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Sample records for chemically induced dynamic

  1. Chemical memory reactions induced bursting dynamics in gene expression.

    Science.gov (United States)

    Tian, Tianhai

    2013-01-01

    Memory is a ubiquitous phenomenon in biological systems in which the present system state is not entirely determined by the current conditions but also depends on the time evolutionary path of the system. Specifically, many memorial phenomena are characterized by chemical memory reactions that may fire under particular system conditions. These conditional chemical reactions contradict to the extant stochastic approaches for modeling chemical kinetics and have increasingly posed significant challenges to mathematical modeling and computer simulation. To tackle the challenge, I proposed a novel theory consisting of the memory chemical master equations and memory stochastic simulation algorithm. A stochastic model for single-gene expression was proposed to illustrate the key function of memory reactions in inducing bursting dynamics of gene expression that has been observed in experiments recently. The importance of memory reactions has been further validated by the stochastic model of the p53-MDM2 core module. Simulations showed that memory reactions is a major mechanism for realizing both sustained oscillations of p53 protein numbers in single cells and damped oscillations over a population of cells. These successful applications of the memory modeling framework suggested that this innovative theory is an effective and powerful tool to study memory process and conditional chemical reactions in a wide range of complex biological systems.

  2. Quantum measurement corrections to chemically induced dynamic nuclear polarization

    CERN Document Server

    Kominis, I K

    2013-01-01

    Chemically induced dynamic nuclear polarization has emerged as a universal signature of spin order in photosynthetic reaction centers. Such polarization, significantly enhanced above thermal equilibrium, is known to result from the nuclear spin sorting inherent in the radical pair mechanism underlying long-lived charge-separated states in photosynthetic reaction centers. We will here show that the recently understood fundamental quantum dynamics of radical-ion-pair reactions open up a new and completely unexpected venue towards obtaining CIDNP signals. The fundamental decoherence mechanism inherent in the recombination process of radical pairs is shown to produce nuclear spin polarizations on the order of $10^4$ times or more higher than thermal equilibrium values at low fields relevant to natural photosynthesis in earth's magnetic field. This opens up the possibility of a fundamentally new exploration of the biological significance of high nuclear polarizations in photosynthesis.

  3. Microchannel-induced change of chemical wave propagation dynamics: importance of ratio between the inlet and the channel sizes.

    Science.gov (United States)

    Nabika, Hideki; Sato, Mami; Unoura, Kei

    2013-01-07

    The ability to control chemical wave propagation dynamics could stimulate the science and technology of artificial and biological spatiotemporal oscillating phenomena. In contrast to the conventional chemical approaches to control the wave front dynamics, here we report a physical approach to tune the propagation dynamics under the same chemical conditions. By using well-designed microchannels with different channel widths and depths, the propagation velocity was successfully controlled based on two independent effects: (i) a transition in the proton diffusion mode and (ii) the formation of a slanted wave front. Numerical analysis yielded a simple relationship between the propagation velocity and the microchannel configuration, which offers a simple and general way of controlling chemical wave propagation.

  4. Elucidating collision induced dissociation products and reaction mechanisms of protonated uracil by coupling chemical dynamics simulations with tandem mass spectrometry experiments.

    Science.gov (United States)

    Molina, Estefanía Rossich; Ortiz, Daniel; Salpin, Jean-Yves; Spezia, Riccardo

    2015-12-01

    In this study we have coupled mixed quantum-classical (quantum mechanics/molecular mechanics) direct chemical dynamics simulations with electrospray ionization/tandem mass spectrometry experiments in order to achieve a deeper understanding of the fragmentation mechanisms occurring during the collision induced dissociation of gaseous protonated uracil. Using this approach, we were able to successfully characterize the fragmentation pathways corresponding to ammonia loss (m/z 96), water loss (m/z 95) and cyanic or isocyanic acid loss (m/z 70). Furthermore, we also performed experiments with isotopic labeling completing the fragmentation picture. Remarkably, fragmentation mechanisms obtained from chemical dynamics simulations are consistent with those deduced from isotopic labeling.

  5. Effect of sucrose on chemically and thermally induced unfolding of domain-I of human serum albumin: Solvation dynamics and fluorescence anisotropy study.

    Science.gov (United States)

    Yadav, Rajeev; Sengupta, Bhaswati; Sen, Pratik

    2016-04-01

    The present study is devoted to understand the effect of sucrose on the hydration dynamics and rotational relaxation dynamics within the domain-I of HSA during chemically as well as thermally induced unfolding. It has been observed that the average solvation time become slower in the presence of sucrose for the lower concentrations of GnHCl, however at higher concentrations of GnHCl the effect of sucrose is almost negligible. From the time resolved fluorescence anisotropy it has been observed that in the lower concentration region of GnHCl the sucrose induced stabilization is small as compared to the higher concentrations of GnHCl. We have concluded that the hydration dynamics plays an important role in the sucrose induced stabilization process at the low concentration region; whereas environmental restriction is responsible at the higher concentration of GnHCl. However, we have observed a negligible stabilizing effect of sucrose towards the temperature induced unfolding.

  6. Probing Chemical Dynamics at Surfaces

    Institute of Scientific and Technical Information of China (English)

    KLEYN, A.W.; KLEYN, A.W

    2001-01-01

    An account is given of recent progress concerning chemical reaction dynamics at surfaces. The goal is to elucidate the reaction dynamics at the molecular level, both as time and distance is concerned. The methods of study include molecular beam scattering, scanning tunnelling microscopy, and (femtosecond) laser spectroscopy. Systems studied include elementary interactions of NO, CO, and O2 at single crystal metal surfaces.

  7. Dynamics of 3D representation of interfaces in UV-induced chemical vapor deposition: experiments, modeling, and simulation for silicon nitride thin layers

    Science.gov (United States)

    Flicstein, Jean; Guillonneau, E.; Marquez, Jose; How Kee Chun, L. S.; Maisonneuve, D.; David, C.; Wang, Zh. Z.; Palmier, Jean F.; Courant, J. L.

    2001-06-01

    We study the surface dynamics of silicon nitride films deposited by UV-induced low pressure chemical vapor pressure. Atomic force microscopy measurements show that the surface reaches a scale invariant stationary state coherent wit the Kardar-Parisi-Zhang (KPZ) equation. Discrete geometry techniques are oriented to extra morphological characteristics of surface and bulk which corresponds to computer simulated photodeposit. This allows to determine the physical origin of KPZ scaling to be al ow value of the surface sticking probability, and connected to the surface concentration of activate charged centers, which permits to start the evaluation of the Monte Carlo-molecular dynamics simulator.

  8. Chemically Induced Dynamic Nuclear Polarization during the Thermolysis of Alkoxyamines: A New Approach to Detect the Occurrence of H-Transfer Reactions

    Directory of Open Access Journals (Sweden)

    Elena Bagryanskaya

    2010-09-01

    Full Text Available Thermal decomposition of alkoxyamines in the presence of scavengers was found to proceed with the formation of chemically induced nuclear polarization detected by 1H NMR. The distinctive Chemically Induced Dynamic Nuclear Polarization (CIDNP features were studied using the example of three alkoxyamines: 4-nitrophenyl 2-(2,2,6,6-tetramethylpiperidin-1-yloxy-2-methylpropanoate (1a, 4-nitrophenyl 2-(2,2-diphenyl-3-phenylimino-2,3-dihydroindol-1-yloxy-2-methylpropanoate (2a and 4-nitrophenyl 2-(2,2,5,5-tetramethyl-4-phenyl-2H-imidazol-1-oxy-2-methylpropanoate (3a in the presence of PhSH. The analysis of CIDNP signs of methacrylate protons allows us to conclude on the occurrence of hydrogen atom transfer reaction in geminate radical pair formed in alkoxyamine thermolysis. Thus, CIDNP is a fast and sensitive method to detect the occurrence of intra/intermolecular hydrogen transfer in alkoxyamine thermolysis.

  9. Kinematically complete chemical reaction dynamics

    Science.gov (United States)

    Trippel, S.; Stei, M.; Otto, R.; Hlavenka, P.; Mikosch, J.; Eichhorn, C.; Lourderaj, U.; Zhang, J. X.; Hase, W. L.; Weidemüller, M.; Wester, R.

    2009-11-01

    Kinematically complete studies of molecular reactions offer an unprecedented level of insight into the dynamics and the different mechanisms by which chemical reactions occur. We have developed a scheme to study ion-molecule reactions by velocity map imaging at very low collision energies. Results for the elementary nucleophilic substitution (SN2) reaction Cl- + CH3I → ClCH3 + I- are presented and compared to high-level direct dynamics trajectory calculations. Furthermore, an improved design of the crossed-beam imaging spectrometer with full three-dimensional measurement capabilities is discussed and characterization measurements using photoionization of NH3 and photodissociation of CH3I are presented.

