packings. An important feature of the method is the integration of the unit-cell parameters with the other packing variables in the definition of the configuration space. The method we present led to previously reported improvements in the densest-known tetrahedron packing. Here, we use the method to reproduce the densest-known lattice sphere packings and the best-known lattice kissing arrangements in up to 14 and 11 dimensions, respectively, providing numerical evidence for their optimality. For nonspherical particles, we report a dense packing of regular four-dimensional simplices with density ϕ=128/219≈0.5845 and with a similar structure to the densest-known tetrahedron packing.

  16. Warm Dense Matter: An Overview

    Energy Technology Data Exchange (ETDEWEB)

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

    2004-04-21

    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

  17. The structure of molecular cloud W51 and dense cores--CO(J=1-0) and HCO+(J=1-0) spectral line mapping

    Institute of Scientific and Technical Information of China (English)

    MA; Hongjun; PEI; Chunchuan; ZENG; Qin

    2005-01-01

    We present a large scale map of about 15′×15′of CO(J=1-0) toward W51 giant molecular cloud (GMC), which covers the most active star-forming region of W51 GMC, and an interferometry HCO+(J=1-0) map of a high spatial resolution (I.e. 8″.7×6″.1) with a field of view (2′×2′) centered at W51IRS1. A structure model of W51GMC is obtained according to the results of the observations and analyses. The observations demonstrate that some small molecular cores generated by the collision between the W51GMC and the 60-73 km·s-1 foreground cloud are collapsing toward their own centers. In addition, 16 new molecular cores are discovered from the HCO+(J=1-0) map.

  18. Experimental performance of semiconductor optical amplifiers and praseodymium-doped fiber amplifiers in 1310-nm dense wavelength division multiplexing system

    Science.gov (United States)

    Chorchos, Lukasz; Turkiewicz, Jaroslaw P.

    2017-04-01

    One of the key optical transmission components is optical amplifiers. Studies on the amplification properties of the 1310-nm optical amplifiers are presented. The evaluated optical amplifiers are semiconductor optical amplifier (SOA) and praseodymium-doped fiber amplifier (PDFA). The study is aimed at the dynamic operation in single- and multiwavelength domains with high rate signals. The maximum obtained gain was 25.0 dB for SOA and 20.9 dB for PDFA. For the SOAs, the minimum achieved value of the receiver sensitivity was -11.5 dBm for a single channel and -11.5 dBm for a dense wavelength division multiplexing case while for PDFA those values were -11.0 dBm and -10.9, respectively. The main advantage of the PDFA in comparison to the measured SOAs is its higher saturation power. The SOAs proved to be viable candidates for high-speed amplification in the 1310-nm wavelength domain.

  19. Characterizing the Transition from Diffuse Atomic to Dense Molecular Clouds in the Magellanic Clouds with [C ii], [C i], and CO

    Science.gov (United States)

    Pineda, Jorge L.; Langer, William D.; Goldsmith, Paul F.; Horiuchi, Shinji; Kuiper, Thomas B. H.; Muller, Erik; Hughes, Annie; Ott, Jürgen; Requena-Torres, Miguel A.; Velusamy, Thangasamy; Wong, Tony

    2017-04-01

    We present and analyze deep Herschel/HIFI observations of the [C ii] 158 μm, [C i] 609 μm, and [C i] 370 μm lines toward 54 lines of sight in the Large Magellanic Cloud (LMC) and Small Magellanic Cloud (SMC). These observations are used to determine the physical conditions of the line-emitting gas, which we use to study the transition from atomic to molecular gas and from C+ to C0 to CO in their low-metallicity environments. We trace gas with molecular fractions in the range 0.1UV absorption (f({{{H}}}2) 0.45 in both the LMC and the SMC. Ionized carbon is the dominant gas-phase form of this element that is associated with molecular gas, with C0 and CO representing a small fraction, implying that most (89% in the LMC and 77% in the SMC) of the molecular gas in our sample is CO-dark H2. The mean {X}{CO} conversion factors in our LMC and SMC sample are larger than the value typically found in the Milky Way. When applying a correction based on the filling factor of the CO emission, we find that the values of {X}{CO} in the LMC and SMC are closer to that in the Milky Way. The observed [C ii] intensity in our sample represents about 1% of the total far-infrared intensity from the lines of sight observed in both Magellanic clouds.

  20. Dense Hypervelocity Plasma Jets

    Science.gov (United States)

    Case, Andrew; Witherspoon, F. Douglas; Messer, Sarah; Bomgardner, Richard; Phillips, Michael; van Doren, David; Elton, Raymond; Uzun-Kaymak, Ilker

    2007-11-01

    We are developing high velocity dense plasma jets for fusion and HEDP applications. Traditional coaxial plasma accelerators suffer from the blow-by instability which limits the mass accelerated to high velocity. In the current design blow-by is delayed by a combination of electrode shaping and use of a tailored plasma armature created by injection of a high density plasma at a few eV generated by arrays of capillary discharges or sparkgaps. Experimental data will be presented for a complete 32 injector gun system built for driving rotation in the Maryland MCX experiment, including data on penetration of the plasma jet through a magnetic field. We present spectroscopic measurements of plasma velocity, temperature, and density, as well as total momentum measured using a ballistic pendulum. Measurements are in agreement with each other and with time of flight data from photodiodes and a multichannel PMT. Plasma density is above 10^15 cm-3, velocities range up to about 100 km/s. Preliminary results from a quadrature heterodyne HeNe interferometer are consistent with these results.

  1. Nuclear reactions in deuterium-saturated palladium under irradiation by 10 MeV γ-quanta, in dense molecular deuterium at 1.2 kbar pressure

    Science.gov (United States)

    Didyk, A. Yu.; Wisniewski, R. S.

    2013-08-01

    A high-pressure chamber with a Pd-rod inside was filled up with 1.2 kbar molecular deuterium (DHPC). Then the saturated by deuterium palladium rod was irradiated during 18 hours by 11 MeV braking γ-quanta at 11-13 μA electron beam using the MT-25 electron accelerator. The element compositions of all the DHPC surfaces which had been in contact with dense deuterium gas were studied using scanning electronic microscopes with Roentgen microprobe analysis. It was determined that all the surfaces, including surfaces of the high-purity Pd-rod (99.995%), were covered either by a partially homogeneous layer or large microparticles of lead. Also, light elements as C, O, Na, Mg, Al, Si, Ti, Mn, Fe, Cu, Zn and heavy metals as Ag, Ta, W, Pt, Au and Pb were observed on the chambers inner surfaces.

  2. 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...

  3. Dense Clumps in Giant Molecular Clouds in the Large Magellanic Cloud: Density and Temperature Derived from $^{13}$CO($J=3-2$) Observations

    CERN Document Server

    Minamidani, Tetsuhiro; Mizuno, Yoji; Mizuno, Norikazu; Kawamura, Akiko; Onishi, Toshikazu; Hasegawa, Tetsuo; Tatematsu, Ken'ichi; Takekoshi, Tatsuya; Sorai, Kazuo; Moribe, Nayuta; Torii, Kazufumi; Sakai, Takeshi; Muraoka, Kazuyuki; Tanaka, Kunihiko; Ezawa, Hajime; Kohno, Kotaro; Kim, Sungeun; Rubio, Mónica; Fukui, Yasuo

    2010-01-01

    In order to precisely determine temperature and density of molecular gas in the Large Magellanic Cloud, we made observations of optically thin $^{13}$CO($J=3-2$) transition by using the ASTE 10m telescope toward 9 peaks where $^{12}$CO($J=3-2$) clumps were previously detected with the same telescope. The molecular clumps include those in giant molecular cloud (GMC) Types I (with no signs of massive star formation), II (with HII regions only), and III (with HII regions and young star clusters). We detected $^{13}$CO($J=3-2$) emission toward all the peaks and found that their intensities are 3 -- 12 times lower than those of $^{12}$CO($J=3-2$). We determined the intensity ratios of $^{12}$CO($J=3-2$) to $^{13}$CO($J=3-2$), $R^{12/13}_{3-2}$, and $^{13}$CO($J=3-2$) to $^{13}$CO($J=1-0$), $R^{13}_{3-2/1-0}$, at 45$\\arcsec$ resolution. These ratios were used for radiative transfer calculations in order to estimate temperature and density of the clumps. The parameters of these clumps range kinetic temperature $T\\ma...

  4. Analysis of Signal-to-Crosstalk Ratio Variations due to Four-Wave Mixing in Dense Wavelength Division Multiplexing Systems Implemented with Standard Single-Mode Fibers

    Directory of Open Access Journals (Sweden)

    Sait Eser KARLIK

    2016-10-01

    Full Text Available In this paper, variation of the signal-to-crosstalk ratio (SXR due to effects of four-wave mixing (FWM has been analyzed on center channels of 5-, 7-, 9-channel dense wavelength division multiplexing (DWDM systems implemented with G.652 standard single-mode fibers (SSMFs for 12.5 GHz, 25 GHz, 50 GHz and 100 GHz equal channel spacing values. Center channels on such systems are the most severely impacted channels by FWM. Therefore, results obtained are the worst-case values for the DWDM system performance and important for system design. Simulations have been performed for systems using three different commercially available SMFs having different design parameter values for chromatic dispersion, dispersion slope, nonlinearity coefficient and attenuation coefficient which are all in the scope of the G.652 Recommendation of Telecommunication Standardization Sector of International Telecommunication Union (ITU-T for SSMFs. In those simulations, under the impact of FWM, variation of SXR with variations in input powers, channel spacings and link lengths have been observed. Simulation results display the combined effect of the optical fiber and system design parameters on FWM performance of DWDM systems and give important clues for not only long-haul but also access network implementations of DWDM systems.

  5. Dynamical Systems and Control Theory Inspired by Molecular Biology

    Science.gov (United States)

    2014-10-02

    in both bacterial and eukaryotic signaling pathways. A common theme in the systems biology literature is that certain systems whose output variables...AFRL-OSR-VA-TR-2014-0282 DYNAMICAL SYSTEMS AND CONTROL THEORY INSPIRED BY MOLECULAR BIOLOGY Eduardo Sontag RUTGERS THE STATE UNIVERSITY OF NEW JERSEY...Standard Form 298 (Re . 8-98) v Prescribed by ANSI Std. Z39.18 DYNAMICAL SYSTEMS AND CONTROL THEORY INSPIRED BY MOLECULAR BIOLOGY AFOSR FA9550-11-1-0247

  6. Time dependent chemistry in dense molecular clouds. III - Infrared band cross sections of molecules in the solid state at 10 K

    Science.gov (United States)

    Dhendecourt, L. B.; Allamandola, L. J.

    1986-01-01

    Thin film transmission infrared spectra and a list of integrated absorbance values (band strengths) of bands in the 2.5 to 20 micron range of various molecular solids deposited on a CsI window cooled to 10 K are presented. These solids include molecules known or suspected to be present on interstellar grains such as H2O, CO, NH3 and CH4 and mixtures of these molecules as well as various hydrocarbons. The method is described by which the absorbance values derived can be used to estimate column densities of species adsorbed on interstellar grains and other solids associated with celestial IR sources.

  7. Modelling dense relational data

    DEFF Research Database (Denmark)

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

    2012-01-01

    Relational modelling classically consider sparse and discrete data. Measures of influence computed pairwise between temporal sources naturally give rise to dense continuous-valued matrices, for instance p-values from Granger causality. Due to asymmetry or lack of positive definiteness they are no......Relational modelling classically consider sparse and discrete data. Measures of influence computed pairwise between temporal sources naturally give rise to dense continuous-valued matrices, for instance p-values from Granger causality. Due to asymmetry or lack of positive definiteness...... 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....

  8. 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.

  9. Spatially Resolved Chemistry in Nearby Galaxies III. Dense Molecular Gas in the Inner Disk of the LIRG IRAS 04296+2923

    CERN Document Server

    Meier, David S; Beck, Sara C

    2014-01-01

    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 LIRGs. Data are from the Owens Valley and CARMA millimeter interferometers. Species detected at ~10 M_sun/yr and is traced by lines of HCN, HCO+, HNC, and CN. A correlation between HCN and star formation rate is observed on sub-kpc 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)/^13CO(1-0) and CO(1-0)/C^18O(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). ^13CO/C^18O abundance ratios are lower than in Galactic clouds, possibly because the C^18O is enriched by massive star ejecta from the starburst. ^13CO is underabundant relative to CO. Extende...

  10. The Transition from Atomic to Molecular Hydrogen in Interstellar Clouds: 21cm Signature of the Evolution of Cold Atomic Hydrogen in Dense Clouds

    CERN Document Server

    Goldsmith, P F; Krco, M; Goldsmith, Paul F.; Li, Di; Krco, Marko

    2006-01-01

    We have investigated the time scale for formation of molecular clouds by examining the conversion of HI to H2 using a time-dependent model. H2 formation on dust grains and cosmic ray and photo destruction are included in one-dimensional model slab clouds which incorporate time-independent density and temperature distributions. We calculate 21cm spectral line profiles seen in absorption against a background provided by general Galactic HI emission, and compare the model spectra with HI Narrow Self-Absorption, or HINSA, profiles absorbed in a number of nearby molecular clouds. The time evolution of the HI and H2 densities is dramatic, with the atomic hydrogen disappearing in a wave propagating from the central, denser regions which have a shorter H2 formation time scale, to the edges, where the density is lower and the time scale for H2 formation longer. The model 21cm spectra are characterized by very strong absorption at early times, when the HI column density through the model clouds is extremely large. The ...

  11. Temporal Performance of Advanced Driver Assistance Systems vis-á-vis Human Driving Behavior in Dense Traffic

    NARCIS (Netherlands)

    Hamberg, R.; Hendriks, T.; Bijlsma, T.

    2015-01-01

    Advanced Driver Assistance Systems (ADAS) are becoming ubiquitous, and gradually take over the role of human drivers in the vision of the automotive sector. Humans are different from most systems: while in general humans exhibit a much higher error rate when performing specific functions, they are a

  12. 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.

  13. Influence of four-wave mixing in short- and medium-range 1310  nm dense wavelength division multiplexing systems.

    Science.gov (United States)

    Markowski, Konrad; Chorchos, Łukasz; Turkiewicz, Jarosław Piotr

    2016-04-10

    In this paper, we demonstrate a comprehensive analysis of the impact of four-wave mixing (FWM) on the quality of transmission in short- and medium-range dense wavelength division multiplexing (DWDM) systems in the 1310 nm wavelength domain. The presented analysis proves that, for the system with uniform power per channel assignment, setting proper input channel power can substantially reduce the influence of the FWM effect on bit error rate in low channel spaced short-range systems, despite the position of the DWDM grid around the zero-dispersion wavelength. Simulations and experimental analysis of the possibility of FWM suppression have been provided. The power penalty measurements show that the influence of FWM on system performance may be as low as 0.3 dB with reasonable input power (i.e., -11  dBm per channel), making possible the transmission of data by fiber over distances of 25 km. Finally, we demonstrate that, for channel spacing as low as 120 GHz, error-free transmission in the 1310 nm wavelength domain is possible, despite high efficiency of FWM generation. The results prove that utilization of the 1310 nm wavelength domain in a system with low channel spacing, i.e., with better bandwidth allocation, is an interesting solution for data storage and processing center applications.

  14. High Density Molecular Gas in the IR-bright Galaxy System VV114

    CERN Document Server

    Iono, D; Yun, M S; Matsushita, S; Peck, A B; Sakamoto, K

    2004-01-01

    New high resolution CO(3-2) interferometric map of the IR-bright interacting galaxy system VV114 observed with the Submillimeter Array (SMA) reveal a substantial amount of warm and dense gas in the IR-bright but optically obscured galaxy, VV114E, and the overlap region connecting the two nuclei. A 1.8 x 1.4 kpc concentration of CO(3-2) emitting gas with a total mass of 4 x 10^9 Msun coincides with the peaks of NIR, MIR, and radio continuum emission found previously by others, identifying the dense fuel for the AGN and/or the starburst activity there. Extensive CO(2-1) emission is also detected, revealing detailed distribution and kinematics that are consistent with the earlier CO(1-0) results. The widely distributed molecular gas traced in CO(2-1) and the distributed discrete peaks of CO(3-2) emission suggest that a spatially extended intense starbursts may contribute significantly to its large IR luminosity. These new observations further support the notion that VV114 is approaching its final stage of merger...

  15. Molecular Dynamics Studies of Energy Transfer Processes in Crystal Systems.

    Science.gov (United States)

    1984-11-30

    Computer molecular dynamics studies have been carried out on the problem of attaining a fundamental understanding of shock-induced initiation of...intramolecular energy exchange in shock-loaded systems are presented. Originator-supplied keywords include: Molecular dynamics , Energy transfer, Shock front, Shock wave, Explosives, Shock structure.

  16. Open quantum system parameters from molecular dynamics

    CERN Document Server

    Wang, Xiaoqing; Wüster, Sebastian; Eisfeld, Alexander

    2015-01-01

    We extract the site energies and spectral densities of the Fenna-Matthews-Olson (FMO) pigment protein complex of green sulphur bacteria from simulations of molecular dynamics combined with energy gap calculations. Comparing four different combinations of methods, we investigate the origin of quantitative differences regarding site energies and spectral densities obtained previously in the literature. We find that different forcefields for molecular dynamics and varying local energy minima found by the structure relaxation yield significantly different results. Nevertheless, a picture averaged over these variations is in good agreement with experiments and some other theory results. Throughout, we discuss how vibrations external- or internal to the pigment molecules enter the extracted quantities differently and can be distinguished. Our results offer some guidance to set up more computationally intensive calculations for a precise determination of spectral densities in the future. These are required to determ...

  17. Detectability comparison of simulated objects within a dense breast phantom using high energy x-ray phase sensitive and conventional imaging systems

    Science.gov (United States)

    Ghani, Muhammad U.; Wong, Molly D.; Wu, Di; Zheng, Bin; Chen, Wei; Fajardo, Laurie L.; Wu, Xizeng; Liu, Hong

    2017-02-01

    The objective of this study was to compare the detectability of simulated objects within a dense breast phantom using high energy x-rays for phase sensitive breast imaging in comparison with a conventional imaging system. A 5 cm thick phantom was used which represented a compressed breast consisting of 70% glandular and 30% adipose tissue ratio in non-uniform background. The phantom had a 6 × 6 matrix of holes with milled depths ranging from 1 to 0.1 mm and diameters ranging from 4.25 to 0.25 mm representing simulated tumors. The in-line phase sensitive prototype was equipped with a micro-focus x-ray source and a flat panel detector with a 50 μm pixel pitch, both mounted on an optical rail. Phase contrast image of the phantom was acquired at 120 kVp, 4.5 mAs at source to object distance (SOD) of 68 cm and source to image detector distance (SIDD) of 170 cm with a geometric magnification (M) of 2.5. A 2.5 mm aluminum (Al) filter was used for beam hardening. The conventional image was acquired using the same porotype with the phantom in contact with the detector at 40 kVp, 12.5 mAs under SID = 68 cm. The mean glandular dose (Dg) for both the acquisitions was 1.3 mGy. The observer study and CNR analyses indicated that the phase contrast image had higher disk detectability as compared to the conventional image. The edge enhancement provided by the phase sensitive images warrants in identifying boundaries of malignant tissues and in providing optimal results in phase retrieval process. The potential demonstrated by this study for imaging a dense breast with a high energy phase sensitive x-ray imaging to improve tumor detection in warrants further investigation of this technique.

  18. Strain and ground-motion monitoring at magmatic areas: ultra-long and ultra-dense networks using fibre optic sensing systems

    Science.gov (United States)

    Jousset, Philippe; Reinsch, Thomas; Henninges, Jan; Blanck, Hanna; Ryberg, Trond

    2016-04-01

    The fibre optic distributed acoustic sensing technology (DAS) is a "new" sensing system for exploring earth crustal elastic properties and monitoring both strain and seismic waves with unprecedented acquisition characteristics. The DAS technology principle lies in sending successive and coherent pulses of light in an optical fibre and measuring the back-scattered light issued from elastic scattering at random defaults within the fibre. The read-out unit includes an interferometer, which measures light interference patterns continuously. The changes are related to the distance between such defaults and therefore the strain within the fibre can be detected. Along an optical fibre, DAS can be used to acquire acoustic signals with a high spatial (every meter over kilometres) and high temporal resolution (thousand of Hz). Fibre optic technologies were, up to now, mainly applied in perimeter surveillance applications and pipeline monitoring and in boreholes. Previous experiments in boreholes have shown that the DAS technology is well suited for probing subsurface elastic properties, showing new ways for cheaper VSP investigations of the Earth crust. Here, we demonstrate that a cable deployed at ground surface can also help in exploring subsurface properties at crustal scale and monitor earthquake activity in a volcanic environment. Within the framework of the EC funded project IMAGE, we observed a >15 km-long fibre optic cable at the surface connected to a DAS read-out unit. Acoustic data was acquired continuously for 9 days. Hammer shots were performed along the surface cable in order to locate individual acoustic traces and calibrate the spatial distribution of the acoustic information. During the monitoring period both signals from on- and offshore explosive sources and natural seismic events could be recorded. We compare the fibre optic data to conventional seismic records from a dense seismic network deployed on Reykjanes. We show that we can probe and monitor earth

  19. A High-Energy, Ultrashort-Pulse X-Ray System for the Dynamic Study of Heavy, Dense Materials

    Energy Technology Data Exchange (ETDEWEB)

    Gibson, David Jeremy [Univ. of California, Davis, CA (United States)

    2004-01-01

    Thomson-scattering based x-ray radiation sources, in which a laser beam is scattered off a relativistic electron beam resulting in a high-energy x-ray beam, are currently being developed by several groups around the world to enable studies of dynamic material properties which require temporal resolution on the order of tens of femtoseconds to tens of picoseconds. These sources offer pulses that are shorter than available from synchrotrons, more tunable than available from so-called Ka sources, and more penetrating and more directly probing than ultrafast lasers. Furthermore, Thomson-scattering sources can scale directly up to x-ray energies in the few MeV range, providing peak brightnesses far exceeding any other sources in this regime. This dissertation presents the development effort of one such source at Lawrence Livermore National Laboratory, the Picosecond Laser-Electron InterAction for the Dynamic Evaluation of Structures (PLEIADES) project, designed to target energies from 30 keV to 200 keV, with a peak brightness on the order of 1018 photons • s-1 • mm-2 • mrad-2 • 0.01% bandwidth-1. A 10 TW Ti:Sapphire based laser system provides the photons for the interaction, and a 100 MeV accelerator with a 1.6 cell S-Band photoinjector at the front end provides the electron beam. The details of both these systems are presented, as is the initial x-ray production and characterization, validating the theory of Thomson scattering. In addition to the systems used to enable PLEIADES, two alternative systems are discussed. An 8.5 GHz X-Band photoinjector, capable of sustaining higher accelerating gradients and producing lower emittance electron beams in a smaller space than the S-Band gun, is presented, and the initial operation and commissioning of this gun is presented. Also, a hybrid chirped-pulse amplification system is presented as an alternative to the standard regenerative amplifier technology in high

  20. An Ammonia Spectral Map of the L1495-B218 Filaments in the Taurus Molecular Cloud : I. Physical Properties of Filaments and Dense cores

    CERN Document Server

    Seo, Young Min; Goldsmith, Paul; Ward-Thompson, Derek; Kirk, Jason M; Schmalzl, Markus; Lee, Jeong-Eun; Friesen, Rachel; Langston, Glen; Masters, Joe; Garwood, Robert W

    2015-01-01

    We present deep NH$_3$ observations of the L1495-B218 filaments in the Taurus molecular cloud covering over a 3 degree angular range using the K-band focal plane array on the 100m Green Bank Telescope. The L1495-B218 filaments form an interconnected, nearby, large complex extending over 8 pc. We observed NH$_3$ (1,1) and (2,2) with a spectral resolution of 0.038 km/s and a spatial resolution of 31$"$. Most of the ammonia peaks coincide with intensity peaks in dust continuum maps at 350 $\\mu$m and 500 $\\mu$m. We deduced physical properties by fitting a model to the observed spectra. We find gas kinetic temperatures of 8 $-$ 15 K, velocity dispersions of 0.05 $-$ 0.25 km/s, and NH$_3$ column densities of 5$\\times$10$^{12}$ $-$ 1$\\times$10$^{14}$ cm$^{-2}$. The CSAR algorithm, which is a hybrid of seeded-watershed and binary dendrogram algorithms, identifies a total of 55 NH$_3$ structures including 39 leaves and 16 branches. The masses of the NH$_3$ sources range from 0.05 M$_\\odot$ to 9.5 M$_\\odot$. The masses...