  10. Nanomotor dynamics in a chemically oscillating medium

    Science.gov (United States)

    Robertson, Bryan; Kapral, Raymond

    2015-04-01

    Synthetic nanomotors powered by chemical reactions have potential uses as cargo transport vehicles in both in vivo and in vitro applications. In many situations, motors will have to operate in out-of-equilibrium complex chemically reacting media, which supply fuel to the motors and remove the products they produce. Using molecular simulation and mean-field theory, this paper describes some of the new features that arise when a chemically powered nanomotor, operating through a diffusiophoretic mechanism, moves in an environment that supports an oscillatory chemical reaction network. It is shown how oscillations in the concentrations in chemical species in the environment give rise to oscillatory motor dynamics. More importantly, since the catalytic reactions on the motor that are responsible for its propulsion couple to the bulk phase reaction network, the motor can change its local environment. This process can give rise to distinctive spatiotemporal structures in reaction-diffusion media that occur as a result of active motor motion. Such locally induced nonequilibrium structure will play an important role in applications that involve motor dynamics in complex chemical media.

  11. Nanomotor dynamics in a chemically oscillating medium

    Energy Technology Data Exchange (ETDEWEB)

    Robertson, Bryan, E-mail: bryan.robertson@mail.utoronto.ca; Kapral, Raymond, E-mail: rkapral@chem.utoronto.ca [Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 (Canada)

    2015-04-21

    Synthetic nanomotors powered by chemical reactions have potential uses as cargo transport vehicles in both in vivo and in vitro applications. In many situations, motors will have to operate in out-of-equilibrium complex chemically reacting media, which supply fuel to the motors and remove the products they produce. Using molecular simulation and mean-field theory, this paper describes some of the new features that arise when a chemically powered nanomotor, operating through a diffusiophoretic mechanism, moves in an environment that supports an oscillatory chemical reaction network. It is shown how oscillations in the concentrations in chemical species in the environment give rise to oscillatory motor dynamics. More importantly, since the catalytic reactions on the motor that are responsible for its propulsion couple to the bulk phase reaction network, the motor can change its local environment. This process can give rise to distinctive spatiotemporal structures in reaction-diffusion media that occur as a result of active motor motion. Such locally induced nonequilibrium structure will play an important role in applications that involve motor dynamics in complex chemical media.

  12. Synchronization Dynamics of Coupled Chemical Oscillators

    Science.gov (United States)

    Tompkins, Nathan

    The synchronization dynamics of complex networks have been extensively studied over the past few decades due to their ubiquity in the natural world. Prominent examples include cardiac rhythms, circadian rhythms, the flashing of fireflies, predator/prey population dynamics, mammalian gait, human applause, pendulum clocks, the electrical grid, and of the course the brain. Detailed experiments have been done to map the topology of many of these systems and significant advances have been made to describe the mathematics of these networks. Compared to these bodies of work relatively little has been done to directly test the role of topology in the synchronization dynamics of coupled oscillators. This Dissertation develops technology to examine the dynamics due to topology within networks of discrete oscillatory components. The oscillatory system used here consists of the photo-inhibitable Belousov-Zhabotinsky (BZ) reaction water-in-oil emulsion where the oscillatory drops are diffusively coupled to one another and the topology is defined by the geometry of the diffusive connections. Ring networks are created from a close-packed 2D array of drops using the Programmable Illumination Microscope (PIM) in order to test Turing's theory of morphogenesis directly. Further technology is developed to create custom planar networks of BZ drops in more complicated topologies which can be individually perturbed using illumination from the PIM. The work presented here establishes the validity of using the BZ emulsion system with a PIM to study the topology induced effects on the synchronization dynamics of coupled chemical oscillators, tests the successes and limitations of Turing's theory of morphogenesis, and develops new technology to further probe the effects of network topology on a system of coupled oscillators. Finally, this Dissertation concludes by describing ongoing experiments which utilize this new technology to examine topology induced transitions of synchronization

  13. Nonlinear Chemical Dynamics and Synchronization

    Science.gov (United States)

    Li, Ning

    Alan Turing's work on morphogenesis, more than half a century ago, continues to motivate and inspire theoretical and experimental biologists even today. That said, there are very few experimental systems for which Turing's theory is applicable. In this thesis we present an experimental reaction-diffusion system ideally suited for testing Turing's ideas in synthetic "cells" consisting of microfluidically produced surfactant-stabilized emulsions in which droplets containing the Belousov-Zhabotinsky (BZ) oscillatory chemical reactants are dispersed in oil. The BZ reaction has become the prototype of nonlinear dynamics in chemistry and a preferred system for exploring the behavior of coupled nonlinear oscillators. Our system consists of a surfactant stabilized monodisperse emulsion of drops of aqueous BZ solution dispersed in a continuous phase of oil. In contrast to biology, here the chemistry is understood, rate constants are measured and interdrop coupling is purely diffusive. We explore a large set of parameters through control of rate constants, drop size, spacing, and spatial arrangement of the drops in lines and rings in one-dimension (1D) and hexagonal arrays in two-dimensions (2D). The Turing model is regarded as a metaphor for morphogenesis in biology but not for prediction. Here, we develop a quantitative and falsifiable reaction-diffusion model that we experimentally test with synthetic cells. We quantitatively establish the extent to which the Turing model in 1D describes both stationary pattern formation and temporal synchronization of chemical oscillators via reaction-diffusion and in 2D demonstrate that chemical morphogenesis drives physical differentiation in synthetic cells.

  14. Level crossing analysis of chemically induced dynamic nuclear polarization: Towards a common description of liquid-state and solid-state cases

    Science.gov (United States)

    Sosnovsky, Denis V.; Jeschke, Gunnar; Matysik, Jörg; Vieth, Hans-Martin; Ivanov, Konstantin L.

    2016-04-01

    Chemically Induced Dynamic Nuclear Polarization (CIDNP) is an efficient method of creating non-equilibrium polarization of nuclear spins by using chemical reactions, which have radical pairs as intermediates. The CIDNP effect originates from (i) electron spin-selective recombination of radical pairs and (ii) the dependence of the inter-system crossing rate in radical pairs on the state of magnetic nuclei. The CIDNP effect can be investigated by using Nuclear Magnetic Resonance (NMR) methods. The gain from CIDNP is then two-fold: it allows one to obtain considerable amplification of NMR signals; in addition, it provides a very useful tool for investigating elusive radicals and radical pairs. While the mechanisms of the CIDNP effect in liquids are well established and understood, detailed analysis of solid-state CIDNP mechanisms still remains challenging; likewise a common theoretical frame for the description of CIDNP in both solids and liquids is missing. Difficulties in understanding the spin dynamics that lead to the CIDNP effect in the solid-state case are caused by the anisotropy of spin interactions, which increase the complexity of spin evolution. In this work, we propose to analyze CIDNP in terms of level crossing phenomena, namely, to attribute features in the CIDNP magnetic field dependence to Level Crossings (LCs) and Level Anti-Crossings (LACs) in a radical pair. This approach allows one to describe liquid-state CIDNP; the same holds for the solid-state case where anisotropic interactions play a significant role in CIDNP formation. In solids, features arise predominantly from LACs, since in most cases anisotropic couplings result in perturbations, which turn LCs into LACs. We have interpreted the CIDNP mechanisms in terms of the LC/LAC concept. This consideration allows one to find analytical expressions for a wide magnetic field range, where several different mechanisms are operative; furthermore, the LAC description gives a way to determine CIDNP sign

  15. Level crossing analysis of chemically induced dynamic nuclear polarization: Towards a common description of liquid-state and solid-state cases.

    Science.gov (United States)

    Sosnovsky, Denis V; Jeschke, Gunnar; Matysik, Jörg; Vieth, Hans-Martin; Ivanov, Konstantin L

    2016-04-14

    Chemically Induced Dynamic Nuclear Polarization (CIDNP) is an efficient method of creating non-equilibrium polarization of nuclear spins by using chemical reactions, which have radical pairs as intermediates. The CIDNP effect originates from (i) electron spin-selective recombination of radical pairs and (ii) the dependence of the inter-system crossing rate in radical pairs on the state of magnetic nuclei. The CIDNP effect can be investigated by using Nuclear Magnetic Resonance (NMR) methods. The gain from CIDNP is then two-fold: it allows one to obtain considerable amplification of NMR signals; in addition, it provides a very useful tool for investigating elusive radicals and radical pairs. While the mechanisms of the CIDNP effect in liquids are well established and understood, detailed analysis of solid-state CIDNP mechanisms still remains challenging; likewise a common theoretical frame for the description of CIDNP in both solids and liquids is missing. Difficulties in understanding the spin dynamics that lead to the CIDNP effect in the solid-state case are caused by the anisotropy of spin interactions, which increase the complexity of spin evolution. In this work, we propose to analyze CIDNP in terms of level crossing phenomena, namely, to attribute features in the CIDNP magnetic field dependence to Level Crossings (LCs) and Level Anti-Crossings (LACs) in a radical pair. This approach allows one to describe liquid-state CIDNP; the same holds for the solid-state case where anisotropic interactions play a significant role in CIDNP formation. In solids, features arise predominantly from LACs, since in most cases anisotropic couplings result in perturbations, which turn LCs into LACs. We have interpreted the CIDNP mechanisms in terms of the LC/LAC concept. This consideration allows one to find analytical expressions for a wide magnetic field range, where several different mechanisms are operative; furthermore, the LAC description gives a way to determine CIDNP sign

  16. Gas-phase chemical dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Weston, R.E. Jr.; Sears, T.J.; Preses, J.M. [Brookhaven National Laboratory, Upton, NY (United States)

    1993-12-01

    Research in this program is directed towards the spectroscopy of small free radicals and reactive molecules and the state-to-state dynamics of gas phase collision, energy transfer, and photodissociation phenomena. Work on several systems is summarized here.