  1. Modeling the role of electron attachment rates on column density ratios for CnH-/CnH (n=4,6,8) in dense molecular clouds

    CERN Document Server

    Gianturco, F A; Wester, R

    2016-01-01

    (abridged) The fairly recent detection of a variety of anions in the Interstellar Molecular Clouds have underlined the importance of realistically modeling the processes governing their abundance. To this aim, our earlier calculations for the radiative electron attachment (REA) rates for C4H-, C6H-, and C8H- are employed to generate the corresponding column density ratios of anion/neutral (A/N) relative abundances. The latter are then compared with those obtained from observational measurements. The calculations involved the time-dependent solutions of a large network of chemical processes over an extended time interval and included a series of runs in which the values of REA rates were repeatedly scaled. Macroscopic parameters for the clouds' modeling were also varied to cover a broad range of physical environments. It was found that, within the range and quality of the processes included in the present network,and selected from state-of-the-art astrophysical databases, the REA values required to match the o...

  2. Study on sustainable redevelopment of a densely built-up area in Tokyo by introducing a distributed local energy supply system

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Hong; Ooka, Ryozo; Huang, Hong [Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505 (Japan); Iwamura, Kazuo [Musashi Institute of Technology, UIA, JIA, Tokyo (Japan); Yoshizawa, Nobufusa; Miisho, Kiyoshi [IWAMURA Atelier Co. Ltd., Tokyo (Japan); Yoshida, Satoshi [Yokohama National University, Yokohama (Japan); Namatame, Sanae; Sakakura, Atsushi; Tanaka, Syunichi [Tokyo Gas Co. Ltd., Tokyo (Japan)

    2008-07-01

    'Distributed local energy systems' had been expected to rationalize the supply of energy to built-up areas, but until now very little research has been performed to estimate the effect of their application to actual cities. In this research, therefore, a future vision for the year 2030 in the Sancha Area (SANCHA VISION 2030), a typical densely built-up area in Tokyo, has been elaborated including a simulation to estimate benefits from the application of distributed energy systems in terms of reduced energy consumption and CO{sub 2} emissions as well as mitigation of the heat-island phenomenon. As a result, it was demonstrated that a 'distributed local energy system', which provides a district with both electrical power and heat through an integrated distribution system, may contribute to a considerable improvement in energy efficiency for those areas. In addition, it may also provide other benefits, including enhancement of living amenity and urban security in times of emergency. (author)

  3. 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.

  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. Novel Raman Parametric Hybrid L-Band Amplifier with Four-Wave Mixing Suppressed Pump for Terabits Dense Wavelength Division Multiplexed Systems

    Directory of Open Access Journals (Sweden)

    Gaganpreet Kaur

    2016-01-01

    Full Text Available We demonstrate improved performance of parametric amplifier cascaded with Raman amplifier for gain of 54.79 dB. We report amplification of L-band using 100 × 10 Gbps Dense Wavelength Division Multiplexed (DWDM system with 25 GHz channel spacing. The gain achieved is the highest reported so far with gain flatness of 3.38 dB without using any gain flattening technique. Hybrid modulated parametric pump is used for suppressing four-wave mixing (FWM around pump region, resulting in improvement of gain flatness by 2.42 dB. The peak to peak variation of gain is achieved less than 1.6 dB. DWDM system with 16-channel, 25 GHz spaced system has been analyzed thoroughly with hybrid modulated parametric pump amplified Raman-FOPA amplifier for gain flatness and improved performance in terms of BER and Q-factor.

  6. pysimm: A python package for simulation of molecular systems

    Science.gov (United States)

    Fortunato, Michael E.; Colina, Coray M.

    In this work, we present pysimm, a python package designed to facilitate structure generation, simulation, and modification of molecular systems. pysimm provides a collection of simulation tools and smooth integration with highly optimized third party software. Abstraction layers enable a standardized methodology to assign various force field models to molecular systems and perform simple simulations. These features have allowed pysimm to aid the rapid development of new applications specifically in the area of amorphous polymer simulations.

  7. Modelling the role of electron attachment rates on column density ratios for C n H-/C n H (n=4,6,8) in dense molecular clouds

    Science.gov (United States)

    Gianturco, F. A.; Grassi, T.; Wester, R.

    2016-10-01

    The fairly recent detection of a variety of anions in the interstellar molecular clouds have underlined the importance of realistically modelling the processes governing their abundance. To pursue this task, our earlier calculations for the radiative electron attachment (REA) rates for C4H-, C6H-, and C8H- are employed in the present work, within a broad network of other concurrent reactions, to generate the corresponding column density ratios of anion/neutral (A/N) relative abundances. The latter are then compared with those obtained in recent years from observational measurements. The calculations involved the time-dependent solutions of a large network of chemical processes over an extended time interval and included a series of runs in which the values of REA rates were repeatedly scaled over several orders of magnitude. Macroscopic parameters for the Clouds’ modelling were also varied to cover a broad range of physical environments. It was found that, within the range and quality of the processes included in the present network,and selected from state-of-the-art astrophysical databases, the REA values required to match the observed A/N ratios needed to be reduced by orders of magnitude for C4H- case, while the same rates for C6H- and C8H- only needed to be scaled by much smaller factors. The results suggest that the generally proposed formation of interstellar anions by REA mechanism is overestimated by current models for the C4H- case, for which is likely to be an inefficient path to formation. This path is thus providing a rather marginal contribution to the observed abundances of C4H-, the latter being more likely to originate from other chemical processes in the network, as we discuss in some detail in the present work. Possible physical reasons for the much smaller differences against observations found instead for the values of the (A/N) ratios in two other, longer members of the series are put forward and analysed within the evolutionary modelling

  8. 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.

  9. A Molecular Communication System Model for Particulate Drug Delivery Systems.

    Science.gov (United States)

    Chahibi, Youssef; Pierobon, Massimiliano; Song, Sang Ok; Akyildiz, Ian F

    2013-12-01

    The goal of a drug delivery system (DDS) is to convey a drug where the medication is needed, while, at the same time, preventing the drug from affecting other healthy parts of the body. Drugs composed of micro- or nano-sized particles (particulate DDS) that are able to cross barriers which prevent large particles from escaping the bloodstream are used in the most advanced solutions. Molecular communication (MC) is used as an abstraction of the propagation of drug particles in the body. MC is a new paradigm in communication research where the exchange of information is achieved through the propagation of molecules. Here, the transmitter is the drug injection, the receiver is the drug delivery, and the channel is realized by the transport of drug particles, thus enabling the analysis and design of a particulate DDS using communication tools. This is achieved by modeling the MC channel as two separate contributions, namely, the cardiovascular network model and the drug propagation network. The cardiovascular network model allows to analytically compute the blood velocity profile in every location of the cardiovascular system given the flow input by the heart. The drug propagation network model allows the analytical expression of the drug delivery rate at the targeted site given the drug injection rate. Numerical results are also presented to assess the flexibility and accuracy of the developed model. The study of novel optimization techniques for a more effective and less invasive drug delivery will be aided by this model, while paving the way for novel communication techniques for Intrabody communication networks.

  10. Probing Cold Dense Nuclear Matter

    Energy Technology Data Exchange (ETDEWEB)

    Subedi, Ramesh; Shneor, R.; Monaghan, Peter; Anderson, Bryon; Aniol, Konrad; Annand, John; Arrington, John; Benaoum, Hachemi; Benmokhtar, Fatiha; Bertozzi, William; Boeglin, Werner; Chen, Jian-Ping; Choi, Seonho; Cisbani, Evaristo; Craver, Brandon; Frullani, Salvatore; Garibaldi, Franco; Gilad, Shalev; Gilman, Ronald; Glamazdin, Oleksandr; Hansen, Jens-Ole; Higinbotham, Douglas; Holmstrom, Timothy; Ibrahim, Hassan; Igarashi, Ryuichi; De Jager, Cornelis; Jans, Eddy; Jiang, Xiaodong; Kaufman, Lisa; Kelleher, Aidan; Kolarkar, Ameya; Kumbartzki, Gerfried; LeRose, John; Lindgren, Richard; Liyanage, Nilanga; Margaziotis, Demetrius; Markowitz, Pete; Marrone, Stefano; Mazouz, Malek; Meekins, David; Michaels, Robert; Moffit, Bryan; Perdrisat, Charles; Piasetzky, Eliazer; Potokar, Milan; Punjabi, Vina; Qiang, Yi; Reinhold, Joerg; Ron, Guy; Rosner, Guenther; Saha, Arunava; Sawatzky, Bradley; Shahinyan, Albert; Sirca, Simon; Slifer, Karl; Solvignon, Patricia; Sulkosky, Vince; Sulkosky, Vincent; Sulkosky, Vince; Sulkosky, Vincent; Urciuoli, Guido; Voutier, Eric; Watson, John; Weinstein, Lawrence; Wojtsekhowski, Bogdan; Wood, Stephen; Zheng, Xiaochao; Zhu, Lingyan

    2008-06-01

    The protons and neutrons in a nucleus can form strongly correlated nucleon pairs. Scattering experiments, in which a proton is knocked out of the nucleus with high-momentum transfer and high missing momentum, show that in carbon-12 the neutron-proton pairs are nearly 20 times as prevalent as proton-proton pairs and, by inference, neutron-neutron pairs. This difference between the types of pairs is due to the nature of the strong force and has implications for understanding cold dense nuclear systems such as neutron stars.

  11. Probing Cold Dense Nuclear Matter

    CERN Document Server

    Subedi, R; Monaghan, P; Anderson, B D; Aniol, K; Annand, J; Arrington, J; Benaoum, H; Benmokhtar, F; Bertozzi, W; Boeglin, W; Chen, J -P; Choi, Seonho; Cisbani, E; Craver, B; Frullani, S; Garibaldi, F; Gilad, S; Gilman, R; Glamazdin, O; Hansen, J -O; Higinbotham, D W; Holmstrom, T; Ibrahim, H; Igarashi, R; De Jager, C W; Jans, E; Jiang, X; Kaufman, L; Kelleher, A; Kolarkar, A; Kumbartzki, G; LeRose, J J; Lindgren, R; Liyanage, N; Margaziotis, D J; Markowitz, P; Marrone, S; Mazouz, M; Meekins, D; Michaels, R; Moffit, B; Perdrisat, C F; Piasetzky, E; Potokar, M; Punjabi, V; Qiang, Y; Reinhold, J; Ron, G; Rosner, G; Saha, A; Sawatzky, B; Shahinyan, A; Širca, S; Slifer, K; Solvignon, P; Sulkosky, V; Urciuoli, G; Voutier, E; Watson, J W; Weinstein, L B; Wojtsekhowski, B; Wood, S; Zheng, X -C; Zhu, L; 10.1126/science.1156675

    2009-01-01

    The protons and neutrons in a nucleus can form strongly correlated nucleon pairs. Scattering experiments, where a proton is knocked-out of the nucleus with high momentum transfer and high missing momentum, show that in 12C the neutron-proton pairs are nearly twenty times as prevalent as proton-proton pairs and, by inference, neutron-neutron pairs. This difference between the types of pairs is due to the nature of the strong force and has implications for understanding cold dense nuclear systems such as neutron stars.

  12. The direct link model for polymer rings using topological field theory and the second topological moment in dense systems

    Energy Technology Data Exchange (ETDEWEB)

    Otto, Matthias [Institut fuer Theoretische Physik, Universitaet Goettingen, Goettingen (Germany)

    2001-03-30

    Polymer rings in solution are either permanently entangled or are not. Permanent topological restrictions give rise to additional entropic interactions apart from the ones arising due to mere chain flexibility or excluded volume. Conversely, entangled polymer rings systems may be formed by closing randomly entangled flexible linear chains. The dependence of linking numbers between randomly entangled rings on the chain length, more specifically the second topological moment , i.e. the average squared linking number, may be determined. In this paper, an approach recently discussed in mathematical physics and called Abelian BF theory, is presented which allows one to express the linking constraint in its simplest form, the Gauss integral, in terms of two gauge fields. The model of Brereton and Shah for a single ring entangled with many other surrounding rings is rederived. The latter model is finally used to calculate the second topological moment, in agreement with a recent result by Ferrari, Kleinert, and Lazzizzera obtained using n-component {phi}{sup 4} theory for the limit n{yields}0. (author)

  13. Stokes Efficiency of Molecular Motor-Cargo Systems

    Directory of Open Access Journals (Sweden)

    Hongyun Wang

    2008-01-01

    Full Text Available A molecular motor utilizes chemical free energy to generate a unidirectional motion through the viscous fluid. In many experimental settings and biological settings, a molecular motor is elastically linked to a cargo. The stochastic motion of a molecular motor-cargo system is governed by a set of Langevin equations, each corresponding to an individual chemical occupancy state. The change of chemical occupancy state is modeled by a continuous time discrete space Markov process. The probability density of a motor-cargo system is governed by a two-dimensional Fokker-Planck equation. The operation of a molecular motor is dominated by high viscous friction and large thermal fluctuations from surrounding fluid. The instantaneous velocity of a molecular motor is highly stochastic: the past velocity is quickly damped by the viscous friction and the new velocity is quickly excited by bombardments of surrounding fluid molecules. Thus, the theory for macroscopic motors should not be applied directly to molecular motors without close examination. In particular, a molecular motor behaves differently working against a viscous drag than working against a conservative force. The Stokes efficiency was introduced to measure how efficiently a motor uses chemical free energy to drive against viscous drag. For a motor without cargo, it was proved that the Stokes efficiency is bounded by 100% [H. Wang and G. Oster, (2002]. Here, we present a proof for the general motor-cargo system.

  14. Probing Interactions in Complex Molecular Systems through Ordered Assembly

    Energy Technology Data Exchange (ETDEWEB)

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

    2002-01-31

    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

  15. Enhanced sampling techniques in molecular dynamics simulations of biological systems.

    Science.gov (United States)

    Bernardi, Rafael C; Melo, Marcelo C R; Schulten, Klaus

    2015-05-01

    Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Electromagnetically induced grating in a crystal of molecular magnets system

    Science.gov (United States)

    Liu, Jibing; Liu, Na; Shan, Chuanjia; Liu, Tangkun; Li, Hong; Zheng, Anshou; Xie, Xiao-Tao

    2016-07-01

    We investigate the response of the molecular system to the magnetic field modulation. Molecular magnets are subjected to a strong standing ac magnetic field and a weak probe magnetic field. The transmission and absorption of the weak probe magnetic field can be changed due to quantum coherence and the spatially modulating of the standing field. And a electromagnetically induced grating is formed in the crystal of molecular magnets via electromagnetically induced transparency (EIT). The diffraction efficiency of the grating can be adjusted efficiently by tuning the intensity of the standing wave field and the single photon detuning.

  17. A molecular dynamics study of polymer/graphene interfacial systems

    Energy Technology Data Exchange (ETDEWEB)

    Rissanou, Anastassia N.; Harmandaris, Vagelis [Department of Mathematics and Applied Mathematics, University of Crete, GR-71409, Heraklion, Crete, Greece and Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), GR-71110, Heraklion, Cret (Greece)

    2014-05-15

    Graphene based polymer nanocomposites are hybrid materials with a very broad range of technological applications. In this work, we study three hybrid polymer/graphene interfacial systems (polystyrene/graphene, poly(methyl methacrylate)/graphene and polyethylene/graphene) through detailed atomistic molecular dynamics (MD) simulations. Density profiles, structural characteristics and mobility aspects are being examined at the molecular level for all model systems. In addition, we compare the properties of the hybrid systems to the properties of the corresponding bulk ones, as well as to theoretical predictions.

  18. Photoelectrochemical solar conversion systems molecular and electronic aspects

    CERN Document Server

    Munoz, Andres G

    2012-01-01

    Providing new insights into the molecular and electronic processes involved in the conversion of sunlight into chemical products, Photoelectrochemical Solar Conversion Systems: Molecular and Electronic Aspects begins with an historical overview and a survey of recent developments in the electrochemistry of semiconductors and spectroscopic techniques. It then provides a comprehensive introduction to the science of conversion cells, reviews current issues and potential directions, and covers a wide range of materials from organic to inorganic cells.Employing a tutorial organization with balanced

  19. 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...

  20. Neutral atomic carbon in dense molecular clouds

    Science.gov (United States)

    Zmuidzinas, J.; Betz, A. L.; Boreiko, R. T.; Goldhaber, D. M.

    1988-01-01

    The 370 micron 3P2-3P1 fine-structure line of neutral carbon was detected in seven sources: OMC 1, NGC 2024, S140, W3, DR 21, M17, and W51. Simultaneous analysis of J = 2-1 data and available observations of the J = 1-0 line make it possible to deduce optical depths and excitation temperatures for these lines. These data indicate that both C I lines are likely to be optically thin, and that the ratio of C I to CO column densities in these clouds is typically about 0.1.

  1. Dense Suspension Splash

    Science.gov (United States)

    Zhang, Wendy; Dodge, Kevin M.; Peters, Ivo R.; Ellowitz, Jake; Klein Schaarsberg, Martin H.; Jaeger, Heinrich M.

    2014-03-01

    Upon impact onto a solid surface at several meters-per-second, a dense suspension plug splashes by ejecting liquid-coated particles. We study the mechanism for splash formation using experiments and a numerical model. In the model, the dense suspension is idealized as a collection of cohesionless, rigid grains with finite surface roughness. The grains also experience lubrication drag as they approach, collide inelastically and rebound away from each other. Simulations using this model reproduce the measured momentum distribution of ejected particles. They also provide direct evidence supporting the conclusion from earlier experiments that inelastic collisions, rather than viscous drag, dominate when the suspension contains macroscopic particles immersed in a low-viscosity solvent such as water. Finally, the simulations reveal two distinct routes for splash formation: a particle can be ejected by a single high momentum-change collision. More surprisingly, a succession of small momentum-change collisions can accumulate to eject a particle outwards. Supported by NSF through its MRSEC program (DMR-0820054) and fluid dynamics program (CBET-1336489).

  2. Dense Axion Stars

    CERN Document Server

    Braaten, Eric; Zhang, Hong

    2015-01-01

    If the dark matter consists of axions, gravity can cause them to coalesce into axion stars, which are stable gravitationally bound Bose-Einstein condensates of axions. In the previously known axion stars, gravity and the attractive force between pairs of axions are balanced by the kinetic pressure.If the axion mass energy is $mc^2= 10^{-4}$ eV, these dilute axion stars have a maximum mass of about $10^{-14} M_\\odot$. We point out that there are also dense axion stars in which gravity is balanced by the mean-field pressure of the axion condensate. We study axion stars using the leading term in a systematically improvable approximation to the effective potential of the nonrelativistic effective field theory for axions. Using the Thomas-Fermi approximation in which the kinetic pressure is neglected, we find a sequence of new branches of axion stars in which gravity is balanced by the mean-field interaction energy of the axion condensate. If $mc^2 = 10^{-4}$ eV, the first branch of these dense axion stars has mas...

  3. Dense Axion Stars

    Science.gov (United States)

    Mohapatra, Abhishek; Braaten, Eric; Zhang, Hong

    2016-03-01

    If the dark matter consists of axions, gravity can cause them to coalesce into axion stars, which are stable gravitationally bound Bose-Einstein condensates of axions. In the previously known axion stars, gravity and the attractive force between pairs of axions are balanced by the kinetic pressure. If the axion mass energy is mc2 =10-4 eV, these dilute axion stars have a maximum mass of about 10-14M⊙ . We point out that there are also dense axion stars in which gravity is balanced by the mean-field pressure of the axion condensate. We study axion stars using the leading term in a systematically improvable approximation to the effective potential of the nonrelativistic effective field theory for axions. Using the Thomas-Fermi approximation in which the kinetic pressure is neglected, we find a sequence of new branches of axion stars in which gravity is balanced by the mean-field interaction energy of the axion condensate. If mc2 =10-4 4 eV, the first branch of these dense axion stars has mass ranging from about 10-11M⊙ toabout M⊙.

  4. ABO System: molecular mimicry of Ascaris lumbricoides

    Directory of Open Access Journals (Sweden)

    Ponce de León Patricia

    2003-01-01

    Full Text Available A. lumbricoides has been associated to the ABO System by various authors. The objective was to detect ABO System epitopes in A. lumbricoides of groups O, A, B and AB patients. 28 adult parasites were obtained from children to be used as assay material. The patients ABO blood groups were determined. Extracts of A. lumbricoides [AE] were prepared by surgical remotion of the cuticle and refrigerated mechanical rupture. Agglutination Inhibition (AI and Hemoagglutination Kinetics (HK tests were used with the [AE]. Of the 28 [AE], eight belonged to O group patients, 15 to A group, three to B group and the remaining two to AB children. The AI Test showed A epitopes in two [AE] of group A patients and B epitopes in two [AE] of group B patients. The HK Test showed B antigenic determiners in two [AE] of group B patients and in two [AE] of group AB patients as well as A antigenic determiners in one [AE] of A group patient. Of the 28 [AE] studied in both tests B epitopes were detected in all [AE] from B and AB patients and A epitopes in three of the 15 [AE] of group A patients. The experiments carried out suggest that A. lumbricoides might absorb A and B antigens from the host, and/or modify the cuticular carbohydrates expression as a kind of antigenic mimicry.

  5. Continuous-terahertz-wave molecular imaging system for biomedical applications

    Science.gov (United States)

    Zhang, Rui; Zhang, Liangliang; Wu, Tong; Wang, Ruixue; Zuo, Shasha; Wu, Dong; Zhang, Cunlin; Zhang, Jue; Fang, Jing

    2016-07-01

    Molecular imaging techniques are becoming increasingly important in biomedical research and potentially in clinical practice. We present a continuous-terahertz (THz)-wave molecular imaging system for biomedical applications, in which an infrared (IR) laser is integrated into a 0.2-THz reflection-mode continuous-THz-wave imaging system to induce surface plasmon polaritons on the nanoparticles and further improve the intensity of the reflected signal from the water around the nanoparticles. A strong and rapid increment of the reflected THz signal in the nanoparticle solution upon the IR laser irradiation is demonstrated, using either gold or silver nanoparticles. This low-cost, simple, and stable continuous-THz-wave molecular imaging system is suitable for miniaturization and practical imaging applications; in particular, it shows great promise for cancer diagnosis and nanoparticle drug-delivery monitoring.