  17. Chemical kinetics and reaction dynamics

    CERN Document Server

    Houston, Paul L

    2006-01-01

    This text teaches the principles underlying modern chemical kinetics in a clear, direct fashion, using several examples to enhance basic understanding. It features solutions to selected problems, with separate sections and appendices that cover more technical applications.Each chapter is self-contained and features an introduction that identifies its basic goals, their significance, and a general plan for their achievement. This text's important aims are to demonstrate that the basic kinetic principles are essential to the solution of modern chemical problems, and to show how the underlying qu

  18. Glucans monomer-exchange dynamics as an open chemical network

    Energy Technology Data Exchange (ETDEWEB)

    Rao, Riccardo, E-mail: riccardo.rao@uni.lu; Esposito, Massimiliano, E-mail: massimiliano.esposito@uni.lu [Complex Systems and Statistical Mechanics, Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg (Luxembourg); Lacoste, David [Laboratoire de Physico-Chimie Théorique, UMR CNRS Gulliver 7083, ESPCI - 10 rue Vauquelin, F-75231 Paris (France)

    2015-12-28

    We describe the oligosaccharides-exchange dynamics performed by the so-called D-enzymes on polysaccharides. To mimic physiological conditions, we treat this process as an open chemical network by assuming some of the polymer concentrations fixed (chemostatting). We show that three different long-time behaviors may ensue: equilibrium states, nonequilibrium steady states, and continuous growth states. We dynamically and thermodynamically characterize these states and emphasize the crucial role of conservation laws in identifying the chemostatting conditions inducing them.

  19. Glucans monomer-exchange dynamics as an open chemical network

    CERN Document Server

    Rao, Riccardo; Esposito, Massimiliano

    2015-01-01

    We describe the oligosaccharides-exchange dynamics performed by so-called D-enzymes on polysaccharides. To mimic physiological conditions, we treat this process as an open chemical network by assuming some of the polymer concentrations fixed (chemostatting). We show that three different long-time behaviors may ensue: equilibrium states, nonequilibrium steady states, and continuous growth states. We dynamically and thermodynamically characterize these states and emphasize the crucial role of conservation laws in identifying the chemostatting conditions inducing them.

  20. Chemical Dynamics at the Advanced Light Source

    Energy Technology Data Exchange (ETDEWEB)

    Baer, T.; Berrah, N.; Fadley, C.; Moore, C.B.; Neumark, D.M.; Ng, C.Y.; Ruscic, B.; Smith, N.V.; Suits, A.G.; Wodtke, A.M.

    1999-02-02

    A day-long retreat was held January 15, 1999 to chart the future directions for chemical dynamics studies at the Advanced Light Source. This represents an important period for the Chemical Dynamics Beamline, as the hardware is well-developed, most of the initial experimental objectives have been realized and the mission is now to identify the future scientific priorities for the beamline and attract users of the highest caliber. To this end, we have developed a detailed scientific program for the near term; identified and prioritized the long range scientific opportunities, identified essential new hardware, and outlined an aggressive outreach program to involve the chemical physics community.

  1. GAS PHASE MOLECULAR DYNAMICS: HIGH-RESOLUTION SPECTROSCOPIC PROBES OF CHEMICAL DYNAMICS.

    Energy Technology Data Exchange (ETDEWEB)

    HALL, G.E.

    2006-05-30

    This research is carried out as part of the Gas Phase Molecular Dynamics group program in the Chemistry Department at Brookhaven National Laboratory. High-resolution spectroscopic tools are developed and applied to problems in chemical dynamics. Recent topics have included the state-resolved studies of collision-induced electronic energy transfer, dynamics of barrierless unimolecular reactions, and the kinetics and spectroscopy of transient species.

  2. Bimatoprost-induced chemical blepharoplasty.

    Science.gov (United States)

    Sarnoff, Deborah S; Gotkin, Robert H

    2015-05-01

    We report significant changes in the appearance of the periorbital area, beyond eyelash enhancement, induced by the topical application of bimatoprost ophthalmic solution, 0.03% (Latisse®, Allergan, Inc., Irvine, CA). To our knowledge, this is the first report in the dermatology or plastic surgery literature describing the rejuvenating effect and overall improvement in the appearance of the periorbital area resulting from applying Latisse to the upper eyelid margins. To date, reports in the literature discuss side-effects and potential complications of topical bimatoprost therapy causing a constellation of findings known as PAP (prostaglandin-associated periorbitopathy). While periorbitopathy implies pathology or a state of disease, we report changes that can be perceived as an improvement in the overall appearance of the periorbital area. We, therefore, propose a name change from PAP to PAPS - prostaglandin- associated periorbital syndrome. This better describes the beneficial, as well as the possible negative effects of topical bimatoprost. Although there is a risk for periorbital disfigurement, when used bilaterally, in properly selected candidates and titrated appropriately, bimatoprost can be beneficial. The striking improvement in the appearance of some individuals warrants further research into the potential use of topical bimatoprost to achieve a "chemical blepharoplasty."

  3. Chemical structure and dynamics. Annual report 1995

    Energy Technology Data Exchange (ETDEWEB)

    Colson, S.D.; McDowell, R.S.

    1996-05-01

    The Chemical Structure and Dynamics program is a major component of Pacific Northwest National Laboratory`s Environmental Molecular Sciences Laboratory (EMSL), providing a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for the characterization of waste tanks and pollutant distributions, and for detection and monitoring of trace atmospheric species.

  4. Chemical structure and dynamics: Annual report 1996

    Energy Technology Data Exchange (ETDEWEB)

    Colson, S.D.; McDowell, R.S.

    1997-03-01

    The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing waste tanks and pollutant distributions, and for detecting and monitoring trace atmospheric species.

  5. Annual Report 2000. Chemical Structure and Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Colson, Steven D.; McDowell, Robin S.

    2001-04-15

    This annual report describes the research and accomplishments of the Chemical Structure and Dynamics Program in the year 2000, one of six research programs at the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) - a multidisciplinary, national scientific user facility and research organization. The Chemical Structure and Dynamics (CS&D) program is meeting the need for a fundamental, molecular-level understanding by 1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; 2) developing a multidisciplinary capability for describing interfacial chemical processes relevant to environmental chemistry; and 3) developing state-of-the-art research and analytical methods for characterizing complex materials of the types found in natural and contaminated systems.

  6. Chemical structure and dynamics: Annual report 1993

    Energy Technology Data Exchange (ETDEWEB)

    Colson, S.D.

    1994-07-01

    The Chemical Structure and Dynamics program responds to the need for a fundamental, molecular-level understanding of chemistry at the wide variety of environmentally-important interfaces. The research program is built around the established relationship between structure, thermodynamics, and kinetics. This research effort continues to evolve into a program of rigorous studies of fundamental molecular processes in model systems (e.g., well-characterized surfaces, single-component solutions, clusters, and biological molecules), and studies of complex systems found in the environment. Experimental studies of molecular and supramolecular structures and thermodynamics are key to understanding the nature of matter, and lead to direct comparison with computational results. Kinetic and mechanistic measurements, combined with real-time dynamics measurements of atomic and molecular motions during chemical reactions, provide for a molecular-level description of chemical reactions. The anticipated results of this work are the achievement of a quantitative understanding of chemical processes at complex interfaces, the development of new techniques for the detection and measurement of species at such interfaces, and the interpretation and extrapolation of the observations in terms of models of interfacial chemistry. The Chemical Structure and Dynamics research program includes five areas described in detail in this report: Reaction mechanisms at solid interfaces; Solution and solution interfaces; Structure and dynamics of biological systems; Analytical methods development; and atmospheric chemistry. Extended abstracts are presented for 23 studies.

  7. Chemical Reaction Dynamics in Nanoscle Environments

    Energy Technology Data Exchange (ETDEWEB)

    Evelyn M. Goldfield

    2006-09-26

    The major focus of the research in this program is the study of the behavior of molecular systems confined in nanoscale environments. The goal is to develop a theoretical framework for predicting how chemical reactions occur in nanoscale environments. To achieve this goal we have employed ab initio quantum chemistry, classical dynamics and quantum dynamics methods. Much of the research has focused on the behavior of molecules confined within single-walled carbon nanotubes (SWCNTs). We have also studied interactions of small molecules with the exterior surface of SWCNTs. Nonequilibrium molecular dynamics of interfaces of sliding surface interfaces have also been performed.

  8. DNA-Encoded Dynamic Combinatorial Chemical Libraries.

    Science.gov (United States)

    Reddavide, Francesco V; Lin, Weilin; Lehnert, Sarah; Zhang, Yixin

    2015-06-26

    Dynamic combinatorial chemistry (DCC) explores the thermodynamic equilibrium of reversible reactions. Its application in the discovery of protein binders is largely limited by difficulties in the analysis of complex reaction mixtures. DNA-encoded chemical library (DECL) technology allows the selection of binders from a mixture of up to billions of different compounds; however, experimental results often show low a signal-to-noise ratio and poor correlation between enrichment factor and binding affinity. Herein we describe the design and application of DNA-encoded dynamic combinatorial chemical libraries (EDCCLs). Our experiments have shown that the EDCCL approach can be used not only to convert monovalent binders into high-affinity bivalent binders, but also to cause remarkably enhanced enrichment of potent bivalent binders by driving their in situ synthesis. We also demonstrate the application of EDCCLs in DNA-templated chemical reactions.

  9. Chemical Structure and Dynamics annual report 1997

    Energy Technology Data Exchange (ETDEWEB)

    Colson, S.D.; McDowell, R.S.

    1998-03-01

    The Chemical Structure and Dynamics (CS and D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. The authors respond to the need for a fundamental, molecular level understanding of chemistry at a wide variety of environmentally important interfaces by: (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing complex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. The focus of the research is defined primarily by DOE`s environmental problems: fate and transport of contaminants in the subsurface environment, processing and storage of waste materials, cellular effects of chemical and radiological insult, and atmospheric chemistry as it relates to air quality and global change. Twenty-seven projects are described under the following topical sections: Reaction mechanisms at interfaces; High-energy processes at environmental interfaces; Cluster models of the condensed phase; and Miscellaneous.

  10. Reactive chemical dynamics through conical intersections

    Indian Academy of Sciences (India)

    S Ghosal; B Jayachander Rao; S Mahapatra

    2007-09-01

    Reaction dynamics of prototypical, D + H2 and Cl (2P) + H2, chemical reactions occurring through the conical intersections of the respective coupled multi-sheeted potential energy surfaces is examined here. In addition to the electronic coupling, nonadiabatic effects due to relativistic spin-orbit coupling are also considered for the latter reaction. A time-dependent wave packet propagation approach is undertaken and the quantum dynamical observables viz., energy resolved reaction probabilities, integral reaction cross-sections and thermal rate constants are reported.

  11. Neural Networks in Chemical Reaction Dynamics

    CERN Document Server

    Raff, Lionel; Hagan, Martin

    2011-01-01

    This monograph presents recent advances in neural network (NN) approaches and applications to chemical reaction dynamics. Topics covered include: (i) the development of ab initio potential-energy surfaces (PES) for complex multichannel systems using modified novelty sampling and feedforward NNs; (ii) methods for sampling the configuration space of critical importance, such as trajectory and novelty sampling methods and gradient fitting methods; (iii) parametrization of interatomic potential functions using a genetic algorithm accelerated with a NN; (iv) parametrization of analytic interatomic

  12. Chemical structure and dynamics. Annual report 1994

    Energy Technology Data Exchange (ETDEWEB)

    Colson, S.D.

    1995-07-01

    The Chemical Structure and Dynamics program was organized as a major component of Pacific Northwest Laboratory`s Environmental and Molecular Sciences Laboratory (EMSL), a state-of-the-art collaborative facility for studies of chemical structure and dynamics. Our program responds to the need for a fundamental, molecular-level understanding of chemistry at the wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces, and (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage. This research effort was initiated in 1989 and will continue to evolve over the next few years into a program of rigorous studies of fundamental molecular processes in model systems, such as well-characterized surfaces, single-component solutions, clusters, and biological molecules; and studies of complex systems found in the environment (multispecies, multiphase solutions; solid/liquid, liquid/liquid, and gas/surface interfaces; colloidal dispersions; ultrafine aerosols; and functioning biological systems). The success of this program will result in the achievement of a quantitative understanding of chemical reactions at interfaces, and more generally in condensed media, that is comparable to that currently available for gas-phase reactions. This understanding will form the basis for the development of a priori theories for predictions of macroscopic chemical behavior in condensed and heterogeneous media, adding significantly to the value of field-scale environmental models, the prediction of short- and long-term nuclear waste storage stabilities, and other problems related to the primary missions of the DOE.

  13. Annual Report 1998: Chemical Structure and Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    SD Colson; RS McDowell

    1999-05-10

    The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Labo- ratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of- the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interracial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in envi- ronmental chemistry and in nuclear waste proc- essing and storage; and (3) developing state-of- the-art analytical methods for characterizing com- plex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. Our program aims at achieving a quantitative understanding of chemical reactions at interfaces and, more generally, in condensed media, compa- rable to that currently available for gas-phase reactions. This understanding will form the basis for the development of a priori theories for pre- dicting macroscopic chemical behavior in con- densed and heterogeneous media, which will add significantly to the value of field-scale envi- ronmental models, predictions of short- and long- term nuclear waste storage stabilities, and other areas related to the primary missions of the U.S. Department of Energy (DOE).

  14. Chemical Detection Based on Adsorption-Induced and Photo-Induced Stresses in MEMS Devices

    Energy Technology Data Exchange (ETDEWEB)

    Datskos, P.G.

    1999-04-05

    Recently there has been an increasing demand to perform real-time in-situ chemical detection of hazardous materials, contraband chemicals, and explosive chemicals. Currently, real-time chemical detection requires rather large analytical instrumentation that are expensive and complicated to use. The advent of inexpensive mass produced MEMS (micro-electromechanical systems) devices opened-up new possibilities for chemical detection. For example, microcantilevers were found to respond to chemical stimuli by undergoing changes in their bending and resonance frequency even when a small number of molecules adsorb on their surface. In our present studies, we extended this concept by studying changes in both the adsorption-induced stress and photo-induced stress as target chemicals adsorb on the surface of microcantilevers. For example, microcantilevers that have adsorbed molecules will undergo photo-induced bending that depends on the number of absorbed molecules on the surface. However, microcantilevers that have undergone photo-induced bending will adsorb molecules on their surfaces in a distinctly different way. Depending on the photon wavelength and microcantilever material, the microcantilever can be made to bend by expanding or contracting the irradiated surface. This is important in cases where the photo-induced stresses can be used to counter any adsorption-induced stresses and increase the dynamic range. Coating the surface of the microstructure with a different material can provide chemical specificity for the target chemicals. However, by selecting appropriate photon wavelengths we can change the chemical selectivity due to the introduction of new surface states in the MEMS device. We will present and discuss our results on the use of adsorption-induced and photo-induced bending of microcantilevers for chemical detection.

  15. Nuclear dynamics induced by antiprotons

    CERN Document Server

    Feng, Zhao-Qing

    2015-01-01

    Reaction dynamics in collisions of antiprotons on nuclei is investigated within the Lanzhou quantum molecular dynamics model. The reaction channels of elastic scattering, annihilation, charge exchange and inelastic collisions of antiprotons on nucleons have been included in the model. Dynamics on particle production, in particular pions, kaons, antikaons and hyperons, is investigated in collisions of $\\overline{p}$ on $^{12}$C, $^{20}$Ne, $^{40}$Ca and $^{181}$Ta from a low to high incident momenta. It is found that the annihilations of $\\overline{p}$ on nucleons are of importance on the dynamics of particle production in phase space. Hyperons are mainly produced via meson induced reactions on nucleons and strangeness exchange collisions, which lead to the delayed emission in antiproton-nucleus collisions.

  16. The Chemical Evolution of Dynamically Hot Galaxies

    Directory of Open Access Journals (Sweden)

    Michael G. Richer

    2001-01-01

    Full Text Available We investigate the chemical properties of M32, the bulges of M31 and the Milky Way, and the dwarf spheroidal galaxies NGC 205, NGC 185, Sagittarius, and Fornax using oxygen abundances for their planetary nebulae. Our principal result is that the mean stellar oxygen abundances correlate very well with thei r mean velocity dispersions, implying that the balance between energy input from type II supernovae and the gravitational potential controls chemical evolution in bulges, ellipticals, and dwarf spheroidals. It appears that chemical evolution ceases once supernovae have injected sufficient energy that a galacti c wind develops. All of the galaxies follow a single relation between oxygen abundance and luminosity, but the dwarf spheroidals have systematically higher [O/Fe] ratios than the other galaxies. Consequently, dynamically hot galaxies do not share a common star formation history nor need to a common chemical evolution, despite attaining similar mean stellar oxygen abundances when formin g similar masses. The oxygen abundances support previous indications that stars in higher luminosity ellipticals and bulges were formed on a shorter time scale than their counterparts in less luminous systems.

  17. Theoretical studies of chemical reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Schatz, G.C. [Argonne National Laboratory, IL (United States)

    1993-12-01

    This collaborative program with the Theoretical Chemistry Group at Argonne involves theoretical studies of gas phase chemical reactions and related energy transfer and photodissociation processes. Many of the reactions studied are of direct relevance to combustion; others are selected they provide important examples of special dynamical processes, or are of relevance to experimental measurements. Both classical trajectory and quantum reactive scattering methods are used for these studies, and the types of information determined range from thermal rate constants to state to state differential cross sections.