  6. Giant Nuclear Systems of Molecular Type

    Science.gov (United States)

    Zagrebaev, Valery; Greiner, Walter

    Low-energy dynamics of heavy nuclear systems is studied within the extended version of the two-center shell model and Langevin type equations of motion. The shell effects lead to the appearance of local minima and deep valleys on the multi-dimensional potential energy surface. It is shown that the local minima on the fission path of a heavy nucleus—so called isomeric states—are nothing else but the two-cluster configurations with magic or semi-magic cores surrounded with a certain number of shared nucleons. Clustering phenomena caused by the shell effects play an important role also in low-energy dynamics of heavy nuclear systems. Fission and quasi-fission are the well-known processes of such kind discussed in the paper. We found that in low-energy damped multi-nucleon transfer reactions the shell effects may significantly enhance the yield of new heavy neutron-rich nuclei located in the unexplored "north-east" area of the nuclear map which is important for astrophysical nucleosynthesis. A possibility for the production of long-living neutron-rich superheavy nuclei in collisions of actinide ions (such as 238U + 248Cm) is another important finding. In these reactions a large mass and charge transfer due to the inverse (anti-symmetrized) quasi-fission process is significantly enhanced by the clustering process with formation of closed shell nuclei around Z = 82 and N = 126. In many such collisions the lifetime of a composite system consisting of two touching actinide nuclei turns out to be rather long (> 10-20S). This time delay is sufficient for the observation of the line structure in spontaneous e + e - production from the supercritical electric field of a giant quasi-atom—a fundamental QED process not observed yet experimentally. In addition, this giant nuclear molecule might undergo to a three-body clusterization (ternary quasi-fission) with formation of two heavy lead-like fragments in the exit channel. The "true ternary fission" is also possible for

  7. A simplified electrophoretic system for determining molecular weights of proteins.

    Science.gov (United States)

    Manwell, C

    1977-09-01

    Electrophoresis of 31 different proteins in commercially prepared polyacrylamide gradient gels, Gradipore, yields a linear relationship between a hypothetical limiting pore size (the reciprocal of a limiting gel concentration, GL) and the cube root of the mol.wt., over the range 13 500-9000 000. A regression analysis of these data reveals that 98.6% of all variability in 1/GL is explained by the molecular weight, and this degree of accuracy compares favourably with existing methods for the determination of molecular weight by retardation of mobility in polyacrylamide. This new procedure has the additional advantages that molecular-weight standards can be obtained from readily available body fluids or tissue extracts by localizing enzymes and other proteins by standard histochemical methods, and that the same electrophoretic system can be used in determining molecular weights as is used in routine surveys of populations for individual and species variation in protein heterogeneity.

  8. 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

  9. Ab initio centroid path integral molecular dynamics: Application to vibrational dynamics of diatomic molecular systems

    Science.gov (United States)

    Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi

    2004-01-01

    An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.

  10. Conductive dense hydrogen.

    Science.gov (United States)

    Eremets, M I; Troyan, I A

    2011-11-13

    Molecular hydrogen is expected to exhibit metallic properties under megabar pressures. This metal is predicted to be superconducting with a very high critical temperature, T(c), of 200-400 K, and it may acquire a new quantum state as a metallic superfluid and a superconducting superfluid. It may potentially be recovered metastably at ambient pressures. However, experiments carried out at low temperatures, Thydrogen remains in the molecular insulating state. Here we report on the transformation of normal molecular hydrogen at room temperature (295 K) to a conductive and metallic state. At 200 GPa the Raman frequency of the molecular vibron strongly decreased and the spectral width increased, evidencing a strong interaction between molecules. Deuterium behaved similarly. Above 220 GPa, hydrogen became opaque and electrically conductive. At 260-270 GPa, hydrogen transformed into a metal as the conductance of hydrogen sharply increased and changed little on further pressurizing up to 300 GPa or cooling to at least 30 K; and the sample reflected light well. The metallic phase transformed back at 295 K into molecular hydrogen at 200 GPa. This significant hysteresis indicates that the transformation of molecular hydrogen into a metal is accompanied by a first-order structural transition presumably into a monatomic liquid state. Our findings open an avenue for detailed and comprehensive studies of metallic hydrogen.

  11. 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.

  12. Molecular biology of the renin-angiotensin system

    Energy Technology Data Exchange (ETDEWEB)

    Dzau, V.J.; Burt, D.W.; Pratt, R.E. (Harvard Medical School, Boston, MA (USA))

    1988-10-01

    This paper reviews the molecular biology of the renin-angiotensin system. The renin gene structure is analyzed in detail, including an examination of the putative regulatory regions. The combined action of these regulatory sequences would result in the complex, tissue-specific expression and regulation observed in vivo. The expression of the tissue renin-angiotensin systems, which may have important physiological functions, is also described. In addition, the pathway of renin biosynthesis and secretion is reviewed. This includes speculation on the fate of circulating prorenin and the physiological role of multiple renin forms and secretory pathways. The molecular approaches described in this paper have greatly advanced our knowledge of the biology of the renin-angiotensin system. Future studies using these and other approaches should provide further insight into this complex system.

  13. Molecular clocks and the early evolution of metazoan nervous systems.

    Science.gov (United States)

    Wray, Gregory A

    2015-12-19

    The timing of early animal evolution remains poorly resolved, yet remains critical for understanding nervous system evolution. Methods for estimating divergence times from sequence data have improved considerably, providing a more refined understanding of key divergences. The best molecular estimates point to the origin of metazoans and bilaterians tens to hundreds of millions of years earlier than their first appearances in the fossil record. Both the molecular and fossil records are compatible, however, with the possibility of tiny, unskeletonized, low energy budget animals during the Proterozoic that had planktonic, benthic, or meiofaunal lifestyles. Such animals would likely have had relatively simple nervous systems equipped primarily to detect food, avoid inhospitable environments and locate mates. The appearance of the first macropredators during the Cambrian would have changed the selective landscape dramatically, likely driving the evolution of complex sense organs, sophisticated sensory processing systems, and diverse effector systems involved in capturing prey and avoiding predation. © 2015 The Author(s).

  14. 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

  15. Viscoelastic behavior of dense microemulsions

    Science.gov (United States)

    Cametti, C.; Codastefano, P.; D'arrigo, G.; Tartaglia, P.; Rouch, J.; Chen, S. H.

    1990-09-01

    We have performed extensive measurements of shear viscosity, ultrasonic absorption, and sound velocity in a ternary system consisting of water-decane-sodium di(2-ethylhexyl)sulfo- succinate(AOT), in the one-phase region where it forms a water-in-oil microemulsion. We observe a rapid increase of the static shear viscosity in the dense microemulsion region. Correspondingly the sound absorption shows unambiguous evidence of a viscoelastic behavior. The absorption data for various volume fractions and temperatures can be reduced to a universal curve by scaling both the absorption and the frequency by the measured static shear viscosity. The sound absorption can be interpreted as coming from the high-frequency tail of the viscoelastic relaxation, describable by a Cole-Cole relaxation formula with unusually small elastic moduli.

  16. Quantum dynamics of bio-molecular systems in noisy environments

    OpenAIRE

    Huelga S.F.; Plenio M.B.

    2012-01-01

    We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental structural elements underlying the quantum dynamics of these systems, identify such elements and explore the resulting interplay of quantum dynamics and environmental decoherence. Secondly, we critically examine some existing approaches to the numerical descripti...

  17. 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.

  18. Molecular absorption cryogenic cooler for liquid hydrogen propulsion systems

    Science.gov (United States)

    Klein, G. A.; Jones, J. A.

    1982-01-01

    A light weight, long life molecular absorption cryogenic cooler (MACC) system is described which can use low temperature waste heat to provide cooling for liquid hydrogen propellant tanks for interplanetary spacecraft. Detailed tradeoff studies were made to evaluate the refrigeration system component interactions in order to minimize the mass of the spacecraft cooler system. Based on this analysis a refrigerator system mass of 31 kg is required to provide the .48 watts of cooling required by a 2.3 meter diameter liquid hydrogen tank.

  19. Control of density fluctuations in atomistic-continuum simulations of dense liquids

    Science.gov (United States)

    Kotsalis, E. M.; Walther, J. H.; Koumoutsakos, P.

    2007-07-01

    We present a control algorithm to eliminate spurious density fluctuations associated with the coupling of atomistic and continuum descriptions for dense liquids. A Schwartz domain decomposition algorithm is employed to couple molecular dynamics for the simulation of the atomistic system with a continuum solver for the simulation of the Navier-Stokes equations. The lack of periodic boundary conditions in the molecular dynamics simulations hinders the proper accounting for the virial pressure leading to spurious density fluctuations at the continuum-atomistic interface. An ad hoc boundary force is usually employed to remedy this situation. We propose the calculation of this boundary force using a control algorithm that explicitly cancels the density fluctuations. The results demonstrate that the present approach outperforms state-of-the-art algorithms. The conceptual and algorithmic simplicity of the method makes it suitable for any type of coupling between atomistic and continuum descriptions of dense fluids.

  20. Molecular system generation with strong resonance optical pumping

    Energy Technology Data Exchange (ETDEWEB)

    Kuntsevich, B.F.; Churakov, V.V.

    1977-03-01

    A study was made of molecular system generation modulated by three oscillating levels with a rotating structure with strong resonance optical pumping. Molecular behavior of the active medium is described by equations for the density matrix. The relationship between the amplification coefficient and pressure at various pumping intensities was examined. In approaching the assigned pumping field, an examination was made of how the generation field is affected by the volumetric density of the pumping energy, partial pressure of the buffer gas and frequency difference in the pumping channel.

  1. Injection of photoelectrons into dense argon gas

    CERN Document Server

    Borghesani, A F

    2010-01-01

    The injection of photoelectrons in a gaseous or liquid sample is a widespread technique to produce a cold plasma in a weakly--ionized system in order to study the transport properties of electrons in a dense gas or liquid. We report here the experimental results of photoelectron injection into dense argon gas at the temperatureT=142.6 K as a function of the externally applied electric field and gas density. We show that the experimental data can be interpreted in terms of the so called Young-Bradbury model only if multiple scattering effects due to the dense environment are taken into account when computing the scattering properties and the energetics of the electrons.

  2. 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

  3. Meaningful timescales from Monte Carlo simulations of molecular systems

    CERN Document Server

    Costa, Liborio I

    2016-01-01

    A new Markov Chain Monte Carlo method for simulating the dynamics of molecular systems with atomistic detail is introduced. In contrast to traditional Kinetic Monte Carlo approaches, where the state of the system is associated with minima in the energy landscape, in the proposed method, the state of the system is associated with the set of paths traveled by the atoms and the transition probabilities for an atom to be displaced are proportional to the corresponding velocities. In this way, the number of possible state-to-state transitions is reduced to a discrete set, and a direct link between the Monte Carlo time step and true physical time is naturally established. The resulting rejection-free algorithm is validated against event-driven molecular dynamics: the equilibrium and non-equilibrium dynamics of hard disks converge to the exact results with decreasing displacement size.

  4. The kinetic chemistry of dense interstellar clouds

    Science.gov (United States)

    Graedel, T. E.; Langer, W. D.; Frerking, M. A.

    1982-01-01

    A model of the time-dependent chemistry of dense interstellar clouds is formulated to study the dominant chemical processes in carbon and oxygen isotope fractionation, the formation of nitrogen-containing molecules, and the evolution of product molecules as a function of cloud density and temperature. The abundances of the dominant isotopes of the carbon- and oxygen-bearing molecules are calculated. The chemical abundances are found to be quite sensitive to electron concentration since the electron concentration determines the ratio of H3(+) to He(+), and the electron density is strongly influenced by the metals abundance. For typical metal abundances and for H2 cloud density not less than 10,000 molecules/cu cm, nearly all carbon exists as CO at late cloud ages. At high cloud density, many aspects of the chemistry are strongly time dependent. Finally, model calculations agree well with abundances deduced from observations of molecular line emission in cold dense clouds.

  5. Heavy mesons in dense matter

    NARCIS (Netherlands)

    Tolos, Laura; Gamermann, Daniel; Garcia-Recio, Carmen; Molina, Raquel; Nieves, Juan; Oset, Eulogio; Ramos, Angels; LlanesEstrada, FJ; Pelaez,

    2011-01-01

    Charmed mesons in dense matter are studied within a unitary coupled-channel approach which takes into account Pauli-blocking effects and meson self-energies in a self-consistent manner. We obtain the open-charm meson spectral functions in this dense medium, and discuss their implications on hidden c

  6. Easy creation of polymeric systems for molecular dynamics with Assemble!

    Science.gov (United States)

    Degiacomi, Matteo T.; Erastova, Valentina; Wilson, Mark R.

    2016-05-01

    We present Assemble!, a program greatly simplifying the preparation of molecular dynamics simulations of polymeric systems. The program is controlled either via command line or an intuitive Graphical User Interface, and runs on all major operating systems. Assemble! allows the creation of a desired system of polymer chains from constituent monomers, packs the chains into a box according to the required concentration and returns all the files needed for simulation with Gromacs. We illustrate the capabilities of Assemble! by demonstrating the easy preparation of a 300 monomers-long polyisoprene in hexane, and a heterogeneous mixture of polybutadiene.

  7. Tailoring approach for obtaining molecular orbitals of large systems

    Indian Academy of Sciences (India)

    Anuja P Rahalkar; Shridhar R Gadre

    2012-01-01

    Molecular orbitals (MO’s) within Hartree-Fock (HF) theory are of vital importance as they provide preliminary information of bonding and features such as electron localization and chemical reactivity. The contemporary literature treats the Kohn-Sham orbitals within density functional theory (DFT) equivalently to the MO's obtained within HF framework. The high scaling order of ab initio methods is the main hurdle in obtaining the MO's for large molecular systems. With this view, an attempt is made in the present work to employ molecular tailoring approach (MTA) for obtaining the complete set of MO's including occupied and virtual orbitals, for large molecules at HF and B3LYP levels of theory. The energies of highest occupied and lowest unoccupied molecular orbitals, and hence the band gaps, are accurately estimated by MTA for most of the test cases benchmarked in this study, which include -conjugated molecules. Typically, the root mean square errors of valence MO's are in range of 0.001 to 0.010 a.u. for all the test cases examined. MTA shows a time advantage factor of 2 to 3 over the corresponding actual calculation, for many of the systems reported.

  8. ANN expert system screening for illicit amphetamines using molecular descriptors

    Science.gov (United States)

    Gosav, S.; Praisler, M.; Dorohoi, D. O.

    2007-05-01

    The goal of this study was to develop and an artificial neural network (ANN) based on computed descriptors, which would be able to classify the molecular structures of potential illicit amphetamines and to derive their biological activity according to the similarity of their molecular structure with amphetamines of known toxicity. The system is necessary for testing new molecular structures for epidemiological, clinical, and forensic purposes. It was built using a database formed by 146 compounds representing drugs of abuse (mainly central stimulants, hallucinogens, sympathomimetic amines, narcotics and other potent analgesics), precursors, or derivatized counterparts. Their molecular structures were characterized by computing three types of descriptors: 38 constitutional descriptors (CDs), 69 topological descriptors (TDs) and 160 3D-MoRSE descriptors (3DDs). An ANN system was built for each category of variables. All three networks (CD-NN, TD-NN and 3DD-NN) were trained to distinguish between stimulant amphetamines, hallucinogenic amphetamines, and nonamphetamines. A selection of variables was performed when necessary. The efficiency with which each network identifies the class identity of an unknown sample was evaluated by calculating several figures of merit. The results of the comparative analysis are presented.

  9. Complement system part I - molecular mechanisms of activation and regulation

    Directory of Open Access Journals (Sweden)

    Nicolas eMerle

    2015-06-01

    Full Text Available Complement is a complex innate immune surveillance system, playing a key role in defense against pathogens and in host homeostasis. The complement system is initiated by conformational changes in recognition molecular complexes upon sensing danger signals. The subsequent cascade of enzymatic reactions is tightly regulated to assure that complement is activated only at specific locations requiring defense against pathogens, thus avoiding host tissue damage. Here we discuss the recent advances describing the molecular and structural basis of activation and regulation of the complement pathways and their implication on physiology and pathology. This article will review the mechanisms of activation of alternative, classical and lectin pathways, the formation of C3 and C5 convertases, the action of anaphylatoxins and the membrane attack complex. We will also discuss the importance of structure-function relationships using the example of atypical hemolytic uremic syndrome. Lastly we will discuss the development and benefits of therapies using complement inhibitors.

  10. Extending Molecular Theory to Steady-State Diffusing Systems

    Energy Technology Data Exchange (ETDEWEB)

    FRINK,LAURA J. D.; SALINGER,ANDREW G.; THOMPSON,AIDAN P.

    1999-10-22

    Predicting the properties of nonequilibrium systems from molecular simulations is a growing area of interest. One important class of problems involves steady state diffusion. To study these cases, a grand canonical molecular dynamics approach has been developed by Heffelfinger and van Swol [J. Chem. Phys., 101, 5274 (1994)]. With this method, the flux of particles, the chemical potential gradients, and density gradients can all be measured in the simulation. In this paper, we present a complementary approach that couples a nonlocal density functional theory (DFT) with a transport equation describing steady-state flux of the particles. We compare transport-DFT predictions to GCMD results for a variety of ideal (color diffusion), and nonideal (uphill diffusion and convective transport) systems. In all cases excellent agreement between transport-DFT and GCMD calculations is obtained with diffusion coefficients that are invariant with respect to density and external fields.

  11. The system of molecular-genetic triggers as self--organizing computing system

    Directory of Open Access Journals (Sweden)

    A. Profir

    2001-05-01

    Full Text Available In this paper is shown, that the system of molecular-genetic triggers can solve the SAT problem. The molecular-genetic trigger represents the self-organizing structure and has attractors. The signal from one attractor is transmitted to other attractor, from the first level to the second level of the system. Molecular-genetic triggers work separately. The system of molecular-genetic triggers represents an example of parallel computing system. Suppose, that the system can receive two types of signals. In the first case, the system switches with the help of signals of a molecular nature (concentration of activators x1, x>sub>2, x3, x4. In the second case, the signals of wave nature of a resonant frequency can be utilized. It is possible to show, that the molecular--genetic system, can recognize images encoded by 2-dimensional vectors. Thus, the cells can be considered as parallel self-organizing system producing, receiving and transmitting the information.

  12. Stokes Efficiency of Molecular Motor-Cargo Systems

    Science.gov (United States)

    2008-01-01

    2655, 1994. 11 F. Reif , Fundamentals of Statistical and Thermal Physics, McGraw-Hill, New York, NY, USA, 1985. 12 H. Kleinert, Path Integrals in...Quantum Mechanics , Statistics , Polymer Physics, and Financial Markets, World Scientific, River Edge, NJ, USA, 3rd edition, 2004. 13 A. Einstein...Efficiency of Molecular Motor-Cargo Systems Hongyun Wang1 and Hong Zhou2 1Department of Applied Mathematics and Statistics , University of California

  13. Efficient construction of nonorthogonal localized molecular orbitals in large systems.

    Science.gov (United States)

    Cui, Ganglong; Fang, Weihai; Yang, Weitao

    2010-08-26

    Localized molecular orbitals (LMOs) are much more compact representations of electronic degrees of freedom than canonical molecular orbitals (CMOs). The most compact representation is provided by nonorthogonal localized molecular orbitals (NOLMOs), which are linearly independent but are not orthogonal. Both LMOs and NOLMOs are thus useful for linear-scaling calculations of electronic structures for large systems. Recently, NOLMOs have been successfully applied to linear-scaling calculations with density functional theory (DFT) and to reformulating time-dependent density functional theory (TDDFT) for calculations of excited states and spectroscopy. However, a challenge remains as NOLMO construction from CMOs is still inefficient for large systems. In this work, we develop an efficient method to accelerate the NOLMO construction by using predefined centroids of the NOLMO and thereby removing the nonlinear equality constraints in the original method ( J. Chem. Phys. 2004 , 120 , 9458 and J. Chem. Phys. 2000 , 112 , 4 ). Thus, NOLMO construction becomes an unconstrained optimization. Its efficiency is demonstrated for the selected saturated and conjugated molecules. Our method for fast NOLMO construction should lead to efficient DFT and NOLMO-TDDFT applications to large systems.

  14. 槽车密相补气式气力输送系统的设计%Design of air conveying system of tank trailer dense phase replenish gas type

    Institute of Scientific and Technical Information of China (English)

    言仿雷; 罗宝东

    2001-01-01

    介绍密相气力输送的基本原理和技术,一种采用密相脉冲补气式气力输送PET切片的槽车贮罐运输、中转、卸料、仓贮的系统的建立,节约投资、降低能耗,提高了经济效益.%Basic principle and technology of dense phase air conve ying were introduced,a system was built which dense phase impluse replenish gas air conveying tank trailer storage was used to transport,transfer,discharge and store PET chip.The investment was saved,the energy consumption was reduced,the ecnomic benefit was improved.

  15. Resolving Ultrafast Heating of Dense Cryogenic Hydrogen

    Science.gov (United States)

    Zastrau, U.; Sperling, P.; Harmand, M.; Becker, A.; Bornath, T.; Bredow, R.; Dziarzhytski, S.; Fennel, T.; Fletcher, L. B.; Förster, E.; Göde, S.; Gregori, G.; Hilbert, V.; Hochhaus, D.; Holst, B.; Laarmann, T.; Lee, H. J.; Ma, T.; Mithen, J. P.; Mitzner, R.; Murphy, C. D.; Nakatsutsumi, M.; Neumayer, P.; Przystawik, A.; Roling, S.; Schulz, M.; Siemer, B.; Skruszewicz, S.; Tiggesbäumker, J.; Toleikis, S.; Tschentscher, T.; White, T.; Wöstmann, M.; Zacharias, H.; Döppner, T.; Glenzer, S. H.; Redmer, R.

    2014-03-01

    We report on the dynamics of ultrafast heating in cryogenic hydrogen initiated by a ≲300 fs, 92 eV free electron laser x-ray burst. The rise of the x-ray scattering amplitude from a second x-ray pulse probes the transition from dense cryogenic molecular hydrogen to a nearly uncorrelated plasmalike structure, indicating an electron-ion equilibration time of ˜0.9 ps. The rise time agrees with radiation hydrodynamics simulations based on a conductivity model for partially ionized plasma that is validated by two-temperature density-functional theory.

  16. High-order-harmonic generation in atomic and molecular systems

    Science.gov (United States)

    Suárez, Noslen; Chacón, Alexis; Pérez-Hernández, Jose A.; Biegert, Jens; Lewenstein, Maciej; Ciappina, Marcelo F.

    2017-03-01

    High-order-harmonic generation (HHG) results from the interaction of ultrashort laser pulses with matter. It configures an invaluable tool to produce attosecond pulses, moreover, to extract electron structural and dynamical information of the target, i.e., atoms, molecules, and solids. In this contribution, we introduce an analytical description of atomic and molecular HHG, that extends the well-established theoretical strong-field approximation (SFA). Our approach involves two innovative aspects: (i) First, the bound-continuum and rescattering matrix elements can be analytically computed for both atomic and multicenter molecular systems, using a nonlocal short range model, but separable, potential. When compared with the standard models, these analytical derivations make possible to directly examine how the HHG spectra depend on the driven media and laser-pulse features. Furthermore, we can turn on and off contributions having distinct physical origins or corresponding to different mechanisms. This allows us to quantify their importance in the various regions of the HHG spectra. (ii) Second, as reported recently [N. Suárez et al., Phys. Rev. A 94, 043423 (2016), 10.1103/PhysRevA.94.043423], the multicenter matrix elements in our theory are free from nonphysical gauge- and coordinate-system-dependent terms; this is accomplished by adapting the coordinate system to the center from which the corresponding time-dependent wave function originates. Our SFA results are contrasted, when possible, with the direct numerical integration of the time-dependent Schrödinger equation in reduced and full dimensionality. Very good agreement is found for single and multielectronic atomic systems, modeled under the single active electron approximation, and for simple diatomic molecular systems. Interference features, ubiquitously present in every strong-field phenomenon involving a multicenter target, are also captured by our model.

  17. The System of Molecular Clouds in the Gould Belt

    CERN Document Server

    Bobylev, V V

    2016-01-01

    Based on high-latitude molecular clouds with highly accurate distance estimates taken from the literature, we have redetermined the parameters of their spatial orientation. This system can be approximated by a 350x235x140 pc ellipsoid inclined by the angle i=17+/-2 degrees to the Galactic plane with the longitude of the ascending node l{\\Omega}=337+/-1 degrees. Based on the radial velocities of the clouds, we have found their group velocity relative to the Sun to be (u0,v0,w0) = (10.6,18.2,6.8)+/-(0.9,1.7,1.5) km/s. The trajectory of the center of the molecular cloud system in the past in a time interval of ~60 Myr has been constructed. Using data on masers associated with low-mass protostars, we have calculated the space velocities of the molecular complexes in Orion, Taurus, Perseus, and Ophiuchus. Their motion in the past is shown to be not random.

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

    Directory of Open Access Journals (Sweden)

    Rietman Edward A

    2011-06-01

    Full Text Available Abstract 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.

  19. 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.

  20. Light scattering from macromolecular systems: Molecular crystals and polymers

    Science.gov (United States)

    Bernstein, E. R.

    1981-11-01

    The research objectives were to: (1) characterize phase transitions theoretically and experimentally in molecular crystal systems; (2) use the above understanding gained by light scattering studies and theoretical interpretation to apply to the more complex system of lyotropic liquid crystals; and (3) then apply knowledge gained on the model systems of increasing complexity to polymer liquid crystals and solid polymers as observed by laser light scattering techniques. Systems experimentally and theoretically discussed are: trioxane, triazine, benzil, and chloranil. Studies of lyotropic liquid crystals (sodium decyl sulfate, sodium sulfate, decanol, water) have progressed. The major findings are: a number of phase transitions occur between 20 and 60 C; these transitions evidence strong critical behavior and long correlation times for fluctuations; and liquid crystals can be studied by light scattering. Spectra of solid powders, ribbons, and liquid crystals of PBT and solid PBO were obtained.

  1. Quantum dynamics of bio-molecular systems in noisy environments

    CERN Document Server

    Plenio, M B

    2012-01-01

    We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental structural elements underlying the quantum dynamics of these systems, identify such elements and explore the resulting interplay of quantum dynamics and environmental decoherence. Secondly, we critically examine some existing approaches to the numerical description of system-environment interaction in the non-perturbative regime and present a promising new method that can overcome some limitations of existing methods. Thirdly, we present an approach towards deciding and quantifying the non-classicality of the action of the environment and the observed system-dynamics. We stress the relevance of these tools for strengthening the interplay between theoretical and experimental research in this field.

  2. 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.

  3. Radiative Corrections and Quantum Gates in Molecular Systems

    Science.gov (United States)

    Reina, John H.; Beausoleil, Ray G.; Spiller, Tim P.; Munro, William J.

    2004-12-01

    We propose a method for quantum information processing using molecules coupled to an external laser field. This utilizes molecular interactions, control of the external field, and an effective energy shift of the doubly excited state of two coupled molecules. Such a level shift has been seen in the two-photon resonance experiments recently reported by Hettich etal. Here we show that this can be explained in terms of the QED Lamb shift. We quantify the performance of the proposed quantum logic gates in the presence of dissipative mechanisms. The unitary transformations required for performing one- and two-qubit operations can be implemented with present day molecular technology. The proposed techniques can also be applied to coupled quantum dot and biomolecular systems.

  4. Densely crosslinked polycarbosiloxanes .1. Synthesis

    NARCIS (Netherlands)

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

    1997-01-01

    Novel densely crosslinked polycarbosiloxanes were obtained by using functional branched prepolymers. Two types of soluble prepolymers were prepared from di- and trifunctional alkoxysilane monomers via cohydrolysis/condensation and for both final crosslinking occurred via hydrosilylation. The prepoly

  5. Optimal probabilistic dense coding schemes

    Science.gov (United States)

    Kögler, Roger A.; Neves, Leonardo

    2017-04-01

    Dense coding with non-maximally entangled states has been investigated in many different scenarios. We revisit this problem for protocols adopting the standard encoding scheme. In this case, the set of possible classical messages cannot be perfectly distinguished due to the non-orthogonality of the quantum states carrying them. So far, the decoding process has been approached in two ways: (i) The message is always inferred, but with an associated (minimum) error; (ii) the message is inferred without error, but only sometimes; in case of failure, nothing else is done. Here, we generalize on these approaches and propose novel optimal probabilistic decoding schemes. The first uses quantum-state separation to increase the distinguishability of the messages with an optimal success probability. This scheme is shown to include (i) and (ii) as special cases and continuously interpolate between them, which enables the decoder to trade-off between the level of confidence desired to identify the received messages and the success probability for doing so. The second scheme, called multistage decoding, applies only for qudits ( d-level quantum systems with d>2) and consists of further attempts in the state identification process in case of failure in the first one. We show that this scheme is advantageous over (ii) as it increases the mutual information between the sender and receiver.

  6. Molecular physiology of vesicular glutamate transporters in the digestive system

    Institute of Scientific and Technical Information of China (English)

    Tao Li; Fayez K. Ghishan; Liqun Bai

    2005-01-01

    Glutamate is the major excitatory neurotransmitter in the mammalian central nervous system (CNS). Packaging and storage of glutamate into glutamatergic neuronal vesicles require ATP-dependent vesicular glutamate uptake systems, which utilize the electrochemical proton gradient as a driving force. Three vesicular glutamate transporters (VGLUT1-3) have been recently identified from neuronal tissue where they play a key role to maintain the vesicular glutamate level. Recently, it has been demonstrated that glutamate signaling is also functional in peripheral neuronal and non-neuronal tissues, and occurs in sites of pituitary, adrenal, pineal glands, bone, GI tract, pancreas,skin, and testis. The glutamate receptors and VGLUTs in digestivesystem have been found in both neuronal and endocrinal cells. The glutamate signaling in the digestive system may have significant relevance to diabetes and GI tract motility disorders. This review will focus on the most recent update of molecular physiology of digestive VGLUTs.

  7. Microscale Symmetrical Electroporator Array as a Versatile Molecular Delivery System

    Science.gov (United States)

    Ouyang, Mengxing; Hill, Winfield; Lee, Jung Hyun; Hur, Soojung Claire

    2017-03-01

    Successful developments of new therapeutic strategies often rely on the ability to deliver exogenous molecules into cytosol. We have developed a versatile on-chip vortex-assisted electroporation system, engineered to conduct sequential intracellular delivery of multiple molecules into various cell types at low voltage in a dosage-controlled manner. Micro-patterned planar electrodes permit substantial reduction in operational voltages and seamless integration with an existing microfluidic technology. Equipped with real-time process visualization functionality, the system enables on-chip optimization of electroporation parameters for cells with varying properties. Moreover, the system’s dosage control and multi-molecular delivery capabilities facilitate intracellular delivery of various molecules as a single agent or in combination and its utility in biological research has been demonstrated by conducting RNA interference assays. We envision the system to be a powerful tool, aiding a wide range of applications, requiring single-cell level co-administrations of multiple molecules with controlled dosages.

  8. A 3D visualization system for molecular structures

    Science.gov (United States)

    Green, Terry J.

    1989-01-01

    The properties of molecules derive in part from their structures. Because of the importance of understanding molecular structures various methodologies, ranging from first principles to empirical technique, were developed for computing the structure of molecules. For large molecules such as polymer model compounds, the structural information is difficult to comprehend by examining tabulated data. Therefore, a molecular graphics display system, called MOLDS, was developed to help interpret the data. MOLDS is a menu-driven program developed to run on the LADC SNS computer systems. This program can read a data file generated by the modeling programs or data can be entered using the keyboard. MOLDS has the following capabilities: draws the 3-D representation of a molecule using stick, ball and ball, or space filled model from Cartesian coordinates, draws different perspective views of the molecule; rotates the molecule on the X, Y, Z axis or about some arbitrary line in space, zooms in on a small area of the molecule in order to obtain a better view of a specific region; and makes hard copy representation of molecules on a graphic printer. In addition, MOLDS can be easily updated and readily adapted to run on most computer systems.

  9. New hybrid method for reactive systems from integrating molecular orbital or molecular mechanics methods with analytical potential energy surfaces.

    Science.gov (United States)

    Espinosa-Garciá, Joaquín; Rangel, Cipriano; Navarrete, Marta; Corchado, José C

    2004-09-15

    A computational approach to calculating potential energy surfaces for reactive systems is presented and tested. This hybrid approach is based on integrated methods where calculations for a small model system are performed by using analytical potential energy surfaces, and for the real system by using molecular orbital or molecular mechanics methods. The method is tested on a hydrogen abstraction reaction by using the variational transition-state theory with multidimensional tunneling corrections. The agreement between the calculated and experimental information depends on the quality of the method chosen for the real system. When the real system is treated by accurate quantum mechanics methods, the rate constants are in excellent agreement with the experimental measurements over a wide temperature range. When the real system is treated by molecular mechanics methods, the results are still good, which is very encouraging since molecular mechanics itself is not at all capable of describing this reactive system. Since no experimental information or additional fits are required to apply this method, it can be used to improve the accuracy of molecular orbital methods or to extend the molecular mechanics method to treat any reactive system with the single constraint of the availability of an analytical potential energy surface that describes the model system.

  10. High-pressure Brillouin scattering in a simple molecular system

    CERN Document Server

    Shimizu, H

    2002-01-01

    Recent developments in high-pressure in situ Brillouin spectroscopy of a simple molecular system are reviewed by demonstrating experimental and analytical methods for the study of acoustic velocities in any direction, adiabatic elastic constants, and elastic anisotropy. Detailed applications to solid argon (Ar) are presented, at pressures up to 70 GPa in a diamond anvil cell, using recently developed approaches that combine the method of in situ Brillouin spectroscopy, for a single crystal of Ar up to 4 GPa, and the envelope method applied to both longitudinal acoustic and transverse acoustic modes, for recrystallized Ar between 4 and 70 GPa.

  11. Splashing onset in dense suspension droplets

    OpenAIRE

    Peters, Ivo; Xu, Qin; Jaeger, Heinrich M.

    2013-01-01

    We investigate the impact of droplets of dense suspensions onto a solid substrate. We show that a global hydrodynamic balance is unable to predict the splash onset and propose to replace it by an energy balance at the level of the particles in the suspension. We experimentally verify that the resulting, particle-based Weber number gives a reliable, particle size and density dependent splash onset criterion. We further show that the same argument also explains why, in bimodal systems, smaller ...

  12. Molecular Evolution of Freshwater Snails with Contrasting Mating Systems.

    Science.gov (United States)

    Burgarella, Concetta; Gayral, Philippe; Ballenghien, Marion; Bernard, Aurélien; David, Patrice; Jarne, Philippe; Correa, Ana; Hurtrez-Boussès, Sylvie; Escobar, Juan; Galtier, Nicolas; Glémin, Sylvain

    2015-09-01

    Because mating systems affect population genetics and ecology, they are expected to impact the molecular evolution of species. Self-fertilizing species experience reduced effective population size, recombination rates, and heterozygosity, which in turn should decrease the efficacy of natural selection, both adaptive and purifying, and the strength of meiotic drive processes such as GC-biased gene conversion. The empirical evidence is only partly congruent with these predictions, depending on the analyzed species, some, but not all, of the expected effects have been observed. One possible reason is that self-fertilization is an evolutionary dead-end, so that most current selfers recently evolved self-fertilization, and their genome has not yet been strongly impacted by selfing. Here, we investigate the molecular evolution of two groups of freshwater snails in which mating systems have likely been stable for several millions of years. Analyzing coding sequence polymorphism, divergence, and expression levels, we report a strongly reduced genetic diversity, decreased efficacy of purifying selection, slower rate of adaptive evolution, and weakened codon usage bias/GC-biased gene conversion in the selfer Galba compared with the outcrosser Physa, in full agreement with theoretical expectations. Our results demonstrate that self-fertilization, when effective in the long run, is a major driver of population genomic and molecular evolutionary processes. Despite the genomic effects of selfing, Galba truncatula seems to escape the demographic consequences of the genetic load. We suggest that the particular ecology of the species may buffer the negative consequences of selfing, shedding new light on the dead-end hypothesis.

  13. Optimal methyl labeling for studies of supra-molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Religa, Tomasz L.; Kay, Lewis E., E-mail: kay@pound.med.utoronto.c [The University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry (Canada)

    2010-07-15

    Selective methyl labeling combined with HMQC spectroscopy that exploits a TROSY effect in {sup 13}CH{sub 3} spin systems has significantly extended the utility of solution NMR spectroscopy in studies of high molecular weight particles. Herein we compare the utility of {sup 13}CH{sub 3}- versus {sup 13}CHD{sub 2}-labeling of Ile, Leu, Val probes in supra-molecular systems through quantification of relative signal-to-noise ratios in optimized spectra of highly deuterated, {sup 13}CH{sub 3}- and {sup 13}CHD{sub 2}-labeled samples of the half proteasome ({alpha}{sub 7}{alpha}{sub 7}, 360 kDa). It is shown that the sensitivity of spectra recorded on Ile, Leu, Val {sup 13}CH{sub 3}-labeled samples is between 1.5 and 2 fold higher than the corresponding data sets obtained on {alpha}{sub 7}{alpha}{sub 7} with {sup 13}CHD{sub 2} probes. Thus, labeling of supra-molecules with {sup 13}CH{sub 3} isotopomers remains the method of choice, but in applications where {sup 13}CHD{sub 2} moieties are required, sensitivity will in general not be limiting.

  14. 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.

  15. Pipe Phantoms With Applications in Molecular Imaging and System Characterization.

    Science.gov (United States)

    Wang, Shiying; Herbst, Elizabeth B; Pye, Stephen D; Moran, Carmel M; Hossack, John A

    2017-01-01

    Pipe (vessel) phantoms mimicking human tissue and blood flow are widely used for cardiovascular related research in medical ultrasound. Pipe phantom studies require the development of materials and liquids that match the acoustic properties of soft tissue, blood vessel wall, and blood. Over recent years, pipe phantoms have been developed to mimic the molecular properties of the simulated blood vessels. In this paper, the design, construction, and functionalization of pipe phantoms are introduced and validated for applications in molecular imaging and ultrasound imaging system characterization. There are three major types of pipe phantoms introduced: 1) a gelatin-based pipe phantom; 2) a polydimethylsiloxane-based pipe phantom; and 3) the "Edinburgh pipe phantom." These phantoms may be used in the validation and assessment of the dynamics of microbubble-based contrast agents and, in the case of a small diameter tube phantom, for assessing imaging system spatial resolution/contrast performance. The materials and procedures required to address each of the phantoms are described.

  16. The generation of meaningful information in molecular systems.

    Science.gov (United States)

    Wills, Peter R

    2016-03-13

    The physico-chemical processes occurring inside cells are under the computational control of genetic (DNA) and epigenetic (internal structural) programming. The origin and evolution of genetic information (nucleic acid sequences) is reasonably well understood, but scant attention has been paid to the origin and evolution of the molecular biological interpreters that give phenotypic meaning to the sequence information that is quite faithfully replicated during cellular reproduction. The near universality and age of the mapping from nucleotide triplets to amino acids embedded in the functionality of the protein synthetic machinery speaks to the early development of a system of coding which is still extant in every living organism. We take the origin of genetic coding as a paradigm of the emergence of computation in natural systems, focusing on the requirement that the molecular components of an interpreter be synthesized autocatalytically. Within this context, it is seen that interpreters of increasing complexity are generated by series of transitions through stepped dynamic instabilities (non-equilibrium phase transitions). The early phylogeny of the amino acyl-tRNA synthetase enzymes is discussed in such terms, leading to the conclusion that the observed optimality of the genetic code is a natural outcome of the processes of self-organization that produced it.

  17. INTERNATIONAL CONFERENCE ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY (ISMB)

    Energy Technology Data Exchange (ETDEWEB)

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

    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.

  18. Characterization of ionic, dipolar and molecular mobility in polymer systems

    Science.gov (United States)

    Guo, Zhenrong

    Changes in the ionic and dipolar molecular mobility in a polymer system are the basis for the changes in the dielectric mechanical properties of polymer materials. Frequency Dependent Dielectric Measurements (FDEMS) and Ion Time-of-Flight (ITOF) are two important techniques to investigate ionic and dipolar molecular mobility in polymer systems. The results can be related to the macro- and molecular dielectric, electrical and dynamic properties of polymeric materials. The combination of these two methods provides a full view of electric, dielectric and dynamic behavior for the systems as they undergo chemical and/or physical changes during polymerization crystallization, vitrification, and/or phase separation. The research on microscopic mass mobility in polymer systems was done on three aspects: (1) ion mobility in an epoxy-amine reaction system; (2) dipolar mobility and relaxation during dimethacrylate resin cure and (3) dye molecule migration and diffusion in polymer films. In the ion mobility study, we separately monitor the changes in the ion mobility and the number of charge carriers during the epoxy-amine polymerization with FDEMS and ITOF measurements. The isolation of the number of carriers and their mobility allows significant improvement in monitoring changes in the state and structure of a material as it cures. For the dipolar mobility and relaxation study, FDEMS measurements were used to detect structural evolution and spatial heterogeneity formation during the polymerization process of dimethacrylate resins. The dielectric spectra, glass transition (Tg) profiles and dynamic mechanical measurements were used to investigate the existence of two cooperative regions of sufficient size to create two alpha-relaxation processes representing oligomer rich and polymer microgel regions during the polymerization. For the dye migration research, we tried to develop a visually color changing paper (VCP) due to dye molecule migration in polymer films. The mobility

  19. Nonlinear Absorption and Refraction in Multilevel Organic Molecular System

    Institute of Scientific and Technical Information of China (English)

    LI Chun-Fei; DENG Xiao-Xu; WANG Yu-Xiao

    2000-01-01

    The nonlinear absorption and refraction in a multilevel organic molecular system is described by using the density matrix theory. The total absorptive coefficient of the system in the low-density case is equal to a linear sum of contributions from each energy level. Similarly, the total refractive index is equal to a linear sum of contributions from each energy level plus the refractive index of the vacuum. The absorption coefficient or refractive index due to each level is proportional to the population of that level, where the constant of proportionality is called the absorption cross-section or the refraction volume, respectively. The relation between the absorption cross-section and the refraction volume for each level is also given.

  20. Unified Concept of Effective One Component Plasma for Hot Dense Plasmas.

    Science.gov (United States)

    Clérouin, Jean; Arnault, Philippe; Ticknor, Christopher; Kress, Joel D; Collins, Lee A

    2016-03-18

    Orbital-free molecular dynamics simulations are used to benchmark two popular models for hot dense plasmas: the one component plasma (OCP) and the Yukawa model. A unified concept emerges where an effective OCP (EOCP) is constructed from the short-range structure of the plasma. An unambiguous ionization and the screening length can be defined and used for a Yukawa system, which reproduces the long-range structure with finite compressibility. Similarly, the dispersion relation of longitudinal waves is consistent with the screened model at vanishing wave number but merges with the OCP at high wave number. Additionally, the EOCP reproduces the overall relaxation time scales of the correlation functions associated with ionic motion. In the hot dense regime, this unified concept of EOCP can be fruitfully applied to deduce properties such as the equation of state, ionic transport coefficients, and the ion feature in x-ray Thomson scattering experiments.

  1. A unified concept of effective one component plasma for hot dense plasmas

    CERN Document Server

    Clérouin, Jean; Ticknor, Christopher; Kress, Joel D; Collins, Lee A

    2016-01-01

    Orbital-free molecular dynamics simulations are used to benchmark two popular models for hot dense plasmas: the one component plasma (OCP) and the Yukawa model. A unified concept emerges where an effective OCP (eOCP) is constructed from the short-range structure of the plasma. An unambiguous ionization and the screening length can be defined and used for a Yukawa system, which reproduces the long range structure with finite compressibility. Similarly, the dispersion relation of longitudinal waves is consistent with the screened model at vanishing wavenumber but merges with the OCP at high wavenumber. Additionally, the eOCP reproduces the overall relaxation timescales of the correlation functions associated with ionic motion. In the hot dense regime, this unified concept of eOCP can be fruitfully applied to deduce properties such as the equation of state, ionic transport coefficients, and the ion feature in x-ray Thomson scattering experiments.

  2. Dense and diffuse gas in dynamically active clouds

    CERN Document Server

    Garrod, R T; Rawlings, J M C

    2006-01-01

    We investigate the chemical and observational implications of repetitive transient dense core formation in molecular clouds. We allow a transient density fluctuation to form and disperse over a period of 1 Myr, tracing its chemical evolution. We then allow the same gas immediately to undergo further such formation and dispersion cycles. The chemistry of the dense gas in subsequent cycles is similar to that of the first, and a limit cycle is reached quickly (2 - 3 cycles). Enhancement of hydrocarbon abundances during a specific period of evolution is the strongest indicator of previous dynamical history. The molecular content of the diffuse background gas in the molecular cloud is expected to be strongly enhanced by the core formation and dispersion process. Such enhancement may remain for as long as 0.5 Myr. The frequency of repetitive core formation should strongly determine the level of background molecular enhancement. We also convolve the emission from a synthesised dark cloud, comprised of ensembles of t...

  3. 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

  4. Dense deposit disease in a child with febrile sore throat

    Directory of Open Access Journals (Sweden)

    Giovanni Conti

    2017-01-01

    Full Text Available Dense deposit disease or membranoproliferative glomerulonephritis type II is a rare glomerulopathy characterized on renal biopsy by deposition of abnormal electron-dense material in the glomerular basement membrane. The pathophysiologic basis is uncontrolled systemic activation of the alternate pathway of the complement cascade. C3 nephritic factor, an autoantibody directed against the C3 convertase of the alternate pathway, plays a key role. In some patients, complement gene mutations have been identified. We report the case of a child who had persistent microscopic hematuria, proteinuria, and hypocomplementemia C3 for over 2 months. Renal biopsy confirmed the diagnosis of dense deposit disease.

  5. 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.

  6. Degree of molecular self-sorting in multicomponent systems.

    Science.gov (United States)

    Saha, Manik Lal; Schmittel, Michael

    2012-06-28

    Self-sorting represents the spontaneous and high fidelity self and/or non-self-recognition of two or more related components within a complex mixture. While the effective management of self-sorting principles perceptibly requires some key expertise in molecular programming, at a higher stage of operation it is of supreme interest to guide the process to increasingly higher degrees of self-sorting. In this article, we present the emerging principles of how to guide several components toward formation of self-sorted multicomponent architectures. To provide further guidance in denominating such systems, we suggest to utilise a systematic classification as well as a formula to evaluate their degree of self-sorting (M).

  7. The large system of molecular clouds in Orion and Monoceros

    Science.gov (United States)

    Maddalena, R. J.; Moscowitz, J.; Thaddeus, P.; Morris, M.

    1986-01-01

    Emission is noted over about one-eighth of an 850-sq deg region centered on Orion and Monoceros that has been surveyed in the J = 1 to 0 line of CO; most of the emission arises from giant molecular clouds associated with Orion A and B, and Mon R2. A much smaller area was surveyed for C-13O emission. A comparison of cloud masses obtained by three independent methods indicates that CO luminosity is as accurate a measure of cloud mass as other indicators. The possible relationships among clouds in the survey are discussed, including the conjecture that the overall Orion complex of clouds is a much larger system than previously considered, incorporating most of the clouds in the present survey.

  8. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Postawa, Z. E-mail: zp@castor.if.uj.edu.pl; Ludwig, K.; Piaskowy, J.; Krantzman, K.; Winograd, N.; Garrison, B.J

    2003-04-01

    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{l_brace}1 1 1{r_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.

  10. Constructing dense genetic linkage maps

    NARCIS (Netherlands)

    Jansen, J.; Jong, de A.G.; Ooijen, van J.W.

    2001-01-01

    This paper describes a novel combination of techniques for the construction of dense genetic linkage maps. The construction of such maps is hampered by the occurrence of even small proportions of typing errors. Simulated annealing is used to obtain the best map according to the optimality criterion:

  11. Unconditional Continuous Variable Dense Coding

    CERN Document Server

    Ralph, T C

    2002-01-01

    We investigate the conditions under which unconditional dense coding can be achieved using continuous variable entanglement. We consider the effect of entanglement impurity and detector efficiency and discuss experimental verification. We conclude that the requirements for a strong demonstration are not as stringent as previously thought and are within the reach of present technology.