  18. The chemical bond structure and dynamics

    CERN Document Server

    Zewail, Ahmed

    1992-01-01

    This inspired book by some of the most influential scientists of our time--including six Nobel laureates--chronicles our emerging understanding of the chemical bond through the last nine decades and into the future. From Pauling's early structural work using x-ray and electron diffraction to Zewail's femtosecond lasers that probe molecular dynamics in real time; from Crick's molecular biology to Rich's molecular recognition, this book explores a rich tradition of scientific heritage and accomplishment. The perspectives given by Pauling, Perutz, Rich, Crick, Porter, Polanyi, Herschbach, Zewail,

  19. Application of synchrotron radiation in chemical dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Heimann, P.; Koike, M.; Kung, A.H.; Ng, C.Y.; White, M.G.; Wodtke, A.

    1993-05-01

    In October 1992, funding was approved to begin construction of a beamline and two end stations to support chemical dynamics experiments at LBL's Advanced Light Source (ALS). This workshop was organized to develop specifications and plans and to select a working team to design and supervise the construction project. Target date for starting the experiments is January 1995. Conclusions of the workshop and representative experiments proposed in earlier workshops to form the basis for beamline plans and end-station designs are summarized in this report. 6 figs.

  20. Application of synchrotron radiation in chemical dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Heimann, P.; Koike, M.; Kung, A.H.; Ng, C.Y.; White, M.G.; Wodtke, A.

    1993-05-01

    In October 1992, funding was approved to begin construction of a beamline and two end stations to support chemical dynamics experiments at LBL`s Advanced Light Source (ALS). This workshop was organized to develop specifications and plans and to select a working team to design and supervise the construction project. Target date for starting the experiments is January 1995. Conclusions of the workshop and representative experiments proposed in earlier workshops to form the basis for beamline plans and end-station designs are summarized in this report. 6 figs.

  1. Theoretical and experimental studies of chemically induced dynamic nuclear polarization kinetics in recombination of radical pairs by the method of switched external magnetic field. II. 13C CIDNP of micellized radical pairs

    Science.gov (United States)

    Fedin, M. V.; Bagryanskaya, E. G.; Purtov, P. A.

    1999-09-01

    The method of 13C chemically induced dynamic nuclear polarization in a switched external magnetic field (SEMF CIDNP) has been applied for the first time in an experimental investigation of micellized radical pairs (RP). Using the examples of three photochemical reactions it has been shown, that SEMF CIDNP allows the investigation of the kinetics of short-lived micellized RPs with high time-resolution in low and intermediate magnetic fields. The experimental kinetics have been analyzed and simulated on the basis of a previously developed theory [Parnachev et al., J. Chem. Phys. 107, 9942 (1997)]. It has been demonstrated that such an analysis provides information on the rates of radical escape from the micelle, on electron relaxation and on the rate of S-T- transitions. The analysis of the estimated rates of S-T- transitions showed that the exchange interaction is essentially anisotropic in the RPs studied.

  2. Study of chemical and radiation induced carcinogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Chmura, A.

    1995-11-01

    The study of chemical and radiation induced carcinogenesis has up to now based many of its results on the detection of genetic aberrations using the fluorescent in situ hybridization (FISH) technique. FISH is time consuming and this tends to hinder its use for looking at large numbers of samples. We are currently developing new technological advances which will increase the speed, clarity and functionality of the FISH technique. These advances include multi-labeled probes, amplification techniques, and separation techniques.

  3. Quantum dynamics of fast chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    Light, J.C. [Univ. of Chicago, IL (United States)

    1993-12-01

    The aims of this research are to explore, develop, and apply theoretical methods for the evaluation of the dynamics of gas phase collision processes, primarily chemical reactions. The primary theoretical tools developed for this work have been quantum scattering theory, both in time dependent and time independent forms. Over the past several years, the authors have developed and applied methods for the direct quantum evaluation of thermal rate constants, applying these to the evaluation of the hydrogen isotopic exchange reactions, applied wave packet propagation techniques to the dissociation of Rydberg H{sub 3}, incorporated optical potentials into the evaluation of thermal rate constants, evaluated the use of optical potentials for state-to-state reaction probability evaluations, and, most recently, have developed quantum approaches for electronically non-adiabatic reactions which may be applied to simplify calculations of reactive, but electronically adiabatic systems. Evaluation of the thermal rate constants and the dissociation of H{sub 3} were reported last year, and have now been published.

  4. Experiences on dynamic simulation software in chemical engineering education

    OpenAIRE

    Komulainen, Tiina M.; Enemark-Rasmussen, Rasmus; Sin, Gürkan; John P Fletcher; Cameron, David

    2012-01-01

    Commercial process simulators are increasing interest in the chemical engineer education. In this paper, the use of commercial dynamic simulation software, D-SPICE® and K-Spice®, for three different chemical engineering courses is described and discussed. The courses cover the following topics: basic chemical engineering, operability and safety analysis and process control. User experiences from both teachers and students are presented. The benefits of dynamic simulation as an additional teac...

  5. Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron

    Energy Technology Data Exchange (ETDEWEB)

    Leone, Stephen R.; Ahmed, Musahid; Wilson, Kevin R.

    2010-03-14

    Scientists at the Chemical Dynamics Beamline of the Advanced Light Source in Berkeley are continuously reinventing synchrotron investigations of physical chemistry and chemical physics with vacuum ultraviolet light. One of the unique aspects of a synchrotron for chemical physics research is the widely tunable vacuum ultraviolet light that permits threshold ionization of large molecules with minimal fragmentation. This provides novel opportunities to assess molecular energetics and reaction mechanisms, even beyond simple gas phase molecules. In this perspective, significant new directions utilizing the capabilities at the Chemical Dynamics Beamline are presented, along with an outlook for future synchrotron and free electron laser science in chemical dynamics. Among the established and emerging fields of investigations are cluster and biological molecule spectroscopy and structure, combustion flame chemistry mechanisms, radical kinetics and product isomer dynamics, aerosol heterogeneous chemistry, planetary and interstellar chemistry, and secondary neutral ion-beam desorption imaging of biological matter and materials chemistry.

  6. Chemically induced mouse models of intestinal inflammation.

    Science.gov (United States)

    Wirtz, Stefan; Neufert, Clemens; Weigmann, Benno; Neurath, Markus F

    2007-01-01

    Animal models of intestinal inflammation are indispensable for our understanding of the pathogenesis of Crohn disease and ulcerative colitis, the two major forms of inflammatory bowel disease in humans. Here, we provide protocols for establishing murine 2,4,6-trinitro benzene sulfonic acid (TNBS)-, oxazolone- and both acute and chronic dextran sodium sulfate (DSS) colitis, the most widely used chemically induced models of intestinal inflammation. In the former two models, colitis is induced by intrarectal administration of the covalently reactive reagents TNBS/oxazolone, which are believed to induce a T-cell-mediated response against hapten-modified autologous proteins/luminal antigens. In the DSS model, mice are subjected several days to drinking water supplemented with DSS, which seems to be directly toxic to colonic epithelial cells of the basal crypts. The procedures for the hapten models of colitis and acute DSS colitis can be accomplished in about 2 weeks but the protocol for chronic DSS colitis takes about 2 months.

  7. Experiences on dynamic simulation software in chemical engineering education

    DEFF Research Database (Denmark)

    Komulainen, Tiina M.; Enemark-rasmussen, Rasmus; Sin, Gürkan

    2012-01-01

    Commercial process simulators are increasing interest in the chemical engineer education. In this paper, the use of commercial dynamic simulation software, D-SPICE® and K-Spice®, for three different chemical engineering courses is described and discussed. The courses cover the following topics......: basic chemical engineering, operability and safety analysis and process control. User experiences from both teachers and students are presented. The benefits of dynamic simulation as an additional teaching tool are discussed and summarized. The experiences confirm that commercial dynamic simulators...

  8. Acute and subacute chemical-induced lung injuries: HRCT findings

    Energy Technology Data Exchange (ETDEWEB)

    Akira, Masanori, E-mail: Akira@kch.hosp.go.jp [Department of Radiology, National Hospital Organization Kinki-Chuo Chest Medical Center, 1180 Nagasone-cho, Kita-ku, Sakai City, Osaka 591-8555 (Japan); Suganuma, Narufumi [Department of Environmental Medicine, Kochi Medical School (Japan)

    2014-08-15

    Lung injury caused by chemicals includes bronchitis, bronchiolitis, chemical pneumonitis, pulmonary edema, acute respiratory distress syndrome, organizing pneumonia, hypersensitivity pneumonitis, acute eosinophilic pneumonia, and sarcoid-like granulomatous lung disease. Each chemical induces variable pathophysiology and the situation resembles to the drug induced lung disease. The HRCT features are variable and nonspecific, however HRCT may be useful in the evaluation of the lung injuries and so we should know about HRCT features of lung parenchymal abnormalities caused by chemicals.