  12. 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.

  13. A method for dense packing discovery

    CERN Document Server

    Kallus, Yoav; Gravel, Simon

    2010-01-01

    The problem of packing a system of particles as densely as possible is foundational in the field of discrete geometry and is a powerful model in the material and biological sciences. As packing problems retreat from the reach of solution by analytic constructions, the importance of an efficient numerical method for conducting de novo (from-scratch) searches for dense packings becomes crucial. In this paper, we use the divide and concur framework to develop a general search method for the solution of periodic constraint problems, and we apply it to the discovery of dense periodic packings. An important feature of the method is the integration of the unit cell parameters with the other packing variables in the definition of the configuration space. The method we present led to improvements in the densest-known tetrahedron packing which are reported in [arXiv:0910.5226]. Here, we use the method to reproduce the densest known lattice sphere packings and the best known lattice kissing arrangements in up to 14 and ...

  14. Dense Correspondences across Scenes and Scales.

    Science.gov (United States)

    Tau, Moria; Hassner, Tal

    2016-05-01

    We seek a practical method for establishing dense correspondences between two images with similar content, but possibly different 3D scenes. One of the challenges in designing such a system is the local scale differences of objects appearing in the two images. Previous methods often considered only few image pixels; matching only pixels for which stable scales may be reliably estimated. Recently, others have considered dense correspondences, but with substantial costs associated with generating, storing and matching scale invariant descriptors. Our work is motivated by the observation that pixels in the image have contexts-the pixels around them-which may be exploited in order to reliably estimate local scales. We make the following contributions. (i) We show that scales estimated in sparse interest points may be propagated to neighboring pixels where this information cannot be reliably determined. Doing so allows scale invariant descriptors to be extracted anywhere in the image. (ii) We explore three means for propagating this information: using the scales at detected interest points, using the underlying image information to guide scale propagation in each image separately, and using both images together. Finally, (iii), we provide extensive qualitative and quantitative results, demonstrating that scale propagation allows for accurate dense correspondences to be obtained even between very different images, with little computational costs beyond those required by existing methods.

  15. Temperature relaxation in dense plasma mixtures

    Science.gov (United States)

    Faussurier, Gérald; Blancard, Christophe

    2016-09-01

    We present a model to calculate temperature-relaxation rates in dense plasma mixtures. The electron-ion relaxation rates are calculated using an average-atom model and the ion-ion relaxation rates by the Landau-Spitzer approach. This method allows the study of the temperature relaxation in many-temperature electron-ion and ion-ion systems such as those encountered in inertial confinement fusion simulations. It is of interest for general nonequilibrium thermodynamics dealing with energy flows between various systems and should find broad use in present high energy density experiments.

  16. Thermal relaxation in a dense liquid under shock compression

    Science.gov (United States)

    Tsai, D. H.; Trevino, S. F.

    1981-11-01

    We have studied by means of molecular dynamics the propagation of a planar shock wave in a dense, three-dimensional column of a simple modified Lennard-Jones liquid. The column is 49.37σ2 in cross section, and 238.5σ in length, where σ is the length parameter in the potential. The column contains approximately 10 000 atoms. It is initially in equilibrium at a density of 0.85σ-3 and temperature of 1.16ɛk, where ɛ is the energy parameter in the potential. Shock compression is effected by causing the column to move in the longitudinal direction with a velocity of - Up and to collide with its mirror image across a mirror located at the origin. From the motion of the atoms in response to this kind of excitation, we calculate the shock velocity and the shock-front structure in the liquid, as well as the profiles of mass density, stress distribution, and energy density behind the shock front. Our shock-front structure agrees well with that obtained from the Navier-Stokes equations, but we also find important differences between our shock profiles and those postulated or computed from the continuum theory. In particular, we find that in 4×10-11 s, the longest time of our calculations, the stress components did not relax to a hydrostatic condition, and the corresponding kinetic temperature profile showed a relaxation process similar to what we found earlier in a crystalline solid. We examine the atomistic mechanisms of the various relaxation processes, and discuss their implications on the shock compression of dense systems of solids and liquids as opposed to rarefield systems of gases.

  17. Parametrizing coarse grained models for molecular systems at equilibrium

    KAUST Repository

    Kalligiannaki, E.

    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.

  18. The Role of the Environment in Molecular Systems

    CERN Document Server

    Kilin, D S

    2000-01-01

    The work is devoted to the investigation of the influence of a heat bath on the physical processes in a quantum system. We use the density matrix theory as one of the most powerfool tool for investigation of quantum relaxation. In the beginning of the work (chapter 2) we mention and recall the most important steps of derivation of the equation of motion for the reduced density matrix (master equation) for an arbitrary quantum system in diabatic representation interacting with the environment modeled by a set of independent harmonic oscillators. Chapter 3 deals with the question of the border between classical and quantum effects and reports on a study of the environmental influence on the time evolution of a coherent state or the superposition of two coherent states of a harmonic oscillator as a simple system displaying the peculiarities of the transition from quantum to classical regime. Chapters 4 and 5 concern the electron transfer (ET) problem, namely the mathematical description of the ET in molecular zi...

  19. Parametrizing coarse grained models for molecular systems at equilibrium

    Science.gov (United States)

    Kalligiannaki, E.; Chazirakis, A.; Tsourtis, A.; Katsoulakis, M. A.; Plecháč, P.; Harmandaris, V.

    2016-10-01

    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.

  20. 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.

  1. Energy conservation in molecular dynamics simulations of classical systems.

    Science.gov (United States)

    Toxvaerd, Søren; Heilmann, Ole J; Dyre, Jeppe C

    2012-06-14

    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 of a "shadow Hamiltonian" H [S. Toxvaerd, Phys. Rev. E 50, 2271 (1994)], i.e., a Hamiltonian close to the original H with the property that the discrete positions of the Verlet algorithm for H lie on the analytic trajectories of H. The shadow Hamiltonian can be obtained from H by an asymptotic expansion in the time step length. Here we use the first non-trivial term in this expansion to obtain an improved estimate of the discrete values of the energy. The investigation is performed for a representative system with Lennard-Jones pair interactions. The simulations show that inclusion of this term reduces the standard deviation of the energy fluctuations by a factor of 100 for typical values of the time step length. Simulations further show that the energy is conserved for at least one hundred million time steps provided the potential and its first four derivatives are continuous at the cutoff. Finally, we show analytically as well as numerically that energy conservation is not sensitive to round-off errors.

  2. 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.

  3. Solving Dense Generalized Eigenproblems on Multi-threaded Architectures

    CERN Document Server

    Aliaga, José I; Davidović, Davor; Di Napoli, Edoardo; Igual, Francisco D; Quintana-Ortí, Enrique S

    2011-01-01

    We compare two approaches to compute a portion of the spectrum of dense symmetric definite generalized eigenproblems: one is based on the reduction to tridiagonal form, and the other on the Krylov-subspace iteration. Two large-scale applications, arising in molecular dynamics and material science, are employed to investigate the contributions of the application, architecture, and parallelism of the method to the performance of the solvers. The experimental results on a state-of-the-art 8-core platform, equipped with a graphics processing unit (GPU), reveal that in real applications, iterative Krylov-subspace methods can be a competitive approach also for the solution of dense problems.

  4. 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

  5. Probing the Physical Structures of Dense Filaments

    Science.gov (United States)

    Li, Di

    2015-08-01

    Filament is a common feature in cosmological structures of various scales, ranging from dark matter cosmic web, galaxy clusters, inter-galactic gas flows, to Galactic ISM clouds. Even within cold dense molecular cores, filaments have been detected. Theories and simulations with (or without) different combination of physical principles, including gravity, thermal balance, turbulence, and magnetic field, can reproduce intriguing images of filaments. The ubiquity of filaments and the similarity in simulated ones make physical parameters, beyond dust column density, a necessity for understanding filament evolution. I report three projects attempting to measure physical parameters of filaments. We derive the volume density of a dense Taurus filament based on several cyanoacetylene transitions observed by GBT and ART. We measure the gas temperature of the OMC 2-3 filament based on combined GBT+VLA ammonia images. We also measured the sub-millimeter polarization vectors along OMC3. These filaments were found to be likely a cylinder-type structure, without dynamic heating, and likely accreting mass along the magnetic field lines.

  6. Bioenhanced dissolution of dense non-aqueous phase of trichloroethylene as affected by iron reducing conditions: model systems and environmental samples.

    Science.gov (United States)

    Paul, Laiby; Smolders, Erik

    2015-01-01

    The anaerobic biotransformation of trichloroethylene (TCE) can be affected by competing electron acceptors such as Fe (III). This study assessed the role of Fe (III) reduction on the bioenhanced dissolution of TCE dense non-aqueous phase liquid (DNAPL). Columns were set up as 1-D diffusion cells consisting of a lower DNAPL layer, a layer with an aquifer substratum and an upper water layer that is regularly refreshed. The substrata used were either inert sand or sand coated with 2-line ferrihydrite (HFO) or two environmental Fe (III) containing samples. The columns were inoculated with KB-1 and were repeatedly fed with formate. In none of the diffusion cells, vinyl chloride or ethene was detected while dissolved and extractable Fe (II) increased strongly during 60 d of incubation. The cis-DCE concentration peaked at 4.0 cm from the DNAPL (inert sand) while it was at 3.4 cm (sand+HFO), 1.7 cm and 2.5 cm (environmental samples). The TCE concentration gradients near the DNAPL indicate that the DNAPL dissolution rate was larger than that in an abiotic cell by factors 1.3 (inert sand), 1.0 (sand+HFO) and 2.2 (both environmental samples). This results show that high bioavailable Fe (III) in HFO reduces the TCE degradation by competitive Fe (III) reduction, yielding lower bioenhanced dissolution. However, Fe (III) reduction in environmental samples was not reducing TCE degradation and the dissolution factor was even larger than that of inert sand. It is speculated that physical factors, e.g. micro-niches in the environmental samples protect microorganisms from toxic concentrations of TCE.

  7. Neurodevelopmental and neuropsychiatric disorders represent an interconnected molecular system.

    Science.gov (United States)

    Cristino, A S; Williams, S M; Hawi, Z; An, J-Y; Bellgrove, M A; Schwartz, C E; Costa, L da F; Claudianos, C

    2014-03-01

    Many putative genetic factors that confer risk to neurodevelopmental disorders such as autism spectrum disorders (ASDs) and X-linked intellectual disability (XLID), and to neuropsychiatric disorders including attention deficit hyperactivity disorder (ADHD) and schizophrenia (SZ) have been identified in individuals from diverse human populations. Although there is significant aetiological heterogeneity within and between these conditions, recent data show that genetic factors contribute to their comorbidity. Many studies have identified candidate gene associations for these mental health disorders, albeit this is often done in a piecemeal fashion with little regard to the inherent molecular complexity. Here, we sought to abstract relationships from our knowledge of systems level biology to help understand the unique and common genetic drivers of these conditions. We undertook a global and systematic approach to build and integrate available data in gene networks associated with ASDs, XLID, ADHD and SZ. Complex network concepts and computational methods were used to investigate whether candidate genes associated with these conditions were related through mechanisms of gene regulation, functional protein-protein interactions, transcription factor (TF) and microRNA (miRNA) binding sites. Although our analyses show that genetic variations associated with the four disorders can occur in the same molecular pathways and functional domains, including synaptic transmission, there are patterns of variation that define significant differences between disorders. Of particular interest is DNA variations located in intergenic regions that comprise regulatory sites for TFs or miRNA. Our approach provides a hypothetical framework, which will help discovery and analysis of candidate genes associated with neurodevelopmental and neuropsychiatric disorders.

  8. Reaction Ensemble Monte Carlo Simulation of Complex Molecular Systems.

    Science.gov (United States)

    Rosch, Thomas W; Maginn, Edward J

    2011-02-08

    Acceptance rules for reaction ensemble Monte Carlo (RxMC) simulations containing classically modeled atomistic degrees of freedom are derived for complex molecular systems where insertions and deletions are achieved gradually by utilizing the continuous fractional component (CFC) method. A self-consistent manner in which to utilize statistical mechanical data contained in ideal gas free energy parameters during RxMC moves is presented. The method is tested by applying it to two previously studied systems containing intramolecular degrees of freedom: the propene metathesis reaction and methyl-tert-butyl-ether (MTBE) synthesis. Quantitative agreement is found between the current results and those of Keil et al. (J. Chem. Phys. 2005, 122, 164705) for the propene metathesis reaction. Differences are observed between the equilibrium concentrations of the present study and those of Lísal et al. (AIChE J. 2000, 46, 866-875) for the MTBE reaction. It is shown that most of this difference can be attributed to an incorrect formulation of the Monte Carlo acceptance rule. Efficiency gains using CFC MC as opposed to single stage molecule insertions are presented.

  9. Dynamic structure of dense krypton gas

    Science.gov (United States)

    Egelstaff, P. A.; Salacuse, J. J.; Schommers, W.; Ram, J.

    1984-07-01

    We have made molecular-dynamics computer simulations of dense krypton gas (10.6×1027 atoms/m3 and 296 K) using reasonably realistic pair potentials. Comparisons are made with the recent experimental data[P. A. Egelstaff et al., Phys. Rev. A 27, 1106 (1983)] for the dynamic structure factor S(q,ω) over the range 0.4

  10. Structural Transitions in Dense Networks

    CERN Document Server

    Lambiotte, R; Bhat, U; Redner, S

    2016-01-01

    We introduce an evolving network model in which a new node attaches to a randomly selected target node and also to each of its neighbors with probability $p$. The resulting network is sparse for $p<\\frac{1}{2}$ and dense (average degree increasing with number of nodes $N$) for $p\\geq \\frac{1}{2}$. In the dense regime, individual networks realizations built by this copying mechanism are disparate and not self-averaging. Further, there is an infinite sequence of structural anomalies at $p=\\frac{2}{3}$, $\\frac{3}{4}$, $\\frac{4}{5}$, etc., where the dependences on $N$ of the number of triangles (3-cliques), 4-cliques, undergo phase transitions. When linking to second neighbors of the target can occur, the probability that the resulting graph is complete---where all nodes are connected---is non-zero as $N\\to\\infty$.

  11. Holographic Renormalization in Dense Medium

    Directory of Open Access Journals (Sweden)

    Chanyong Park

    2014-01-01

    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.

  12. Radiative properties of dense nanofluids.

    Science.gov (United States)

    Wei, Wei; Fedorov, Andrei G; Luo, Zhongyang; Ni, Mingjiang

    2012-09-01

    The radiative properties of dense nanofluids are investigated. For nanofluids, scattering and absorbing of electromagnetic waves by nanoparticles, as well as light absorption by the matrix/fluid in which the nanoparticles are suspended, should be considered. We compare five models for predicting apparent radiative properties of nanoparticulate media and evaluate their applicability. Using spectral absorption and scattering coefficients predicted by different models, we compute the apparent transmittance of a nanofluid layer, including multiple reflecting interfaces bounding the layer, and compare the model predictions with experimental results from the literature. Finally, we propose a new method to calculate the spectral radiative properties of dense nanofluids that shows quantitatively good agreement with the experimental results.

  13. Dilatons for Dense Hadronic Matter

    CERN Document Server

    Lee, Hyun Kyu

    2009-01-01

    The idea that the explicit breaking of scale invariance by the trace anomaly of QCD can be rephrased as a spontaneous breaking has been recently exploited to capture the low-energy strong interaction dynamics of dense (and also hot) matter in terms of two dilaton fields, the "soft" (chi_s) and the "hard" (chi_h) fields, in the frame work of the hidden local gauge symmetry. In the Freund-Nambu model, the spontaneous symmetry breaking of scale symmetry is induced by an explicitly breaking term, while the spontaneous symmetry breaking is possible in the flat potential model which is scale symmetric. We discuss the interplay of the soft and hard dilatons using the spontaneously broken scale symmetry schemes and uncover a novel structure of dense matter hitherto unexplored.

  14. Carbon nanotubes as nanodelivery systems an insight through molecular dynamics simulations

    CERN Document Server

    Lim, Melvin Choon Giap

    2013-01-01

    This book showcases the application of carbon nanotubes as nanodelivery systems for copper atoms, using molecular dynamics simulations as a means of investigation. The nanodelivery system of the carbon nanotube presents the possible usage of the carbon structure in many areas in the future. This book is comprehensive and informative, and serves as a guide for any reader who wishes to perform a molecular dynamics simulation of his own and to conduct an analytical study of a molecular system.

  15. Design of optimal collimation for dedicated molecular breast imaging systems

    Energy Technology Data Exchange (ETDEWEB)

    Weinmann, Amanda L.; Hruska, Carrie B.; O' Connor, Michael K. [Department of Radiology, Division of Nuclear Medicine, Mayo Clinic, Rochester, Minnesota 55905 (United States)

    2009-03-15

    Molecular breast imaging (MBI) is a functional imaging technique that uses specialized small field-of-view gamma cameras to detect the preferential uptake of a radiotracer in breast lesions. MBI has potential to be a useful adjunct method to screening mammography for the detection of occult breast cancer. However, a current limitation of MBI is the high radiation dose (a factor of 7-10 times that of screening mammography) associated with current technology. The purpose of this study was to optimize the gamma camera collimation with the aim of improving sensitivity while retaining adequate resolution for the detection of sub-10-mm lesions. Square-hole collimators with holes matched to the pixilated cadmium zinc telluride detector elements of the MBI system were designed. Data from MBI patient studies and parameters of existing dual-head MBI systems were used to guide the range of desired collimator resolutions, source-to-collimator distances, pixel sizes, and collimator materials that were examined. General equations describing collimator performance for a conventional gamma camera were used in the design process along with several important adjustments to account for the specialized imaging geometry of the MBI system. Both theoretical calculations and a Monte Carlo model were used to measure the geometric efficiency (or sensitivity) and resolution of each designed collimator. Results showed that through optimal collimation, collimator sensitivity could be improved by factors of 1.5-3.2, while maintaining a collimator resolution of either {<=}5 or {<=}7.5 mm at a distance of 3 cm from the collimator face. These gains in collimator sensitivity permit an inversely proportional drop in the required dose to perform MBI.

  16. Theoretical Studies of the Relaxation Matrix for Molecular Systems

    Science.gov (United States)

    Ma, Qiancheng; Boulet, C.

    2016-06-01

    The phenomenon of collisional transfer of intensity due to line mixing has an increasing importance for atmospheric monitoring. From a theoretical point of view, all relevant information about the collisional processes is contained in the relaxation matrix where the diagonal elements give half-widths and shifts, and the off-diagonal elements correspond to line interferences. For simple systems such as those consisting of diatom-atom or diatom-diatom, accurate fully quantum calculations based on interaction potentials are feasible. However, fully quantum calculations become unrealistic for more complex systems. On the other hand, the semi-classical Robert-Bonamy formalism, which has been widely used to calculate half-widths and shifts for decades, fails in calculating the off-diagonal matrix elements resulting from applying the isolated line approximation. As a result, in order to simulate atmospheric spectra where the effects from line mixing are important, semi-empirical fitting or scaling laws such as the energy corrected sudden (ECS) and the infinite order sudden (IOS) models are commonly used. Recently, we have found that in developing this semi-classical line shape theory, to rely on the isolated line approximation is not necessary. By eliminating this unjustified assumption, and accurately evaluating matrix elements of the exponential operators, we have developed a more capable formalism that enables one not only to reduce uncertainties for calculated half-widths and shifts, but also to calculate the whole relaxation matrix. This implies that we can address the line mixing with the semi-classical theory based on interaction potentials between molecular absorber and molecular perturber. We have applied this formalism for Raman and infrared spectra of linear and asymmetric-top molecules. Recently, the method has been extended into symmetric-tops with inverse symmetry such as the NH3 molecule. Our calculated half-widths of NH3 lines in the νb{1} and the pure

  17. RESEARCH ON DENSITY STABILITY OF AIR DENSE MEDIUM FLUIDIZED BED

    Institute of Scientific and Technical Information of China (English)

    骆振福; 陈清如

    1994-01-01

    In this papcr on thc basis of studying the distribution of fine coal in the dense medium fluidized bed, the optimal size range of fine coal, which constitutes a fluidized bed together with the dense medium, has been found. In the separating process the fine coal will continuously accumulate in fluidized bed, thus inevitably reducing the density of the bed. In order to keep bed density stable, the authors adopted such measures as split-flow of used medium and complement of fresh dense medium. The experiment results in both lab and pilot systems of the air-dense medium fluidized bed show that these measures are effective and satisfactory. Then authors also have established some relative dynamic mathematical models for it.

  18. Gravity-driven dense granular flows

    Energy Technology Data Exchange (ETDEWEB)

    ERTAS,DENIZ; GREST,GARY S.; HALSEY,THOMAS C.; DEVINE,DOV; SILBERT,LEONARDO E.

    2000-03-29

    The authors report and analyze the results of numerical studies of dense granular flows in two and three dimensions, using both linear damped springs and Hertzian force laws between particles. Chute flow generically produces a constant density profile that satisfies scaling relations suggestive of a Bagnold grain inertia regime. The type for force law has little impact on the behavior of the system. Failure is not initiated at the surface, consistent with the absence of surface flows and different principal stress directions at vs. below the surface.

  19. 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

  20. The roles of integration in molecular systems biology.

    Science.gov (United States)

    O'Malley, Maureen A; Soyer, Orkun S

    2012-03-01

    A common way to think about scientific practice involves classifying it as hypothesis- or data-driven. We argue that although such distinctions might illuminate scientific practice very generally, they are not sufficient to understand the day-to-day dynamics of scientific activity and the development of programmes of research. One aspect of everyday scientific practice that is beginning to gain more attention is integration. This paper outlines what is meant by this term and how it has been discussed from scientific and philosophical points of view. We focus on methodological, data and explanatory integration, and show how they are connected. Then, using some examples from molecular systems biology, we will show how integration works in a range of inquiries to generate surprising insights and even new fields of research. From these examples we try to gain a broader perspective on integration in relation to the contexts of inquiry in which it is implemented. In today's environment of data-intensive large-scale science, integration has become both a practical and normative requirement with corresponding implications for meta-methodological accounts of scientific practice. We conclude with a discussion of why an understanding of integration and its dynamics is useful for philosophy of science and scientific practice in general.

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

    Science.gov (United States)

    Fillat, Cristina; Jose, Anabel; Ros, Xavier Bofill-De; Mato-Berciano, Ana; Maliandi, Maria Victoria; Sobrevals, Luciano

    2011-01-01

    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. PMID:24212620

  2. Inducibility of a molecular bioreporter system by heavy metals

    Energy Technology Data Exchange (ETDEWEB)

    Klimowski, L.; Rayms-Keller, A.; Olson, K.E.; Yang, R.S.H.; Tessari, J.; Carlson, J.; Beaty, B. [Colorado State Univ., Fort Collins, CO (United States)

    1996-02-01

    The authors have developed a molecular bioreporter model for detecting an invertebrate response to heavy metals in streams. The bioreporter system, pMt2-luc, utilizes a Drosophila melanogaster metallothionein promoter to regulate luciferase expression in stably transformed mosquito cells.The LucC5 clone, which was isolated from pMt2-luc transformed, hygromycin-resistant C6/36 (Aedes albopictus) cells, demonstrated a 12-fold increase in luciferase-specific activity 48 h after exposure to 13 ppm copper (Cu). In addition to Cu, exposure of LucC5 cells to 19 ppm lead (Pb) or 3 ppm mercury (Hg) for 48 h induced luciferase expression threefold and fourfold, respectively. Exposures of up to 30 ppm arsenic (As), 8 ppm cadmium (Cd), 7 ppm chromium (Cr), or 5 ppm nickel (Ni) had no effect on luciferase induction. LucC5 cells exposed to metal mixtures of 13 ppm Cu and 19 ppm Pb yielded an additive response with a 14-fold increase in luciferase expression. When organic chemicals such as phenol (3 ppm) were mixed with 13 ppm Cu, 19 ppm Pb, or 3 ppm Hg a significant reduction in luciferase activity was noted. Additionally, atomic absorption spectroscopy suggested that two of the metals, Cu and Pb, show marked differences in accumulation within the LucC5 cell line.

  3. Development of a Molecular System for Studying Microbial Arsenate Respiration

    Science.gov (United States)

    Saltikov, C. W.; Newman, D. K.

    2002-12-01

    The toxic element arsenic is a major contaminant of many groundwaters and surface waters throughout the world. Arsenic enrichment is primarily of geological origin resulting from weathering processes and geothermal activity. Not surprisingly, microorganisms inhabiting anoxic arsenic-contaminated environments have evolved to exploit arsenate during respiration. Numerous bacteria have been isolated that use arsenate as a terminal electron acceptor for respiratory growth. The diversity of this metabolism appears to be widespread throughout the microbial tree of life, suggesting respiratory arsenate reduction is ancient in origin. Yet little is known about the molecular mechanisms for how these organisms respire arsenate. We have developed a model system in Shewanella trabarsenatis, strain ANA-3, a facultative anaerobe that respires arsenate and tolerates high concentrations of arsenite (10 mM). Through loss-of-function studies, we have identified genes involved in both arsenic resistance and arsenate respiration. The genes that confer resistance to arsenic are homologous to the well-characterized ars operon of E. coli. However, the respiratory arsenate reductase is predicted to encode a novel protein that shares homologous regions (~ 40 % similarity) to molybdopterin anaerobic reductases specific for DMSO, thiosulfate, nitrate, and polysulfide. I will discuss our emerging model for how strain ANA-3 respires arsenate and the relationship between arsenite resistance and arsenate respiration. I will also highlight the relevance of this type of analysis for biogeochemical studies.

  4. Plant systems for recognition of pathogen-associated molecular patterns.

    Science.gov (United States)

    Postel, Sandra; Kemmerling, Birgit

    2009-12-01

    Research of the last decade has revealed that plant immunity consists of different layers of defense that have evolved by the co-evolutional battle of plants with its pathogens. Particular light has been shed on PAMP- (pathogen-associated molecular pattern) triggered immunity (PTI) mediated by pattern recognition receptors. Striking similarities exist between the plant and animal innate immune system that point for a common optimized mechanism that has evolved independently in both kingdoms. Pattern recognition receptors (PRRs) from both kingdoms consist of leucine-rich repeat receptor complexes that allow recognition of invading pathogens at the cell surface. In plants, PRRs like FLS2 and EFR are controlled by a co-receptor SERK3/BAK1, also a leucine-rich repeat receptor that dimerizes with the PRRs to support their function. Pathogens can inject effector proteins into the plant cells to suppress the immune responses initiated after perception of PAMPs by PRRs via inhibition or degradation of the receptors. Plants have acquired the ability to recognize the presence of some of these effector proteins which leads to a quick and hypersensitive response to arrest and terminate pathogen growth.

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

    Directory of Open Access Journals (Sweden)

    Maria Victoria Maliandi

    2011-01-01

    Full Text Available 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.

  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. A Novel Multi-Point Fiber Optics Acetylene Sensing System Based on Dense Wavelength Division Multiplexers%基于波分复用的多点光纤乙炔传感系统

    Institute of Scientific and Technical Information of China (English)

    余贶琭; 吴重庆; 郭旋; 王智; 石梅荣; 武文彬

    2011-01-01

    The Beer-Lambert law, taking into account the pressure broadening of the absorption lines function is analyzed, then it is used for multi-point acetylene gas detection. A fiber optical multi-point acetylene sensing system using dense wavelength division multiplexers, which takes advantage of different absorption lines to tag different probes in the system, is put forward. This system is easy to build and operate, while it does not need to modulate the light source. In addition, the system has a much smaller system loss and cross talks as the consequences of employing the dense wavelength division multiplexers. Theoretical results show that the maximum sensor number of the system is eighteen with a 0.5 % sensitivity using the absorption lines from 1510 to 1540 nm. A three-point sensing system is experimentally demonstrated and the errors of the measured results are within 1.8 %.%理论分析了考虑吸收线型函数展宽时的Beer-Lambert定律,作了进一步推导并应用于多点乙炔气体监测.提出一种采用波分复用器、利用吸收峰区分不同传感点的多点光纤乙炔传感系统,系统简单易操作,无需对光源进行调制,且系统损耗与串扰小.理论分析表明当目标检测灵敏度为0.5%时,在1510~1540 nm范围内该系统最大可监测18个传感点.搭建了一个3个监测点的乙炔传感系统并验证了上述理论的可行性,各传感点的测量误差均小于1.8%.

  8. 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.

  9. Duality principle from rarefied to dense gas and extended thermodynamics with six fields

    Science.gov (United States)

    Arima, Takashi; Ruggeri, Tommaso; Sugiyama, Masaru

    2017-01-01

    We present an extended thermodynamics (ET) theory of dissipative dense gases. In particular, we study the ET theory with six fields, where we neglect shear viscosity and heat conductivity. We postulate a simple principle of duality between rarefied and dense gases. This principle is based on the microscopic analysis of the energy exchange between different modes of the molecular motion. The basic system of equations satisfies all principles of ET, that is, Galilean invariance, entropy principle, and thermodynamic stability (entropy convexity), and, as in the ET theory of rarefied gases, the constitutive equations are completely determined by the thermal and caloric equations of state. The system is simplest after the Euler system, but, in contrast to the Euler system, we may have a global smooth solution due to the fact that the system is dissipative symmetric hyperbolic and satisfies the so-called K condition. There emerge two nonequilibrium temperatures; one is due to the translational modes, and the other is due to the internal modes such as rotation and vibration of a molecule. This viewpoint allows us to understand the origin of the dynamic pressure in a more clear way. Furthermore we evaluate the characteristic velocities associated with the hyperbolic system and address the fluctuation-dissipation relation of the bulk viscosity. As a typical example, we analyze van der Waals fluids based on the present theory.

  10. Dilatons in Dense Baryonic Matter

    CERN Document Server

    Lee, Hyun Kyu

    2013-01-01

    We discuss the role of dilaton, which is supposed to be representing a special feature of scale symmetry of QCD, trace anomaly, in dense baryonic matter. The idea that the scale symmetry breaking of QCD is responsible for the spontaneous breaking of chiral symmetry is presented along the similar spirit of Freund-Nambu model. The incorporation of dilaton field in the hidden local symmetric parity doublet model is briefly sketched with the possible role of dilaton at high density baryonic matter, the emergence of linear sigma model in dilaton limit.

  11. Equilibration dynamics and conductivity of warm dense hydrogen

    Science.gov (United States)

    Zastrau, U.; Sperling, P.; Becker, A.; Bornath, T.; Bredow, R.; Döppner, T.; Dziarzhytski, S.; Fennel, T.; Fletcher, L. B.; Förster, E.; Fortmann, C.; Glenzer, S. H.; Göde, S.; Gregori, G.; Harmand, M.; Hilbert, V.; Holst, B.; Laarmann, T.; Lee, H. J.; Ma, T.; Mithen, J. P.; Mitzner, R.; Murphy, C. D.; Nakatsutsumi, M.; Neumayer, P.; Przystawik, A.; Roling, S.; Schulz, M.; Siemer, B.; Skruszewicz, S.; Tiggesbäumker, J.; Toleikis, S.; Tschentscher, T.; White, T.; Wöstmann, M.; Zacharias, H.; Redmer, R.

    2014-07-01

    We investigate subpicosecond dynamics of warm dense hydrogen at the XUV free-electron laser facility (FLASH) at DESY (Hamburg). Ultrafast impulsive electron heating is initiated by a ≤300-fs short x-ray burst of 92-eV photon energy. A second pulse probes the sample via x-ray scattering at jitter-free variable time delay. We show that the initial molecular structure dissociates within (0.9±0.2) ps, allowing us to infer the energy transfer rate between electrons and ions. We evaluate Saha and Thomas-Fermi ionization models in radiation hydrodynamics simulations, predicting plasma parameters that are subsequently used to calculate the static structure factor. A conductivity model for partially ionized plasma is validated by two-temperature density-functional theory coupled to molecular dynamic simulations and agrees with the experimental data. Our results provide important insights and the needed experimental data on transport properties of dense plasmas.

  12. 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}

  13. 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.

  14. Variational path integral molecular dynamics and hybrid Monte Carlo algorithms using a fourth order propagator with applications to molecular systems

    Science.gov (United States)

    Kamibayashi, Yuki; Miura, Shinichi

    2016-08-01

    In the present study, variational path integral molecular dynamics and associated hybrid Monte Carlo (HMC) methods have been developed on the basis of a fourth order approximation of a density operator. To reveal various parameter dependence of physical quantities, we analytically solve one dimensional harmonic oscillators by the variational path integral; as a byproduct, we obtain the analytical expression of the discretized density matrix using the fourth order approximation for the oscillators. Then, we apply our methods to realistic systems like a water molecule and a para-hydrogen cluster. In the HMC, we adopt two level description to avoid the time consuming Hessian evaluation. For the systems examined in this paper, the HMC method is found to be about three times more efficient than the molecular dynamics method if appropriate HMC parameters are adopted; the advantage of the HMC method is suggested to be more evident for systems described by many body interaction.

  15. 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.

  16. Compton scattering measurements from dense plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Glenzer, S H; Neumayer, P; Doeppner, T; Landen, L; Lee, R W; Wallace, R; Weber, S; Lee, H J; Kritcher, A L; Falcone, R; Regan, S P; Sawada, H; Meyerhofer, D D; Gregori, G; Fortmann, C; Schwarz, V; Redmer, R

    2007-10-02

    Compton scattering has been developed for accurate measurements of densities and temperatures in dense plasmas. One future challenge is the application of this technique to characterize compressed matter on the National Ignition Facility where hydrogen and beryllium will approach extremely dense states of matter of up to 1000 g/cc. In this regime, the density, compressibility, and capsule fuel adiabat may be directly measured from the Compton scattered spectrum of a high-energy x-ray line source. Specifically, the scattered spectra directly reflect the electron velocity distribution. In non-degenerate plasmas, the width provides an accurate measure of the electron temperatures, while in partially Fermi degenerate systems that occur in laser-compressed matter it provides the Fermi energy and hence the electron density. Both of these regimes have been accessed in experiments at the Omega laser by employing isochorically heated solid-density beryllium and moderately compressed beryllium foil targets. In the latter experiment, compressions by a factor of 3 at pressures of 40 Mbar have been measured in excellent agreement with radiation hydrodynamic modeling.

  17. Compton scattering measurements from dense plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Glenzer, S H; Neumayer, P; Doeppner, T; Landen, O L; Lee, R W; Wallace, R J; Weber, S [Lawrence Livermore National Laboratory, Livermore, CA (United States); Lee, H J; Kritcher, A L; Falcone, R [University of California Berkeley, Berkeley, CA 94709 (United States); Regan, S P; Sawada, H; Meyerhofer, D D [Laboratory for Laser Energetics, Rochester, NY (United States); Gregori, G [Clarendon Laboratory, University of Oxford, Oxford OX1 3PU (United Kingdom); Fortmann, C; Schwarz, V; Redmer, R [Institut fuer Physik, Universitaet Rostock, D-18051 Rostock (Germany)], E-mail: glenzer1@llnl.gov

    2008-05-15

    Compton scattering techniques have been developed for accurate measurements of densities and temperatures in dense plasmas. One future challenge is the application of this technique to characterize compressed matter on the National Ignition Facility where hydrogen and beryllium will approach extremely dense states of matter of up to 1000 g/cc. In this regime, the density, compressibility, and capsule fuel adiabat may be directly measured from the Compton scattered spectrum of a high-energy x-ray line source. Specifically, the scattered spectra directly reflect the electron velocity distribution. In non-degenerate plasmas, the width provides an accurate measure of the electron temperatures, while in partially Fermi degenerate systems that occur in laser-compressed matter it provides the Fermi energy and hence the electron density. Both of these regimes have been accessed in experiments at the Omega laser by employing isochorically heated solid-density beryllium and moderately compressed beryllium foil targets. In the latter experiment, compressions by a factor of 3 at pressures of 40 Mbar have been measured in excellent agreement with radiation hydrodynamic modeling.

  18. Transport diffusion in one dimensional molecular systems: Power law and validity of Fick's law

    Science.gov (United States)

    Xu, Zhi-cheng; Zheng, Dong-qin; Ai, Bao-quan; Hu, Bambi; Zhong, Wei-rong

    2015-10-01

    The transport diffusion in one-dimensional molecular systems is investigated through non-equilibrium molecular dynamics and Monte Carlo methods. We have proposed the power law relationship of the transport diffusion coefficient with the temperature, the mass and the transport length, D* ∝ T*m*-1L*β, where β equals to 0.8 for small systems and zero for large systems. It is found that Fick's law is valid in long transport length but invalid in short transport length. Our results can provide a new perspective for understanding the microscopic mechanism of the molecular transport phenomena in low-dimensional systems.

  19. Preface - From molecules to molecular materials, biological molecular systems and nanostructures: A collection of contributions presented at the XIIIth International Conference on Molecular Spectroscopy

    Science.gov (United States)

    Ratajczak, Henryk; Drozd, Marek; Fausto, Rui

    2016-12-01

    This volume contains a series of selected contributions presented at the XIIIth International Conference on Molecular Spectroscopy (ICMS): "From Molecules to Molecular Materials, Biological Molecular Systems and Nanostructures" held in Wrocław, Poland, 9-12 September 2015, under the auspices of the Mayor of Wrocław and the European Academy of Sciences, Arts and Humanities. Wrocław was chosen not accidentally as venue for the conference. With more than a thousand years of history, Wrocław is the location of one of the oldest universities in Central Europe. Being a place where education and science play major roles in the daily life of its inhabitants, Wrocław is also a privileged center for spectroscopy in Poland.

  20. Charge and Energy Transfer Dynamics in Molecular Systems

    CERN Document Server

    May, Volkhard

    2004-01-01

    This second edition is based on the successful concept of the first edition in presenting a unified perspective on molecular charge and energy transfer processes. The authors bridge the regimes of coherent and dissipative dynamics, thus establishing the connection between classic rate theories and modern treatments of ultrafast phenomena. The book serves as an introduction for graduate students and researchers. Among the new topics of this second edition are. - semiclassical and quantum-classical hybrid formulations of molecular dynamics. - the basics of femtosecond nonlinear spectroscopy. - e

  1. Chemical pathways and kinetic rates of the N(4S) + N2 → N3 solid phase reaction: could the N3 radical be a temperature sensor of nitrogen ices in dense molecular clouds?

    Science.gov (United States)

    Mencos, Alejandro; Nourry, Sendres; Krim, Lahouari

    2017-05-01

    Even though the N3 radical has not yet been detected in the interstellar medium, its formation still remains a challenge. For a long time, bombardments of N2 ices by energetic particles were the only way to from the azide radical as it was thought that ultraviolet (UV) photons were not strong enough to fragment the molecular nitrogen into N atoms. Consequently, it had been suggested that N3 could be used as discriminator between ice radiolysis and ice photolysis until a very recent study that has shown that photodecomposition of molecular nitrogen by UV photons might also be a source of the azide radical. In contrast to all these nitrogen ice bombarding experiments, only two laboratory studies have investigated the N3 formation where the reactants N and N2 mixed in the gas phase were co-condensed at 12 K, and this raised a new question concerning whether N + N2 → N3 took place in the solid phase or in the gas phase. The experimental results of these two studies are contradictory and the problem of the characterization of N3 formation by co-condensing atomic N and molecular N2 has persisted to the present day. In this paper, we give a clear answer to this question, by investigating the kinetic rates of the N(4S) + N2 → N3 reaction in the solid phase in the temperature range of 3-35 K. We find a rate constant of 7.7 × 10-23 s-1 molecule-1 cm3 for the azide radical formation in the solid phase and we provide new information on the N3 infrared signature, which could be used to characterize the temperature and the structure of nitrogen ices.

  2. 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.

  3. Theory of the equation of state of hot dense matter

    Energy Technology Data Exchange (ETDEWEB)

    Barbee, T W; Surh, M; Yang, L H

    1999-07-23

    Ab initio molecular dynamics calculations are adapted to treat dense plasmas for temperatures exceeding the electronic Fermi temperature. Extended electronic states are obtained in a plane wave basis by using pseudopotentials for the ion cores in the local density approximation to density functional theory. The method reduces to conventional first principles molecular dynamics at low temperatures with the expected high level of accuracy. The occurrence of thermally excited ion cores at high temperatures is treated by means of final state pseudopotentials. The method is applied to the shock compression Hugoniot equation of state for aluminum. Good agreement with experiment is found for temperatures ranging from zero through 105K.

  4. 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

  5. Neutrino Oscillations in Dense Matter

    Science.gov (United States)

    Lobanov, A. E.

    2017-03-01

    A modification of the electroweak theory, where the fermions with the same electroweak quantum numbers are combined in multiplets and are treated as different quantum states of a single particle, is proposed. In this model, mixing and oscillations of particles arise as a direct consequence of the general principles of quantum field theory. The developed approach enables one to calculate the probabilities of the processes taking place in the detector at long distances from the particle source. Calculations of higher-order processes, including computation of the contributions due to radiative corrections, can be performed in the framework of the perturbation theory using the regular diagram technique. As a result, the analog to the Dirac-Schwinger equation of quantum electrodynamics describing neutrino oscillations and its spin rotation in dense matter can be obtained.

  6. DPIS for warm dense matter

    Energy Technology Data Exchange (ETDEWEB)

    Kondo, K.; Kanesue, T.; Horioka, K.; Okamura, M.

    2010-05-23

    Warm Dense Matter (WDM) offers an challenging problem because WDM, which is beyond ideal plasma, is in a low temperature and high density state with partially degenerate electrons and coupled ions. WDM is a common state of matter in astrophysical objects such as cores of giant planets and white dwarfs. The WDM studies require large energy deposition into a small target volume in a shorter time than the hydrodynamical time and need uniformity across the full thickness of the target. Since moderate energy ion beams ({approx} 0.3 MeV/u) can be useful tool for WDM physics, we propose WDM generation using Direct Plasma Injection Scheme (DPIS). In the DPIS, laser ion source is connected to the Radio Frequency Quadrupole (RFQ) linear accelerator directly without the beam transport line. DPIS with a realistic final focus and a linear accelerator can produce WDM.

  7. Photoproduction of molecular hydrogen by a plant-algal symbiotic system

    Energy Technology Data Exchange (ETDEWEB)

    Newton, J.W.

    1976-02-13

    The rapidly growing water fern Azolla, which contains a nitrogen-fixing blue-green algal symbiont, has been studied as a possible system for photoproduction of molecular hydrogen. When this plant is grown on a combined nitrogen supply, photochemically generated hydrogen can be diverted through the algal nitrogenase system, which serves as a source of molecular hydrogen generated from water. This symbiosis has several advantages as a possible biological energy conversion system. (auth)

  8. DENSE PHASE REBURN COMBUSTION SYSTEM (DPRCS) DEMONSTRATION ON A 154 MWE TANGENTIAL FURNACE: ADDITIONAL AREA OF INTEREST-TO DEVELOP AND DEMONSTRATE AN IN-FURNACE MULTI-POLLUTANT REDUCTION TECHNOLOGY TO REDUCE NOx, SO2 & Hg

    Energy Technology Data Exchange (ETDEWEB)

    Allen C. Wiley; Steven Castagnero; Geoff Green; Kevin Davis; David White

    2004-03-01

    Semi-dense phase pneumatic delivery and injection of calcium and sodium sorbents, and microfine powdered coal, at various sidewall elevations of an online operating coal-fired power plant, was investigated for the express purpose of developing an in-furnace, economic multi-pollutant reduction methodology for NO{sub x}, SO{sub 2} & Hg. The 154 MWe tangentially-fired furnace that was selected for a full-scale demonstration, was recently retrofitted for NO{sub x} reduction with a high velocity rotating-opposed over-fire air system. The ROFA system, a Mobotec USA technology, has a proven track record of breaking up laminar flow along furnace walls, thereby enhancing the mix of all constituents of combustion. The knowledge gained from injecting sorbents and micronized coal into well mixed combustion gases with significant improvement in particulate retention time, should serve well the goals of an in-furnace multi-pollutant reduction technology; that of reducing back-end cleanup costs on a wide variety of pollutants, on a cost per ton basis, by first accomplishing significant in-furnace reductions of all pollutants.

  9. How molecular should your molecular model be? On the level of molecular detail required to simulate biological networks in systems and synthetic biology.

    Science.gov (United States)

    Gonze, Didier; Abou-Jaoudé, Wassim; Ouattara, Djomangan Adama; Halloy, José

    2011-01-01

    The recent advance of genetic studies and the rapid accumulation of molecular data, together with the increasing performance of computers, led researchers to design more and more detailed mathematical models of biological systems. Many modeling approaches rely on ordinary differential equations (ODE) which are based on standard enzyme kinetics. Michaelis-Menten and Hill functions are indeed commonly used in dynamical models in systems and synthetic biology because they provide the necessary nonlinearity to make the dynamics nontrivial (i.e., limit-cycle oscillations or multistability). For most of the systems modeled, the actual molecular mechanism is unknown, and the enzyme equations should be regarded as phenomenological. In this chapter, we discuss the validity and accuracy of these approximations. In particular, we focus on the validity of the Michaelis-Menten function for open systems and on the use of Hill kinetics to describe transcription rates of regulated genes. Our discussion is illustrated by numerical simulations of prototype systems, including the Repressilator (a genetic oscillator) and the Toggle Switch model (a bistable system). We systematically compare the results obtained with the compact version (based on Michaelis-Menten and Hill functions) with its corresponding developed versions (based on "elementary" reaction steps and mass action laws). We also discuss the use of compact approaches to perform stochastic simulations (Gillespie algorithm). On the basis of these results, we argue that using compact models is suitable to model qualitatively biological systems.

  10. 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...

  11. Adiabatic bias molecular dynamics: A method to navigate the conformational space of complex molecular systems

    Science.gov (United States)

    Marchi, Massimo; Ballone, Pietro

    1999-02-01

    This study deals with a novel molecular simulation technique, named adiabatic bias molecular dynamics (MD), which provides a simple and reasonably inexpensive route to generate MD trajectories joining points in conformational space separated by activation barriers. Because of the judicious way the biasing potential is updated during the MD runs, the technique allows with some additional effort the computation of the free energy change experienced during the trajectory. The adiabatic bias method has been applied to a nontrivial problem: The unfolding of an atomistic model of lysozyme. Here, the radius of gyration (Rg) was used as a convenient reaction coordinate. For changes in Rg between 19.7 and 28 Å, we observe a net loss of the native tertiary structure of lysozyme. At the same time, secondary structure elements such as α-helices are retained although some of the original order is diminished. The calculated free energy profile for the unfolding transition shows a monotonous increase with Rg and depends crucially on the nonbonded cutoff used in the potential model.

  12. 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…

  13. The challenges for molecular nutrition research 4: the "nutritional systems biology level"

    NARCIS (Netherlands)

    Ommen, B. van; Cavallieri, D.; Roche, H.M.; Klein, U.I.; Daniel, H.

    2008-01-01

    Nutritional systems biology may be defined as the ultimate goal of molecular nutrition research, where all relevant aspects of regulation of metabolism in health and disease states at all levels of its complexity are taken into account to describe the molecular physiology of nutritional processes. T

  14. Teaching Applied Genetics and Molecular Biology to Agriculture Engineers. Application of the European Credit Transfer System

    Science.gov (United States)

    Weiss, J.; Egea-Cortines, M.