  9. Dynamic Reaction Figures: An Integrative Vehicle for Understanding Chemical Reactions

    Science.gov (United States)

    Schultz, Emeric

    2008-01-01

    A highly flexible learning tool, referred to as a dynamic reaction figure, is described. Application of these figures can (i) yield the correct chemical equation by simply following a set of menu driven directions; (ii) present the underlying "mechanism" in chemical reactions; and (iii) help to solve quantitative problems in a number of different…

  10. Chemically induced compaction bands in geomaterials

    Science.gov (United States)

    Stefanou, Ioannis; Sulem, Jean

    2013-04-01

    Compaction bands play an important role in oil production and may provide useful information on various geological processes. Various mechanisms can be involved at different scales: the micro scale (e.g. the grain scale), the meso scale (e.g. the Representative Element Volume) and the macro scale (e.g. the structure). Moreover, hydro-chemo-mechanical couplings might play an important role in triggering instabilities in the form of compaction bands. Compaction bands can be seen as an instability of the underneath mathematical problem leading to localization of deformation [1,2,3]. Here we explore the conditions of compaction banding in quartz-based geomaterials by considering the effect of chemical dissolution and precipitation [4,5]. In due course of the loading process grain crushing affects the residual strength, the porosity and the permeability of the material. Moreover, at the micro-level, grain crushing results in an increase of the grain specific surface, which accelerates the dissolution [6]. Consequently, the silica is removed more rapidly from the grain skeleton and the overall mechanical properties are degraded due to chemical factors. The proposed model accounts for these phenomena. In particular, the diffusion of the diluted in the water silica is considered through the mass balance equation of the porous medium. The reduction of the mechanical strength of the material is described through a macroscopic failure criterion with chemical softening. The grain size reduction is related to the total energy input [7]. A grain size and porosity dependent permeability law is adopted. These degradation mechanisms are coupled with the dissolution/precipitation reaction kinetics. The obtained hydro-chemo-mechanical model is used to investigate the conditions, the material parameters and the chemical factors inducing compaction bands formation. References [1] J.W. Rudnicki, and J.R. Rice. "Conditions for the Localization of Deformation in Pressure

  11. Catalysis of Dynamical Chiral Symmetry Breaking by Chiral Chemical Potential

    CERN Document Server

    Braguta, V V

    2016-01-01

    In this paper we study the properties of media with chiral imbalance parameterized by chiral chemical potential. It is shown that depending on the strength of interaction between constituents in the media the chiral chemical potential either creates or enhances dynamical chiral symmetry breaking. Thus the chiral chemical potential plays a role of the catalyst of dynamical chiral symmetry breaking. Physically this effect results from the appearance of the Fermi surface and additional fermion states on this surface which take part in dynamical chiral symmetry breaking. An interesting conclusion which can be drawn is that at sufficiently small temperature chiral plasma is unstable with respect to condensation of Cooper pairs and dynamical chiral symmetry breaking even for vanishingly small interactions between constituents.

  12. Laboratory chemical dynamics and outer planets

    Science.gov (United States)

    Kaiser, Ralf I.

    Reactions of CN (2Σ+) and C2H (2Σ+) radicals with unsaturated hydrocarbons are of fundamental relevance to form complex nitriles and polyynes in hydrocarbon rich atmospheres, planets, and moons. Here we present results on crossed molecular beams experiments combined with electronic structure calculations on the reactions of C2H and CN radicals with acetylene, methylacetylene, allene, and benzene. Our investigation show that both radicals attack the unsaturated bond without entrance barrier in exothermic reactions. The collision complex decomposes to form the hydrocarbon and a H atom or shows a H atom migration prior to hydrogen atom loss. The identification of this C2H /CN - H exchange opens a versatile route to form unsaturated nitriles and polyynes and predicts their formation in hydrocarbon rich planetary atmospheres. Further, our studies provide a solid database on reaction products and shall guide chemical investigation of the NASA-ESA Cassini-Huygens mission to identify unsaturated hydrocarbons in Titan. Most important, these experiments verify unambiguously that the knowledge of reaction rate constants only is insufficient for detailed chemical models of planetary atmospheres. Reaction products and most important reactive intermediates MUST be included to get a plausible chemical model of planetary atmospheres.

  13. Chemical leukoderma induced by dimethyl sulfate*

    Science.gov (United States)

    Gozali, Maya Valeska; Zhang, Jia-an; Yi, Fei; Zhou, Bing-rong; Luo, Dan

    2016-01-01

    Chemical leukoderma occurs due to the toxic effect of a variety of chemical agents. Mechanisms include either destruction or inhibition of melanocytes. We report two male patients (36 and 51 years old) who presented with multiple hypopigmented macules and patches on the neck, wrist, and legs after exposure to dimethyl sulfate in a chemical industry. Physical examination revealed irregular depigmentation macules with sharp edges and clear hyperpigmentation around the lesions. History of repeated exposure to a chemical agent can help the clinical diagnosis of chemical leukoderma. This diagnosis is very important for prognosis and therapeutic management of the disease.

  14. Cluster dynamics transcending chemical dynamics toward nuclear fusion.

    Science.gov (United States)

    Heidenreich, Andreas; Jortner, Joshua; Last, Isidore

    2006-07-11

    Ultrafast cluster dynamics encompasses femtosecond nuclear dynamics, attosecond electron dynamics, and electron-nuclear dynamics in ultraintense laser fields (peak intensities 10(15)-10(20) W.cm(-2)). Extreme cluster multielectron ionization produces highly charged cluster ions, e.g., (C(4+)(D(+))(4))(n) and (D(+)I(22+))(n) at I(M) = 10(18) W.cm(-2), that undergo Coulomb explosion (CE) with the production of high-energy (5 keV to 1 MeV) ions, which can trigger nuclear reactions in an assembly of exploding clusters. The laser intensity and the cluster size dependence of the dynamics and energetics of CE of (D(2))(n), (HT)(n), (CD(4))(n), (DI)(n), (CD(3)I)(n), and (CH(3)I)(n) clusters were explored by electrostatic models and molecular dynamics simulations, quantifying energetic driving effects, and kinematic run-over effects. The optimization of table-top dd nuclear fusion driven by CE of deuterium containing heteroclusters is realized for light-heavy heteroclusters of the largest size, which allows for the prevalence of cluster vertical ionization at the highest intensity of the laser field. We demonstrate a 7-orders-of-magnitude enhancement of the yield of dd nuclear fusion driven by CE of light-heavy heteroclusters as compared with (D(2))(n) clusters of the same size. Prospective applications for the attainment of table-top nucleosynthesis reactions, e.g., (12)C(P,gamma)(13)N driven by CE of (CH(3)I)(n) clusters, were explored.

  15. NATO Advanced Study Institute on Advances in Chemical Reaction Dynamics

    CERN Document Server

    Capellos, Christos

    1986-01-01

    This book contains the formal lectures and contributed papers presented at the NATO Advanced Study Institute on. the Advances in Chemical Reaction Dynamics. The meeting convened at the city of Iraklion, Crete, Greece on 25 August 1985 and continued to 7 September 1985. The material presented describes the fundamental and recent advances in experimental and theoretical aspects of, reaction dynamics. A large section is devoted to electronically excited states, ionic species, and free radicals, relevant to chemical sys­ tems. In addition recent advances in gas phase polymerization, formation of clusters, and energy release processes in energetic materials were presented. Selected papers deal with topics such as the dynamics of electric field effects in low polar solutions, high electric field perturbations and relaxation of dipole equilibria, correlation in picosecond/laser pulse scattering, and applications to fast reaction dynamics. Picosecond transient Raman spectroscopy which has been used for the elucidati...

  16. Can Natural Sunlight Induce Coherent Exciton Dynamics?

    CERN Document Server

    Olšina, Jan; Wang, Chen; Cao, Jianshu

    2014-01-01

    Excitation of a model photosynthetic molecular aggregate by incoherent sunlight is systematically examined. For a closed system, the excited state coherence induced by the sunlight oscillates with an average amplitude that is inversely proportional to the excitonic gap, and reaches a stationary amplitude that depends on the temperature and coherence time of the radiation field. For an open system, the light-induced dynamical coherence relaxes to a static coherence determined by the non-canonical thermal distribution resulting from the entanglement with the phonon bath. The decay of the excited state population to the common ground state establishes a non-equilibrium steady-state flux driven by the sunlight, and it defines a time window to observe the transition from dynamical to static coherence. For the parameters relevant to photosynthetic systems, the exciton dynamics initiated by the sunlight exhibits a non-negligible amount of dynamical coherence (quantum beats) on the sub-picosecond timescale; however, ...

  17. Chemically induced intestinal damage models in zebrafish larvae.

    Science.gov (United States)

    Oehlers, Stefan H; Flores, Maria Vega; Hall, Christopher J; Okuda, Kazuhide S; Sison, John Oliver; Crosier, Kathryn E; Crosier, Philip S

    2013-06-01

    Several intestinal damage models have been developed using zebrafish, with the aim of recapitulating aspects of human inflammatory bowel disease (IBD). These experimentally induced inflammation models have utilized immersion exposure to an array of colitogenic agents (including live bacteria, bacterial products, and chemicals) to induce varying severity of inflammation. This technical report describes methods used to generate two chemically induced intestinal damage models using either dextran sodium sulfate (DSS) or trinitrobenzene sulfonic acid (TNBS). Methods to monitor intestinal damage and inflammatory processes, and chemical-genetic methods to manipulate the host response to injury are also described.