    2008-01-01

    We have been teaching applied molecular genetics to engineers and adapted the teaching methodology to the European Credit Transfer System. We teach core principles of genetics that are universal and form the conceptual basis of most molecular technologies. The course then teaches widely used techniques and finally shows how different techniques…

  15. 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…

  16. Molecular Iodine-Mediated Cyclization of Tethered Heteroatom-Containing Alkenyl or Alkynyl Systems

    Directory of Open Access Journals (Sweden)

    Malose Jack Mphahlele

    2009-11-01

    Full Text Available Molecular iodine has established itself as a readily available and easy-to-handle electrophilic and oxidizing reagent used in various organic transformations. In this review attention is focused on the use of molecular iodine in promoting cyclization (iodocyclization and cyclodehydroiodination of tethered heteroatom-containing alkenyl or alkynyl systems.

  17. Evolution of dust and molecular hydrogen in the Magellanic System

    CERN Document Server

    Yozin, Cameron

    2014-01-01

    We investigate the evolution of the interstellar medium (ISM) in self-consistent, chemodynamical simulations of the Magellanic Clouds (MCs) during their recent (z<0.3) past. An explicit modelling of dust and molecular hydrogen lifecycles enables the comparison of our models against the observed properties of the ISM, including elemental depletion from the gas-phase. Combining this model with a tidal-dominated paradigm for the formation for the Magellanic Stream and Bridge, we reproduce the age-metallicity relations, long gas depletion timescales, and presently observed dust and molecular hydrogen masses of the MCs to within their respective uncertainties. We find that these models' enrichment depends sensitively on the processing of dust within the ISM and the dynamical influence of external tides/stellar bars. The ratio of characteristic dust destruction timescales in our SMC and LMC models, a governing parameter of our models' evolution, is consistent with estimates based on observed supernova (SN) rates...

  18. 5G Ultra-Dense Cellular Networks

    OpenAIRE

    Ge, Xiaohu; Tu, Song; Mao, Guoqiang; Wang, Cheng-xiang; Han, Tao

    2015-01-01

    Traditional ultra-dense wireless networks are recommended as a complement for cellular networks and are deployed in partial areas, such as hotspot and indoor scenarios. Based on the massive multiple-input multi-output (MIMO) antennas and the millimeter wavecommunication technologies, the 5G ultra-dense cellular network is proposed to deploy in overall cellular scenarios. Moreover, a distribution network architecture is presented for 5G ultra-dense cellular networks. Furthermore, the backhaul ...

  19. Interference Coordination for Dense Wireless Networks

    DEFF Research Database (Denmark)

    Soret, Beatriz; Pedersen, Klaus I.; Jørgensen, Niels T.K.

    2015-01-01

    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 ...... simply react to an identified interference problem. As an example, we propose two algorithms to apply time domain and frequency domain small cell interference coordination in a DenseNet....

  20. HOW GOOD IS A DENSE SHOP SCHEDULE?

    Institute of Scientific and Technical Information of China (English)

    陈礴; 俞文(鱼此)

    2001-01-01

    In this paper, we study a class of simple and easy-to-construct shop schedules, known as dense schedules. We present tight bounds on the maximum deviation in makespan of dense flow-shop and job-shop schedules from their optimal ones. For dense open-shop schedules, we do the same for the special case of four machines and thus add a stronger supporting case for proving a standing conjecture.

  1. Modeling molecular hydrogen emission in M dwarf exoplanetary systems

    Science.gov (United States)

    Evonosky, William; France, Kevin; Kruczek, Nick E.; Youngblood, Allison; Measurements of the Ultraviolet Spectral Characteristics of Low-mass Exoplanet host Stars (MUSCLES)

    2017-01-01

    Exoplanets orbiting low-mass stars are prime candidates for atmospheric characterization due to their astronomical abundance and short orbital periods. These planets orbit stars that are often more active than main sequence solar-type stars. They are exposed to differing levels of ultraviolet radiation which can cause traditional “biosignature” gases to be generated abiotically, potentially causing false-positive identifications of life. We modeled the recently discovered molecular hydrogen emission in the ultraviolet spectra (1350 - 1650 Å) as arising from the stellar surface, excited by radiation generated in the upper chromosphere. The model was compared with observed hydrogen emission from the “Measurements of the Ultraviolet Spectral Characteristics of Low-mass Exoplanet host Stars” (MUSCLES) survey by conducting a grid search and implementing a chi-squared minimization routine. We considered only progressions from the [1, 4] and [1, 7] first excited electronic levels. Our modeling procedure varied the atomic hydrogen column density (in the chromosphere) as well as the photospheric molecular hydrogen column density and temperature. The model required as an input a reconstructed intrinsic Lyman α profile which served as the pumping radiation for the molecular hydrogen. We found that an atomic hydrogen column density of log10N(H I) = 14.13 ± 0.16 cm-2 represents a breaking point above which there is not enough Lyman α flux available to excite a significant molecular hydrogen population into the [1, 7] state. We also present H2 temperatures which may suggest that star spots on low mass stars persist longer, and encompass more area than star spots on solar-type stars.

  2. Weak links between fast mobility and local structure in molecular and atomic liquids

    CERN Document Server

    Bernini, S; Leporini, D

    2016-01-01

    We investigate by Molecular-Dynamics simulations the fast mobility - the rattling amplitude of the particles temporarily trapped by the cage of the neighbors - in mildly supercooled states of dense molecular (linear trimers) and atomic (binary mixtures) liquids. The mixture particles interact by the Lennard-Jones potential. The non-bonded particles of the molecular system are coupled by the more general Mie potential with variable We investigate by Molecular-Dynamics simulations the fast mobility - the rattling amplitude of the particles temporarily trapped by the cage of the neighbors - in mildly supercooled states of dense molecular (linear trimers) and atomic (binary mixtures) liquids. The mixture particles interact by the Lennard-Jones potential. The non-bonded particles of the molecular system are coupled by the more general Mie potential with variable repulsive and attractive exponents in a range which is characteristic of small $n$-alkanes and $n$-alcohols. Possible links between the fast mobility and ...

  3. The ionization fraction in dense clouds

    CERN Document Server

    De Boisanger, C B; Van Dishoeck, E F

    1995-01-01

    We present submillimeter observations of various molecular ions toward two dense clouds, NGC 2264 IRS1 and W 3 IRS5, in order to investigate their ionization fraction. Analysis of the line intensity ratios by the way of statistical equilibrium calculations allows determination of the physical parameters: n(H2)~(1-2)e6 cm-3 and T(kin)~50-100 K. Column densities and abundances are also derived. Together, the abundances of the observed ions provide a lower limit to the ionization fraction, which is (2-3)e-9 in both clouds. In order to better constrain the electron abundance, a simple chemical model is built which calculates the steady state abundances of the major positive ions, using the observed abundances wherever available. With reasonable assumptions, good agreement within a factor of two with the observations can be achieved. The calculated electron fraction is x(e)= (1.0-3.3)e-8 in the case of NGC 2264 and x(e)=(0.5-1.1)e-8 for W 3 IRS5. In the first case, the high abundance of N2H+ requires a rather high...

  4. 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)

  5. On the Evolution of the Dense Core Mass Function

    CERN Document Server

    Williams, Jonathan J Swift Jonathan P

    2008-01-01

    The mass distributions of dense cores in star-forming regions are measured to have a shape similar to the initial mass function of stars. This has been generally interpreted to mean that the constituent cores will form individual stars or stellar systems at a nearly constant star formation efficiency. This article presents a series of numerical experiments evolving distributions of dense cores into stars to quantify the effects of stellar multiplicity, global core fragmentation, and a varying star formation efficiency. We find that the different evolutionary schemes have an overall small effect on the shape of the resultant distribution of stars. Our results imply that at the current level of observational accuracy the comparison between the mass functions of dense cores and stars alone is insufficient to discern between different evolutionary models. Observations over a wide range of mass scales including the high or low-mass tails of these distributions have the largest potential for discerning between diff...

  6. 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.

  7. Dense Focal Plane Arrays for Pushbroom Satellite Radiometers

    DEFF Research Database (Denmark)

    Iupikov, O. A.; Ivashina, M. V.; Pontoppidan, K.

    2014-01-01

    Performance of a dense focal plane array feeding an offset toroidal reflector antenna system is studied and discussed in the context of a potential application in multi-beam radiometers for ocean surveillance. We present a preliminary design of the array feed for the 5-m diameter antenna at X...

  8. The JCMT Gould Belt Survey: Dense Core Clusters in Orion A

    CERN Document Server

    Lane, J; Johnstone, D; Mairs, S; Di Francesco, J; 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 {\\mu}m and 450 {\\mu}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.

  9. The JCMT Gould Belt Survey: Dense Core Clusters in Orion A

    Science.gov (United States)

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

    2016-12-01

    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 μm 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.

  10. HaerWuSu Dense Medium Washing System Shunt Adjusting Device Applications%重介浅槽洗选系统分流调整装置的研制与应用

    Institute of Scientific and Technical Information of China (English)

    秦平

    2011-01-01

    介绍了哈尔乌素露天煤矿选煤厂重介浅槽洗选工艺,针对该生产系统中重介质密度调整存在诸多问题,提出技术革新方案。设计了一套适合现场环境、空间使用要求的分流装置,对其工作原理、结构特点以及在生产实践过程中的应用和使用效果进行科学阐述。%this paper introduces open-pit coal WuSu Haer dense medium shallow groove wash process,according to the production systems exist heavy medium density adjusted can not control in effective limits,design of a suitable site environment,space requirements of the use of distributary equipment,its working principle,structural characteristics,in the production practice process application and use effects scientifically elaboration.

  11. NEW METHOD FOR CALCULATING MOLECULAR ORBITALS WITH APPLICATION TO CYCLIC SYSTEMS,

    Science.gov (United States)

    New method for calculating molecular orbitals with application to cyclic systems: Stud; of the quantum mechanical problem of an electron bound to a configuration of N overlapping potentials. Reprinted from ’The Physical Review ’.

  12. 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 ...

  13. 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 ...

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

    Science.gov (United States)

    Merindol, Rémi; Walther, Andreas

    2017-01-30

    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.

  15. Interactions of mercury with different molecular weight fractions of humic substances in aquatic systems.

    Digital Repository Service at National Institute of Oceanography (India)

    Chakraborty, P.; Yao, K.M.; Chennuri, K.; Vudamala, K.; Babu, P.V.R.

    Interactions of mercury (Hg) with different molecular weight fractions of humic substances (HS) play an important role in controlling distribution, diffusion, speciation, and bioavailability of Hg in natural systems. This study suggests that Hg...

  16. Optical and transport properties of complex molecular systems

    OpenAIRE

    2009-01-01

    Esta Tesis presenta el estudio de las propiedades ópticas y de transporte de sistemas de baja dimensionalidad a través de modelos de enlace fuerte. Nuestro trabajo se centra en dos tipos de sistemas: agregados moleculares lineales y moléculas de ADN.En los Capítulos 2, 3 y 4 se estudian las propiedades de localización de un Hamiltoniano de Frenkel desordenado unidimensional. El desorden se introduce en las energías de sitio y es correlacionado de largo alcance. Para correlaciones fuertes, se ...

  17. Controllable Optical Bistability in a Crystal of Molecular Magnets System

    Institute of Scientific and Technical Information of China (English)

    LIU Ji-Bing; LU Xin-You; HAO Xiang-Ying; SI Liu-Gang; YANG Xiao-Xue

    2008-01-01

    We investigate the formation of opticai bistability (OB) in a crystal of molecular magnets contained in a unidirectional ring cavity. The crystal is subjected to one de magnetic field and two (probe and coupling) ac resonant magnetic field. The results show that OB can be controlled efficiently by adjusting the intensity of the control field, the detuning of probe magnetic field and the cooperation parameter. Furthermore, within certain parameter range, the optical multistablity (OM) can also be observed in the crystal medium. This investigation can be used for designing new types of nonelectronic devices for realizing switching process.

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

    Science.gov (United States)

    2005-10-01

    Molecular Genetics Division, Ohio State University. For reporting purpose, the ’Smad2’ sign indicates a disabled copy of ’Smad2’ gene while the ’+’ sign...skeletal mass in third- and fourth-grade children : Effects of age, gender, ethnicity and body composition. Bone 20:73-78. 18. Thomas, T. and Burguera, B...strand buffer mix (250 mM Tris HCI (pH 8.3 at RT), 375 mM KCI, 15 mM MgCI, I ul of 0.1 M DTT and 1 ul of RNAse Out, recombinant RNAse inhibitor

  19. Radiative corrections and quantum gates in molecular systems

    CERN Document Server

    Huffenberger, Kevin M

    2004-01-01

    We propose a method for quantum information processing using molecules coupled to an external laser field. This utilizes molecular interactions, control of the external field and an effective energy shift of the doubly-excited state of two coupled molecules. Such a level shift has been seen in the two-photon resonance experiments recently reported in Ref. [1]. Here we show that this can be explained in terms of the QED Lamb shift. We quantify the performance of the proposed quantum logic gates in the presence of dissipative mechanisms. The unitary transformations required for performing one- and two-qubit operations can be implemented with present day technology.

  20. Charge Transport by Superexchange in Molecular Host-Guest Systems

    Science.gov (United States)

    Symalla, Franz; Friederich, Pascal; Massé, Andrea; Meded, Velimir; Coehoorn, Reinder; Bobbert, Peter; Wenzel, Wolfgang

    2016-12-01

    Charge transport in disordered organic semiconductors is generally described as a result of incoherent hopping between localized states. In this work, we focus on multicomponent emissive host-guest layers as used in organic light-emitting diodes (OLEDs), and show using multiscale ab initio based modeling that charge transport can be significantly enhanced by the coherent process of molecular superexchange. Superexchange increases the rate of emitter-to-emitter hopping, in particular if the emitter molecules act as relatively deep trap states, and allows for percolation path formation in charge transport at low guest concentrations.

  1. STAR FORMATION IN DENSE CLUSTERS

    Energy Technology Data Exchange (ETDEWEB)

    Myers, Philip C., E-mail: pmyers@cfa.harvard.edu [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States)

    2011-12-10

    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 {approx}1 Myr. The protostar accretion luminosity is typically less than its steady spherical value by a factor of {approx}2, consistent with models of episodic disk accretion.

  2. Star formation in dense clusters

    CERN Document Server

    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 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 luminosi...

  3. YJ19卷烟机紧头位置自动调整机构的改进%Improvement of Automatic Dense End Location Adjusting System in YJ19 Cigarette Maker

    Institute of Scientific and Technical Information of China (English)

    李少平; 范磊; 王秋领; 胡宏帅; 李浩亮; 孙二明; 巢珍

    2012-01-01

    The automatic dense end location monitoring system in YJ19 cigarette maker exists "skip" and "dwell" phenomena, which affects the reliability of the system and results in high rate of loose end cigarettes and low accuracy of cigarette weight control. In light of the principle of velocity compensation, the original adjusting device was improved by using a planet gear differential mechanism as its transmission mechanism. The results of application showed that: after improvement, the qualified rate of weight difference between cigarettes of inside and outside rows increased by 23.6 percentage points, the rate of loose end cigarette decreased by 0.3 percentage points, the amount of cut tobacco loss from cigarette end reduced by 1.84 mg/cig., and the precision and stability of the control system were effectively improved.%YJ19卷烟机原紧头跟踪系统调整机构采用的相位调节,在使用中存在“跳齿”、“卡死”等现象,影响紧头位置跟踪和自动调整的可靠性,造成烟支空头率高、烟支重量控制精度差等问题.为此,根据速度补偿原理,应用行星差动机构作为传动机构对原紧头自动调整装置进行了改进.应用效果表明,改进后里外排烟支重量差异合格率提高23.6百分点,烟支空头率降低0.30百分点,端部落丝量降低1.84 mg/支,有效提高了紧头自动控制系统的准确性和稳定性.

  4. Simulation of the initiation of detonation in an energetic molecular crystal

    Science.gov (United States)

    Tsai, D. H.; Trevino, S. F.

    1984-12-01

    A molecular dynamical study of the detonation process in a dense system is presented. The model is a filament of a molecular crystal capable of undergoing exothermic dissociation. When the model is heated at one end, dissociation reactions start at that end and propagate along the filament. The accompanying expansion of the heated region drives a shock wave into the filament, causing further reactions due to shock heating. The results thus obtained provide a molecular description of the initiation of detonation.

  5. Characterizing the Dense Gas in the Eagle and Pelican Pillars

    Science.gov (United States)

    Grand, Erin; Pound, M. W.; Mundy, L. G.

    2014-01-01

    We observed two regions with molecular pillars, the Eagle and the Pelican, in order to understand the morphology of dense gas in these structures. Molecular pillars are formed in HII regions at the boundary between ionized gas and molecular clouds through the effects of photoionization, ablation, and recombination. Two sets of models exist for the formation mechanism of the pillars: (1) the growth of radiative hydrodynamic instabilities and (2) shadowing of the ionization front due to clumps in the molecular cloud. We have CARMA observations of the two sources in HCN J=1-0, N2H+ J=1-0, HCO+ J=1-0 and CS J=2-1 with resolutions of 9x6’’ for the Eagle and 4x4’’ for the Pelican. The dense gas follows the structure outlined in the optical images and seen in CO emission, throughout the pillars, with an increase in emission in the heads of the pillars. The differencing morphologies among the molecules are consistent with typical photo-disassociation region behavior. The velocity field shows a distinct gradient from head-to-tail for the majority of the pillars. We find that the morphology and the kinematics of the pillars are consistent with the shadowing model.

  6. Molecular Cloning of Human Gene(s) Directing the Synthesis of Nervous System Cholinesterases

    Science.gov (United States)

    1987-09-01

    Report No. 4 If MOLECULAR CLONING OF O HUMAN GENE(S) DIRECTING qTHE SYNTHESIS OF NERVOUS SYSTEM CHOLINESTERASES cc Annual/Final Report 0 N November...62734A I734A875 IAl 451 MOLECULAR CLONING OF HUMAN GEME(S) DIRECTING THE SYNTHESIS OF NERVOUS SYSTEM CHOLINESTERASE 12. PERSONAL AUTHOR(S) Hermona Soreq...important roles in regulating the pace and mode of function of particular types of synapses. For example, molecular cloning of the nicotinic (44-46) and the

  7. A Survey of Dense Cores in the Orion B Cloud

    Science.gov (United States)

    Ikeda, Norio; Kitamura, Yoshimi; Sunada, Kazuyoshi

    2009-02-01

    We have carried out an H13CO+(J = 1 - 0) core survey in a large area of 1 deg2, covering most of the dense region in the Orion B molecular cloud, using the Nobeyama 45 m radio telescope with the 25-BEam Array Receiver System. We cataloged 151 dense cores using the clumpfind method. The cores have mean radius, velocity width, and mass of 0.10 ± 0.02 pc, 0.53 ± 0.15 km s-1, and 8.1 ± 6.4 M sun, respectively, which are very similar to those in the Orion A cloud. We examined the spatial relation between our H13CO+ cores and the 850 μm cores observed by Johnstone and colleagues in 2001 and 2006, and found that there are two types of spatial relationships: H13CO+ cores with and without the 850 μm cores. Since the mean density of the 850 μm cores is higher than that of the H13CO+ cores, we can interpret the H13CO+ cores with 850 μm cores as being more centrally concentrated and hence more evolved, compared with those without. Considering the relationship between the masses of the H13CO+ and 850 μm cores, we estimate the 850 μm core mass function (CMF) using the H13CO+ CMF through the generalization of the confusion model proposed by Ikeda and colleagues in 2007. Our predicted 850 μm CMF is found to be quite consistent with that directly derived by Johnstone and colleagues. Furthermore, we predict the initial mass function (IMF) by the generalized confusion model assuming a star formation efficiency of 40% for the H13CO+ cores, and found that our predicted IMF is consistent with the Galactic field-averaged IMF within uncertainties. This agreement may indicate that the origin of the IMF goes back to the cloud structures with densities of less than 104 cm-3.

  8. On a strong dense periodicity property of shifts of finite type

    Energy Technology Data Exchange (ETDEWEB)

    Dzul-Kifli, Syahida Che; Al-Muttairi, Hassan [School of Mathematical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (Malaysia)

    2015-10-22

    There are various definitions of chaotic dynamical systems. The most utilized definition of chaos is Devaney chaos which isolates three components as being the essential features of chaos; transitivity, dense periodic points and sensitive dependence on initial conditions. In this paper, we focus on a strong dense periodicity property i.e. the set of points with prime period at least n is dense for each n. On shift of finite type over two symbols Σ{sub 2}, we show that the strong dense periodicity property implies another strong chaotic notions; locally everywhere onto (also called exact) and totally transitive.

  9. Heavy meson production in hot dense matter

    NARCIS (Netherlands)

    Tolos, Laura; Gamermann, Daniel; Garcia-Recio, Carmen; Molina, Raquel; Nieves, Juan; Oset, Eulogio; Ramos, Angels; Nieves, JM; Oset, E; Vacas, MJV

    2010-01-01

    The properties of charmed mesons in dense matter are studied using a unitary coupled-channel approach in the nuclear medium which takes into account Pauli-blocking effects and meson self-energies in a self-consistent manner. We obtain the open-charm meson spectral functions in this dense nuclear env

  10. Finding dense locations in indoor tracking data

    DEFF Research Database (Denmark)

    Ahmed, Tanvir; Pedersen, Torben Bach; Lu, Hua

    2014-01-01

    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 mode...

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

    Science.gov (United States)

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

    2014-11-18

    CONSPECTUS: In chemical and biological systems, various interactions that govern the chemical and physical properties of molecules, assembling phenomena, and electronic transport properties compete and control the microscopic structure of materials. The well-controlled manipulation of each component can allow researchers to design receptors or sensors, new molecular architectures, structures with novel morphology, and functional molecules or devices. In this Account, we describe the structures and electronic and spintronic properties of π-molecular systems that are important for controlling the architecture of a variety of carbon-based systems. Although DFT is an important tool for describing molecular interactions, the inability of DFT to accurately represent dispersion interactions has made it difficult to properly describe π-interactions. However, the recently developed dispersion corrections for DFT have allowed us to include these dispersion interactions cost-effectively. We have investigated noncovalent interactions of various π-systems including aromatic-π, aliphatic-π, and non-π systems based on dispersion-corrected DFT (DFT-D). In addition, we have addressed the validity of DFT-D compared with the complete basis set (CBS) limit values of coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)] and Møller-Plesset second order perturbation theory (MP2). The DFT-D methods are still unable to predict the correct ordering in binding energies within the benzene dimer and the cyclohexane dimer. Nevertheless, the overall DFT-D predicted binding energies are in reasonable agreement with the CCSD(T) results. In most cases, results using the B97-D3 method closely reproduce the CCSD(T) results with the optimized energy-fitting parameters. On the other hand, vdW-DF2 and PBE0-TS methods estimate the dispersion energies from the calculated electron density. In these approximations, the interaction energies around the equilibrium

  12. 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.

  13. Classical molecular simulations of complex industrially-important systems on the Intel Paragon

    Energy Technology Data Exchange (ETDEWEB)

    Cochran, H.D.; LoCascio, P.F.; Cummings, P.T. [Univ. of Tennessee, Knoxville, TN (United States)

    1996-06-01

    Advances in parallel supercomputing now make possible molecular-based engineering and science calculations that will soon revolutionize many technologies, such as those involving polymers and those involving aqueous electrolytes. We have developed a suite of message-passing codes for classical molecular simulation of such complex fluids and amorphous materials and have completed a number of demonstration calculations of problems of scientific and technological importance with each. In this overview paper we will outline the techniques for classical molecular simulation of these industrially-important systems on the Inter Paragon and we will summarize some of the important scientific and technical results of the varied applications, including the following: (1) Parallel codes for quatemion dynamics using techniques for handling long-range Coulombic forces allow study of ion pairing in supercritical aqueous electrolyte solutions. Ion pairing lies at the heart of technological problems with corrosion and solids deposition in industrial processes utilizing high temperature water. (2) Non-equilibrium, multiple time step molecular dynamics lets us investigate the rheology of molecular fluids. Such calculations enable the molecular-based design of new synthetic lubricants of importance in the automotive engines of the future. (3) Chain molecule Monte Carlo simulations in the Gibbs ensemble now permit calculation of phase equilibrium of long-chain molecular systems. With complementary equilibrium molecular dynamics (with multiple time steps) we have been able to gain fundamental insight into the technologically-important problem of liquid-liquid phase separation in polymer blends.