  18. Noise-induced multistability in chemical systems: Discrete versus continuum modeling.

    Science.gov (United States)

    Duncan, Andrew; Liao, Shuohao; Vejchodský, Tomáš; Erban, Radek; Grima, Ramon

    2015-04-01

    The noisy dynamics of chemical systems is commonly studied using either the chemical master equation (CME) or the chemical Fokker-Planck equation (CFPE). The latter is a continuum approximation of the discrete CME approach. It has recently been shown that for a particular system, the CFPE captures noise-induced multistability predicted by the CME. This phenomenon involves the CME's marginal probability distribution changing from unimodal to multimodal as the system size decreases below a critical value. We here show that the CFPE does not always capture noise-induced multistability. In particular we find simple chemical systems for which the CME predicts noise-induced multistability, whereas the CFPE predicts monostability for all system sizes.

  19. Chemical dynamics in the gas phase: Time-dependent quantum mechanics of chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    Gray, S.K. [Argonne National Laboratory, IL (United States)

    1993-12-01

    A major goal of this research is to obtain an understanding of the molecular reaction dynamics of three and four atom chemical reactions using numerically accurate quantum dynamics. This work involves: (i) the development and/or improvement of accurate quantum mechanical methods for the calculation and analysis of the properties of chemical reactions (e.g., rate constants and product distributions), and (ii) the determination of accurate dynamical results for selected chemical systems, which allow one to compare directly with experiment, determine the reliability of the underlying potential energy surfaces, and test the validity of approximate theories. This research emphasizes the use of recently developed time-dependent quantum mechanical methods, i.e. wave packet methods.

  20. Dynamical mean-field theory from a quantum chemical perspective.

    Science.gov (United States)

    Zgid, Dominika; Chan, Garnet Kin-Lic

    2011-03-07

    We investigate the dynamical mean-field theory (DMFT) from a quantum chemical perspective. Dynamical mean-field theory offers a formalism to extend quantum chemical methods for finite systems to infinite periodic problems within a local correlation approximation. In addition, quantum chemical techniques can be used to construct new ab initio Hamiltonians and impurity solvers for DMFT. Here, we explore some ways in which these things may be achieved. First, we present an informal overview of dynamical mean-field theory to connect to quantum chemical language. Next, we describe an implementation of dynamical mean-field theory where we start from an ab initio Hartree-Fock Hamiltonian that avoids double counting issues present in many applications of DMFT. We then explore the use of the configuration interaction hierarchy in DMFT as an approximate solver for the impurity problem. We also investigate some numerical issues of convergence within DMFT. Our studies are carried out in the context of the cubic hydrogen model, a simple but challenging test for correlation methods. Finally, we finish with some conclusions for future directions.

  1. Applications of laser-induced gratings to spectroscopy and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Rohlfing, E.A. [Sandia National Laboratories, Livermore, CA (United States)

    1993-12-01

    This program has traditionally emphasized two principal areas of research. The first is the spectroscopic characterization of large-amplitude motion on the ground-state potential surface of small, transient molecules. The second is the reactivity of carbonaceous clusters and its relevance to soot and fullerene formation in combustion. Motivated initially by the desire to find improved methods of obtaining stimulated emission pumping (SEP) spectra of transients, most of our recent work has centered on the use of laser-induced gratings or resonant four-wave mixing in free-jet expansions. These techniques show great promise for several chemical applications, including molecular spectroscopy and photodissociation dynamics. The author describes recent applications of two-color laser-induced grating spectroscopy (LIGS) to obtain background-free SEP spectra of transients and double resonance spectra of nonfluorescing species, and the use of photofragment transient gratings to probe photodissociation dynamics.

  2. Single-molecule chemical reaction reveals molecular reaction kinetics and dynamics.

    Science.gov (United States)

    Zhang, Yuwei; Song, Ping; Fu, Qiang; Ruan, Mingbo; Xu, Weilin

    2014-06-25

    Understanding the microscopic elementary process of chemical reactions, especially in condensed phase, is highly desirable for improvement of efficiencies in industrial chemical processes. Here we show an approach to gaining new insights into elementary reactions in condensed phase by combining quantum chemical calculations with a single-molecule analysis. Elementary chemical reactions in liquid-phase, revealed from quantum chemical calculations, are studied by tracking the fluorescence of single dye molecules undergoing a reversible redox process. Statistical analyses of single-molecule trajectories reveal molecular reaction kinetics and dynamics of elementary reactions. The reactivity dynamic fluctuations of single molecules are evidenced and probably arise from either or both of the low-frequency approach of the molecule to the internal surface of the SiO2 nanosphere or the molecule diffusion-induced memory effect. This new approach could be applied to other chemical reactions in liquid phase to gain more insight into their molecular reaction kinetics and the dynamics of elementary steps.

  3. 75 FR 76460 - Lymphohematopoietic Cancers Induced by Chemicals and Other Agents: Overview and Implications for...

    Science.gov (United States)

    2010-12-08

    ... AGENCY Lymphohematopoietic Cancers Induced by Chemicals and Other Agents: Overview and Implications for..., ``Lymphohematopoietic Cancers Induced by Chemicals and Other Agents: Overview and Implications for Risk Assessment.... ADDRESSES: The draft ``Lymphohematopoietic Cancers Induced by Chemicals and Other Agents: Overview...

  4. Molecular Dynamics Simulations of Solutions at Constant Chemical Potential

    CERN Document Server

    Perego, Claudio; Parrinello, Michele

    2015-01-01

    Molecular Dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, that range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, that influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a Grand-Canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work we propose the C$\\mu$MD method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the C$\\mu$MD method to the paradigmatic case of urea crystall...

  5. 2-D Chemical-Dynamical Modeling of Venus's Sulfur Variability

    Science.gov (United States)

    Bierson, Carver J.; Zhang, Xi

    2016-10-01

    Over the last decade a combination of ground based and Venus Express observations have been made of the concentration of sulfur species in Venus's atmosphere, both above [1, 2] and below the clouds [3, 4]. These observations put constraints on both the vertical and meridional variations of the major sulfur species in Venus's atmosphere.. It has also been observed that SO2 concentrations varies on both timescales of hours and years [1,4]. The spatial and temporal distribution of tracer species is owing to two possibilities: mutual chemical interaction and dynamical tracer transport.Previous Chemical modeling of Venus's middle atmosphere has only been explored in 1-D. We will present the first 2-D (altitude and latitude) chemical-dynamical model for Venus's middle atmosphere. The sulfur chemistry is based on of the 1D model of Zhang et al. 2012 [5]. We do model runs over multiple Venus decades testing two scenarios: first one with varying sulfur fluxes from below, and second with secular dynamical perturbations in the atmosphere [6]. By comparing to Venus Express and ground based observations, we put constraints on the dynamics of Venus's middle atmosphere.References: [1] Belyaev et al. Icarus 2012 [2] Marcq et al. Nature geoscience, 2013 [3] Marcq et al. JGR:Planets, 2008 [4] Arney et al. JGR:Planets, 2014 [5] Zhang et al. Icarus 2012 [6] Parish et al. Icarus 2012

  6. One-Directional Fluidic Flow Induced by Chemical Wave Propagation in a Microchannel.

    Science.gov (United States)

    Arai, Miyu; Takahashi, Kazuhiro; Hattori, Mika; Hasegawa, Takahiko; Sato, Mami; Unoura, Kei; Nabika, Hideki

    2016-05-26

    A one-directional flow induced by chemical wave propagation was investigated to understand the origin of its dynamic flow. A cylindrical injection port was connected with a straight propagation channel; the chemical wave was initiated at the injection port. Chemical waves propagated with a constant velocity irrespective of the channel width, indicating that the dynamics of the chemical waves were governed by a geometry-independent interplay between the chemical reaction and diffusion. In contrast, the velocity of the one-directional flow was dependent on the channel width. Furthermore, enlargement of the injection port volume increased the flow velocity and volume flux. These results imply that the one-directional flow in the microchannel is due to a hydrodynamic effect induced in the injection port. Spectroscopic analysis of a pH indicator revealed the simultaneous behavior between the pH increase near the injection port and the one-directional flow. Hence, we can conclude that the one-directional flow in the microchannel with chemical wave propagation was caused by a proton consumption reaction in the injection port, probably through liquid volume expansion by the reaction products and the reaction heat. It is a characteristic feature of the present system that the hydrodynamic flow started from the chemical wave initiation point and not the propagation wavefront, as observed for previous systems.

  7. The hunt for the dynamical resonances in chemical reaction dynamics: a perspective on historical advances

    Directory of Open Access Journals (Sweden)

    Yu Angyang

    2015-06-01

    Full Text Available The theoretical background and basic definition of the resonances in chemical reaction dynamics have been introduced in this article. The historical breakthrough in the experimental search for the reaction resonances has been reviewed in this report, with an emphasis on the crossed molecular beam apparatus. The research of the chemical reaction resonances has attracted many scientists’ attention from 80s of last century. The chemical reaction resonances in the F+H2 reaction were firstly observed by the researchers of the Chinese Academy of Sciences in 2006. Besides, the partial wave resonances in the chemical reactions have been observed for the first time in 2010.