  14. 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

    Molecular junctions are promising candidates for thermoelectric devices due to the potential to tune the electronic and thermal transport properties. However, a high figure of merit is hard to achieve, without reducing the phononic contribution to thermal conductance. Here, we propose a strategy...... 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...... molecular junction. Phonon transmission of pi-stacked systems is largely attenuated in the whole frequency range, and the remaining transmission occurs mainly below 5 THz, where out-of-plane channels dominate. The figure of merit (ZT) of the pi-stacked molecular junction is dramatically enhanced because...

  15. Molecular techniques in the diagnosis of deep and systemic mycosis.

    Science.gov (United States)

    Springer, Jan; Einsele, Hermann; Loeffler, Juergen

    2012-01-01

    Making an early and sensitive diagnosis of invasive fungal infections in high-risk patients is mandatory, because it has major consequences on the effectiveness of antifungal therapy. Molecular assays have the potential to become the cornerstone of diagnosis, allowing for rapid, reliable detection of minute amounts of fungal DNA in various specimens at a low cost. PCR is gaining popularity as the platforms become more automated and commercially available; however, further studies are needed to explore the diagnostic value in patient subgroups (ie, children) and to define whether the underlying disease or the use of antifungal prophylaxis may influence assay results. Individualized management of high-risk patients would be desirable to integrate preemptive therapy strategies, and individual host and genetic factors. Pharmacological and epidemiological considerations should also be evaluated.

  16. System among the corticosteroids: specificity and molecular dynamics

    Science.gov (United States)

    Brookes, Jennifer C.; Galigniana, Mario D.; Harker, Anthony H.; Stoneham, A. Marshall; Vinson, Gavin P.

    2012-01-01

    Understanding how structural features determine specific biological activities has often proved elusive. With over 161 000 steroid structures described, an algorithm able to predict activity from structural attributes would provide manifest benefits. Molecular simulations of a range of 35 corticosteroids show striking correlations between conformational mobility and biological specificity. Thus steroid ring A is important for glucocorticoid action, and is rigid in the most specific (and potent) examples, such as dexamethasone. By contrast, ring C conformation is important for the mineralocorticoids, and is rigid in aldosterone. Other steroids that are less specific, or have mixed functions, or none at all, are more flexible. One unexpected example is 11-deoxycorticosterone, which the methods predict (and our activity studies confirm) is not only a specific mineralocorticoid, but also has significant glucocorticoid activity. These methods may guide the design of new corticosteroid agonists and antagonists. They will also have application in other examples of ligand–receptor interactions. PMID:21613285

  17. 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...... an improved stability with a factor of , but the overhead of computer time is a factor of at least two. The conclusion is that the second-order “Verlet”-algorithm, most commonly used in MD, is superior. It gives the exact dynamics within the limit of the asymptotic expansion and this limit can be estimated...

  18. Bulk superconductivity at 38 K in a molecular system.

    Science.gov (United States)

    Ganin, Alexey Y; Takabayashi, Yasuhiro; Khimyak, Yaroslav Z; Margadonna, Serena; Tamai, Anna; Rosseinsky, Matthew J; Prassides, Kosmas

    2008-05-01

    C(60)-based solids are archetypal molecular superconductors with transition temperatures (Tc) as high as 33 K (refs 2-4). Tc of face-centred-cubic (f.c.c.) A(3)C(60) (A=alkali metal) increases monotonically with inter C(60) separation, which is controlled by the A(+) cation size. As Cs(+) is the largest such ion, Cs(3)C(60) is a key material in this family. Previous studies revealing trace superconductivity in Cs(x)C(60) materials have not identified the structure or composition of the superconducting phase owing to extremely small shielding fractions and low crystallinity. Here, we show that superconducting Cs(3)C(60) can be reproducibly isolated by solvent-controlled synthesis and has the highest Tc of any molecular material at 38 K. In contrast to other A(3)C(60) materials, two distinct cubic Cs(3)C(60) structures are accessible. Although f.c.c. Cs(3)C(60) can be synthesized, the superconducting phase has the A15 structure based uniquely among fullerides on body-centred-cubic packing. Application of hydrostatic pressure controllably tunes A15 Cs(3)C(60) from insulating at ambient pressure to superconducting without crystal structure change and reveals a broad maximum in Tc at approximately 7 kbar. We attribute the observed Tc maximum as a function of inter C(60)separation--unprecedented in fullerides but reminiscent of the atom-based cuprate superconductors--to the role of strong electronic correlations near the metal-insulator transition onset.

  19. Including Quantum Effects in the Dynamics of Complex (i.e., Large)Molecular Systems

    Energy Technology Data Exchange (ETDEWEB)

    Miller, William H.

    2006-04-27

    The development in the 1950's and 60's of crossed molecular beam methods for studying chemical reactions at the single-collision molecular level stimulated the need and desire for theoretical methods to describe these and other dynamical processes in molecular systems. Chemical dynamics theory has made great strides in the ensuing decades, so that methods are now available for treating the quantum dynamics of small molecular systems essentially completely. For the large molecular systems that are of so much interest nowadays (e.g. chemical reactions in solution, in clusters, in nano-structures, in biological systems, etc.), however, the only generally available theoretical approach is classical molecular dynamics (MD) simulations. Much effort is currently being devoted to the development of approaches for describing the quantum dynamics of these complex systems. This paper reviews some of these approaches, especially the use of semiclassical approximations for adding quantum effects to classical MD simulations, also showing some new versions that should make these semiclassical approaches even more practical and accurate.

  20. Development of ocular drug delivery systems using molecularly imprinted soft contact lenses.

    Science.gov (United States)

    Tashakori-Sabzevar, Faezeh; Mohajeri, Seyed Ahmad

    2015-05-01

    Recently, significant advances have been made in order to optimize drug delivery to ocular tissues. The main problems in ocular drug delivery are poor bioavailability and uncontrollable drug delivery of conventional ophthalmic preparations (e.g. eye drops). Hydrogels have been investigated since 1965 as new ocular drug delivery systems. Increase of hydrogel loading capacity, optimization of drug residence time on the ocular surface and biocompatibility with the eye tissue has been the main focus of previous studies. Molecular imprinting technology provided the opportunity to fulfill the above-mentioned objectives. Molecularly imprinted soft contact lenses (SCLs) have high potentials as novel drug delivery systems for the treatment of eye disorders. This technique is used for the preparation of polymers with specific binding sites for a template molecule. Previous studies indicated that molecular imprinting technology could be successfully applied for the preparation of SCLs as ocular drug delivery systems. Previous research, particularly in vivo studies, demonstrated that molecular imprinting is a versatile and effective method in optimizing the drug release behavior and enhancing the loading capacity of SCLs as new ocular drug delivery systems. This review highlights various potentials of molecularly imprinted contact lenses in enhancing the drug-loading capacity and controlling the drug release, compared to other ocular drug delivery systems. We have also studied the effects of contributing factors such as the type of comonomer, template/functional monomer molar ratio, crosslinker concentration in drug-loading capacity, and the release properties of molecularly imprinted hydrogels.

  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. Parameter estimation method for improper fractional models and its application to molecular biological systems.

    Science.gov (United States)

    Tian, Li-Ping; Liu, Lizhi; Wu, Fang-Xiang

    2010-01-01

    Derived from biochemical principles, molecular biological systems can be described by a group of differential equations. Generally these differential equations contain fractional functions plus polynomials (which we call improper fractional model) as reaction rates. As a result, molecular biological systems are nonlinear in both parameters and states. It is well known that it is challenging to estimate parameters nonlinear in a model. However, in fractional functions both the denominator and numerator are linear in the parameters while polynomials are also linear in parameters. Based on this observation, we develop an iterative linear least squares method for estimating parameters in biological systems modeled by improper fractional functions. The basic idea is to transfer optimizing a nonlinear least squares objective function into iteratively solving a sequence of linear least squares problems. The developed method is applied to the estimation of parameters in a metabolism system. The simulation results show the superior performance of the proposed method for estimating parameters in such molecular biological systems.

  3. Aspectos moleculares do Sistema Sangüíneo ABO Molecular aspects of ABO Blood Group System

    Directory of Open Access Journals (Sweden)

    Ana Carla Batissoco

    2003-03-01

    Full Text Available O sistema ABO é o mais importante grupo sangüíneo na medicina transfusional. O gene ABO codifica as glicosiltransferases responsáveis pela transferência dos resíduos específicos de açúcar, GalNaca1-3 e Gala 1-3, ao substrato H e os convertem ao antígeno A ou B respectivamente. A estrutura do DNA dos três principais alelos do sistema ABO, A¹, B e O foi primeiramente descrita em 1990. Os avanços da genética molecular permitiram o entendimento da base molecular dos genes ABO e o conhecimento do polimorfismo dos alelos comuns a esse locus. Essa revisão tem como objetivo o estudo dos alelos variantes desse sistema, assim como a compreensão das mutações, deleções ou rearranjo de genes responsáveis pela ocorrência de alguns dos subgrupos do sistema ABO. As técnicas mais comumente utilizadas para a genotipagem ABO também são avaliadas, bem como suas vantagens e limitações.The ABO blood group is the most important blood group system in transfusion medicine. Antigens of the ABO system consist of A or B carbohydrate structure carried on the substrate H antigen The ABO gene is responsible for encoding for glycosyltransferases A or B that defines which specific carbohydrate is added to the end of H substance oligosaccharide chains, GalNacalpha1-3 and Galalpha1-3, respectively. The DNA structure of the three major alleles of the human blood group ABO system, A¹ and B, was first described in 1990. Advances of molecular genetics have allowed understanding of the molecular basis of the ABO blood group system and the knowledge of the common alleles polymorphisms of this locus. This review article has the purpose of describing the variants of these alleles and the underlying mutations, deletions or rearrangement of the genes responsible for the occurrence of ABO subgroups and O transferases inactivation. Finally, various methods available for ABO genotyping are also evaluated, as well as its advantages and limitations.

  4. Modeling of molecular photocells: Application to two-level photovoltaic system with electron-hole interaction.

    Science.gov (United States)

    Nemati Aram, Tahereh; Anghel-Vasilescu, Petrutza; Asgari, Asghar; Ernzerhof, Matthias; Mayou, Didier

    2016-09-28

    We present a novel simple model to describe molecular photocells where the energy conversion process takes place by a single molecular donor-acceptor complex attached to electrodes. By applying quantum scattering theory, an open quantum system method, the coherent molecular photocell is described by a wave function. We analyze photon absorption, energy conversion, and quantum yield of a molecular photocell by considering the effects of electron-hole interaction and non-radiative recombination. We model the exciton creation, dissociation, and subsequent effects on quantum yield in the energy domain. We find that depending on the photocell structure, the electron-hole interaction can normally decrease or abnormally increase the cell efficiency. The proposed model helps to understand the mechanisms of molecular photocells, and it can be used to optimize their yield.

  5. 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.

  6. The molecular identity of the mitochondrial Ca2+ sequestration system.

    Science.gov (United States)

    Starkov, Anatoly A

    2010-09-01

    There is ample evidence to suggest that a dramatic decrease in mitochondrial Ca(2+) retention may contribute to the cell death associated with stroke, excitotoxicity, ischemia and reperfusion, and neurodegenerative diseases. Mitochondria from all studied tissues can accumulate and store Ca(2+) , but the maximum Ca(2+) storage capacity varies widely and exhibits striking tissue specificity. There is currently no explanation for this fact. Precipitation of Ca(2+) and phosphate in the mitochondrial matrix has been suggested to be the major form of storage of accumulated Ca(2+) in mitochondria. How this precipitate is formed is not known. The molecular identity of almost all proteins involved in Ca(2+) transport, storage and formation of the permeability transition pore is also unknown. This review summarizes studies aimed at identifying these proteins, and describes the properties of a known mitochondrial protein that may be involved in Ca(2+) transport and the structure of the permeability transition pore. © 2010 The Author Journal compilation © 2010 FEBS.

  7. Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems.

    Science.gov (United States)

    Chiu, Matt; Herbordt, Martin C

    2010-11-01

    The acceleration of molecular dynamics (MD) simulations using high-performance reconfigurable computing (HPRC) has been much studied. Given the intense competition from multicore and GPUs, there is now a question whether MD on HPRC can be competitive. We concentrate here on the MD kernel computation: determining the short-range force between particle pairs. In one part of the study, we systematically explore the design space of the force pipeline with respect to arithmetic algorithm, arithmetic mode, precision, and various other optimizations. We examine simplifications and find that some have little effect on simulation quality. In the other part, we present the first FPGA study of the filtering of particle pairs with nearly zero mutual force, a standard optimization in MD codes. There are several innovations, including a novel partitioning of the particle space, and new methods for filtering and mapping work onto the pipelines. As a consequence, highly efficient filtering can be implemented with only a small fraction of the FPGA's resources. Overall, we find that, for an Altera Stratix-III EP3ES260, 8 force pipelines running at nearly 200 MHz can fit on the FPGA, and that they can perform at 95% efficiency. This results in an 80-fold per core speed-up for the short-range force, which is likely to make FPGAs highly competitive for MD.

  8. Theory and simulation of strong correlations in quantum Coulomb systems

    CERN Document Server

    Bonitz, M; Filinov, A V; Golubnychiy, V O; Kremp, D; Gericke, D O; Murillo, M S; Filinov, V S; Fortov, V; Hoyer, W; Koch, S W

    2003-01-01

    Strong correlations in quantum Coulomb systems (QCS) are attracting increasing interest in many fields ranging from dense plasmas and semiconductors to metal clusters and ultracold trapped ions. Examples are bound states in dense plasmas (atoms, molecules, clusters) and semiconductors (excitons, trions, biexcitons) or Coulomb crystals. We present first-principle simulation results of these systems including path integral Monte Carlo simulations of the equilibrium behaviour of dense hydrogen and electron-hole plasmas and molecular dynamics and quantum kinetic theory simulations of the nonequilibrium properties of QCS. Finally, we critically assess potential and limitations of the various methods in their application to Coulomb systems.

  9. 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.

  10. Coherent control of non-resonant two-photon transition in molecular system

    Institute of Scientific and Technical Information of China (English)

    Zhang Hui; Zhang Shi-An; Wang Zu-Geng; Sun Zhen-Rong

    2010-01-01

    In this paper,we study theoretically and experimentally the coherent control of non-resonant two-photon transition in a molecular system (Perylene dissolved in chloroform solution) by shaping the femtosecond pulses with simple phase patterns (cosinusoidal and π phase step-function shape).The control efficiency of the two-photon transition probability is correlated with both the laser field and the molecular absorption bandwidth.Our results demonstrate that,the two-photon transition probability in a molecular system can be reduced but not completely eliminated by manipulating the laser field,and the control efficiency is minimal when the molecular absorption bandwidth is larger than twice the laser spectral bandwidth.

  11. 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.

  12. The type II secretion system: biogenesis, molecular architecture and mechanism.

    Science.gov (United States)

    Korotkov, Konstantin V; Sandkvist, Maria; Hol, Wim G J

    2012-04-02

    Many gram-negative bacteria use the sophisticated type II secretion system (T2SS) to translocate a wide range of proteins from the periplasm across the outer membrane. The inner-membrane platform of the T2SS is the nexus of the system and orchestrates the secretion process through its interactions with the periplasmic filamentous pseudopilus, the dodecameric outer-membrane complex and a cytoplasmic secretion ATPase. Here, recent structural and biochemical information is reviewed to describe our current knowledge of the biogenesis and architecture of the T2SS and its mechanism of action.

  13. Crystal structures and dynamical properties of dense CO2.

    Science.gov (United States)

    Yong, Xue; Liu, Hanyu; Wu, Min; Yao, Yansun; Tse, John S; Dias, Ranga; Yoo, Choong-Shik

    2016-10-04

    Structural polymorphism in dense carbon dioxide (CO2) has attracted significant attention in high-pressure physics and chemistry for the past two decades. Here, we have performed high-pressure experiments and first-principles theoretical calculations to investigate the stability, structure, and dynamical properties of dense CO2 We found evidence that CO2-V with the 4-coordinated extended structure can be quenched to ambient pressure below 200 K-the melting temperature of CO2-I. CO2-V is a fully coordinated structure formed from a molecular solid at high pressure and recovered at ambient pressure. Apart from confirming the metastability of CO2-V (I-42d) at ambient pressure at low temperature, results of ab initio molecular dynamics and metadynamics (MD) simulations provided insights into the transformation processes and structural relationship from the molecular to the extended phases. In addition, the simulation also predicted a phase V'(Pna21) in the stability region of CO2-V with a diffraction pattern similar to that previously assigned to the CO2-V (P212121) structure. Both CO2-V and -V' are predicted to be recoverable and hard with a Vicker hardness of ∼20 GPa. Significantly, MD simulations found that the CO2 in phase IV exhibits large-amplitude bending motions at finite temperatures and high pressures. This finding helps to explain the discrepancy between earlier predicted static structures and experiments. MD simulations clearly indicate temperature effects are critical to understanding the high-pressure behaviors of dense CO2 structures-highlighting the significance of chemical kinetics associated with the transformations.

  14. Quantitative Assessment of Molecular Dynamics Sampling for Flexible Systems.

    Science.gov (United States)

    Nemec, Mike; Hoffmann, Daniel

    2017-02-14

    Molecular dynamics (MD) simulation is a natural method for the study of flexible molecules but at the same time is limited by the large size of the conformational space of these molecules. We ask by how much the MD sampling quality for flexible molecules can be improved by two means: the use of diverse sets of trajectories starting from different initial conformations to detect deviations between samples and sampling with enhanced methods such as accelerated MD (aMD) or scaled MD (sMD) that distort the energy landscape in controlled ways. To this end, we test the effects of these approaches on MD simulations of two flexible biomolecules in aqueous solution, Met-Enkephalin (5 amino acids) and HIV-1 gp120 V3 (a cycle of 35 amino acids). We assess the convergence of the sampling quantitatively with known, extensive measures of cluster number Nc and cluster distribution entropy Sc and with two new quantities, conformational overlap Oconf and density overlap Odens, both conveniently ranging from 0 to 1. These new overlap measures quantify self-consistency of sampling in multitrajectory MD experiments, a necessary condition for converged sampling. A comprehensive assessment of sampling quality of MD experiments identifies the combination of diverse trajectory sets and aMD as the most efficient approach among those tested. However, analysis of Odens between conventional and aMD trajectories also reveals that we have not completely corrected aMD sampling for the distorted energy landscape. Moreover, for V3, the courses of Nc and Odens indicate that much higher resources than those generally invested today will probably be needed to achieve convergence. The comparative analysis also shows that conventional MD simulations with insufficient sampling can be easily misinterpreted as being converged.

  15. Development of design information for molecular-sieve type regenerative CO2-removal systems

    Science.gov (United States)

    Wright, R. M.; Ruder, J. M.; Dunn, V. B.; Hwang, K. C.

    1973-01-01

    Experimental and analytic studies were conducted with molecular sieve sorbents to provide basic design information, and to develop a system design technique for regenerable CO2-removal systems for manned spacecraft. Single sorbate equilibrium data were obtained over a wide range of conditions for CO2, water, nitrogen, and oxygen on several molecular sieve and silica gel sorbents. The coadsorption of CO2 with water preloads, and with oxygen and nitrogen was experimentally evaluated. Mass-transfer, and some limited heat-transfer performance evaluations were accomplished under representative operating conditions, including the coadsorption of CO2 and water. CO2-removal system performance prediction capability was derived.

  16. Structural aspects of molecular recognition in the immune system. Part II: Pattern recognition receptors

    OpenAIRE

    2014-01-01

    The vertebrate immune system uses pattern recognition receptors (PRRs) to detect a large variety of molecular signatures (pathogen-associated molecular patterns, PAMPs) from a broad range of different invading pathogens. The PAMPs range in size from relatively small molecules, to others of intermediate size such as bacterial lipopolysaccharide, lipopeptides, and oligosaccharides, to macromolecules such as viral DNA, RNA, and pathogen-derived proteins such as flagellin. Underlying this functio...

  17. Systems vaccinology : molecular signatures of immunity to Bordetella pertussis

    NARCIS (Netherlands)

    Raeven, R.H.M.

    2016-01-01

    The worldwide resurgence of whooping cough (pertussis), even in highly vaccinated populations, demands improved pertussis vaccines. In this thesis a systems vaccinology approach is applied to deepen knowledge of the immune responses evoked by different pertussis vaccines and compare this with a Bord

  18. Exp6-polar thermodynamics of dense supercritical water

    Energy Technology Data Exchange (ETDEWEB)

    Bastea, S; Fried, L E

    2007-12-13

    We introduce a simple polar fluid model for the thermodynamics of dense supercritical water based on a Buckingham (exp-6) core and point dipole representation of the water molecule. The proposed exp6-polar thermodynamics, based on ideas originally applied to dipolar hard spheres, performs very well when tested against molecular dynamics simulations. Comparisons of the model predictions with experimental data available for supercritical water yield excellent agreement for the shock Hugoniot, isotherms and sound speeds, and are also quite good for the self-diffusion constant and relative dielectric constant. We expect the present approach to be also useful for other small polar molecules and their mixtures.

  19. The Dense Gas in the Central Kiloparsec of NGC 6946

    CERN Document Server

    Levine, E S; Meijerink, R; Blitz, Leo

    2007-01-01

    We present observations of the HCN and HCO+ J=1-0 transitions in the center of the nearby spiral galaxy NGC 6946 made with the BIMA and CARMA interferometers. Using the BIMA SONG CO map, we investigate the change in the I_HCN/I_CO and I_ HCO/I_CO integrated intensity ratios as a function of radius in the central kiloparsec of the galaxy, and find that they are strongly concentrated at the center. We use the 2MASS K_S band image to find the stellar surface density, and then construct a map of the hydrostatic midplane pressure. We apply a PDR model to the observed I_HCN/I_HCO+ integrated intensity ratio to calculate the number density of molecular hydrogen in the dense gas tracer emitting region, and find that it is roughly constant at 10^5 cm^-3 across our map. We explore two hypotheses for the distribution of the dense gas. If the HCN and HCO+ emission comes from self-gravitating density peaks inside of a less dense gas distribution, there is a linear proportionality between the internal velocity dispersion o...

  20. Gas dynamics in Massive Dense Cores in Cygnus-X

    CERN Document Server

    Csengeri, T; Schneider, N; Motte, F; Dib, S

    2010-01-01

    We study the kinematic properties of dense gas surrounding massive protostars recognized by Bontemps et a. (2010) in a sample of five Massive Dense Cores in Cygnus-X. We investigate whether turbulent support plays a major role in stabilizing the core against fragmentation into Jeans-mass objects or alternatively, the observed kinematics could indicate a high level of dynamics. We present IRAM 30m single-dish (HCO+ and H13CO+) and IRAM PdBI high angular-resolution observations of dense gas tracers (H13CO+ and H13CN) to reveal the kinematics of molecular gas at scales from 0.03 to 0.1 pc. Radiative transfer modeling shows that H13CO+ is depleted within the envelopes of massive protostars and traces the bulk of material surrounding the protostars rather than their inner envelopes. H13CN shows a better correspondence with the peak of the continuum emission, possibly due to abundance anomalies and specific chemistry in the close vicinity of massive protostars. Analyzing the line-widths we show that the observed li...