  8. Coriolis coupling and nonadiabaticity in chemical reaction dynamics.

    Science.gov (United States)

    Wu, Emilia L

    2010-12-01

    The nonadiabatic quantum dynamics and Coriolis coupling effect in chemical reaction have been reviewed, with emphasis on recent progress in using the time-dependent wave packet approach to study the Coriolis coupling and nonadiabatic effects, which was done by K. L. Han and his group. Several typical chemical reactions, for example, H+D(2), F+H(2)/D(2)/HD, D(+)+H(2), O+H(2), and He+H(2)(+), have been discussed. One can find that there is a significant role of Coriolis coupling in reaction dynamics for the ion-molecule collisions of D(+)+H(2), Ne+H(2)(+), and He+H(2)(+) in both adiabatic and nonadiabatic context.

  9. Dynamics of prebiotic RNA reproduction illuminated by chemical game theory.

    Science.gov (United States)

    Yeates, Jessica A M; Hilbe, Christian; Zwick, Martin; Nowak, Martin A; Lehman, Niles

    2016-05-03

    Many origins-of-life scenarios depict a situation in which there are common and potentially scarce resources needed by molecules that compete for survival and reproduction. The dynamics of RNA assembly in a complex mixture of sequences is a frequency-dependent process and mimics such scenarios. By synthesizing Azoarcus ribozyme genotypes that differ in their single-nucleotide interactions with other genotypes, we can create molecules that interact among each other to reproduce. Pairwise interplays between RNAs involve both cooperation and selfishness, quantifiable in a 2 × 2 payoff matrix. We show that a simple model of differential equations based on chemical kinetics accurately predicts the outcomes of these molecular competitions using simple rate inputs into these matrices. In some cases, we find that mixtures of different RNAs reproduce much better than each RNA type alone, reflecting a molecular form of reciprocal cooperation. We also demonstrate that three RNA genotypes can stably coexist in a rock-paper-scissors analog. Our experiments suggest a new type of evolutionary game dynamics, called prelife game dynamics or chemical game dynamics. These operate without template-directed replication, illustrating how small networks of RNAs could have developed and evolved in an RNA world.

  10. A model for chemically-induced mechanical loading on MEMS

    DEFF Research Database (Denmark)

    Amiot, Fabien

    2007-01-01

    The development of full displacement field measurements as an alternative to the optical lever technique to measure the mechanical response for microelectro-mechanical systems components in their environment calls for a modeling of chemically-induced mechanical fields (stress, strain, and displac......The development of full displacement field measurements as an alternative to the optical lever technique to measure the mechanical response for microelectro-mechanical systems components in their environment calls for a modeling of chemically-induced mechanical fields (stress, strain...

  11. Solution of Chemical Dynamic Optimization Using the Simultaneous Strategies

    Institute of Scientific and Technical Information of China (English)

    LIU Xinggao; CHEN Long; HU Yunqing

    2013-01-01

    An approach of simultaneous strategies with two novel techniques is proposed to improve the solution accuracy of chemical dynamic optimization problems.The first technique is to handle constraints on control variables based on the finite-element collocation so as to control the approximation error for discrete optimal problems,where a set of control constraints at element knots are integrated with the procedure for optimization leading to a significant gain in the accuracy of the simultaneous strategies.The second technique is to make the mesh refinement more feasible and reliable by introducing length constraints and guideline in designing appropriate element length boundaries,so that the proposed approach becomes more efficient in adjusting elements to track optimal control profile breakpoints and ensure accurate state and control profiles.Four classic benchmarks of dynamic optimization problems are used as illustrations,and the proposed approach is compared with literature reports.The research results reveal that the proposed approach is preferable in improving the solution accuracy of chemical dynamic optimization problem.

  12. DNA and RNA induced enantioselectivity in chemical synthesis

    NARCIS (Netherlands)

    Roelfes, Gerard

    One of the hallmarks of DNA and RNA structures is their elegant chirality. Using these chiral structures to induce enantioselectivity in chemical synthesis is as enticing as it is challenging. In recent years, three general approaches have been developed to achieve this, including chirality transfer

  13. The Coupled Chemical and Physical Dynamics Model of MALDI

    Science.gov (United States)

    Knochenmuss, Richard

    2016-06-01

    The coupled physical and chemical dynamics model of ultraviolet matrix-assisted laser desorption/ionization (MALDI) has reproduced and explained a wide variety of MALDI phenomena. The rationale behind and elements of the model are reviewed, including the photophysics, kinetics, and thermodynamics of primary and secondary reaction steps. Experimental results are compared with model predictions to illustrate the foundations of the model, coupling of ablation and ionization, differences between and commonalities of matrices, secondary charge transfer reactions, ionization in both polarities, fluence and concentration dependencies, and suppression and enhancement effects.

  14. Wettability Induced Crack Dynamics and Morphology

    CERN Document Server

    Ghosh, Udita Uday; Bhandari, Aditya Bikram; Chakraborty, Suman; DasGupta, Sunando

    2014-01-01

    Substrate wettability alteration induced control over crack formation process in thin colloidal films has been addressed in the present study. Colloidal nanosuspension (53nm, mean particle diameter) droplets have been subjected to natural drying to outline the effects of substrate surface energies over the dry-out characteristics with emphasis on crack dynamics, crack morphology and underlying particle arrangements. Experimental findings indicate that number of cracks formed decreases with increase in substrate hydrophobicity. These physical phenomena have been explained based on the magnitude of stress dissipation incurred by the substrate. DLVO predictions are also found to be in tune with the reported experimental investigations.

  15. DYNSYL: a general-purpose dynamic simulator for chemical processes

    Energy Technology Data Exchange (ETDEWEB)

    Patterson, G.K.; Rozsa, R.B.

    1978-09-05

    Lawrence Livermore Laboratory is conducting a safeguards program for the Nuclear Regulatory Commission. The goal of the Material Control Project of this program is to evaluate material control and accounting (MCA) methods in plants that handle special nuclear material (SNM). To this end we designed and implemented the dynamic chemical plant simulation program DYNSYL. This program can be used to generate process data or to provide estimates of process performance; it simulates both steady-state and dynamic behavior. The MCA methods that may have to be evaluated range from sophisticated on-line material trackers such as Kalman filter estimators, to relatively simple material balance procedures. This report describes the overall structure of DYNSYL and includes some example problems. The code is still in the experimental stage and revision is continuing.

  16. Multiple time scale based reduction scheme for nonlinear chemical dynamics

    Science.gov (United States)

    Das, D.; Ray, D. S.

    2013-07-01

    A chemical reaction is often characterized by multiple time scales governing the kinetics of reactants, products and intermediates. We eliminate the fast relaxing intermediates in autocatalytic reaction by transforming the original system into a new one in which the linearized part is diagonal. This allows us to reduce the dynamical system by identifying the associated time scales and subsequent adiabatic elimination of the fast modes. It has been shown that the reduced system sustains the robust qualitative signatures of the original system and at times the generic form of the return map for the chaotic system from which complex dynamics stems out in the original system can be identified. We illustrate the scheme for a three-variable cubic autocatalytic reaction and four-variable peroxidase-oxidase reaction.

  17. Perspective: On the relevance of slower-than-femtosecond time scales in chemical structural-dynamics studies

    Directory of Open Access Journals (Sweden)

    Philip Coppens

    2015-03-01

    Full Text Available A number of examples illustrate structural-dynamics studies of picosecond and slower photo-induced processes. They include molecular rearrangements and excitations. The information that can be obtained from such studies is discussed. The results are complementary to the information obtained from femtosecond studies. The point is made that all pertinent time scales should be covered to obtain comprehensive insight in dynamic processes of chemical and biological importance.

  18. SPH code for dynamical and chemical evolution of disk galaxies

    CERN Document Server

    Berczik, P

    1998-01-01

    The problem of chemical and dynamical evolution of galaxies is one of the most attracting and complex problems of modern astrophysics. Within the framework of the given work the standard dynamic Smoothed Particle Hydrodynamics (SPH) code (Monaghan J.J. 1992, ARAA, 30, 543) is noticeably expanded. Our investigation concernes with the changes and incorporation of new ideas into the algorithmic inclusion of Star Formation (SF) and Super Novae (SN) explosions in SPH (Berczik P. & Kravchuk S.G., 1996, ApSpSci, 245, 27). The proposed energy criterion for definition of a place and efficiency of SF results in the successfully explain Star Formation History (SFH) in isolated galaxies of different types. On the base of original ideas we expand a code in a more realistic way of the description of effects of return of a hot, chemical enriched gas in Interstellar Matter (ISM). In addition to the account of SNII, we offer the self-agreed account of SNIa and PN. This allows to describe not only the ISM content of $ O^{1...

  19. A model for chemically-induced mechanical loading on MEMS

    DEFF Research Database (Denmark)

    Amiot, Fabien

    2007-01-01

    , and displacements). As these phenomena usually arise from species adsorption, adsorbate modification or surface reconstruction, they are surface-related by nature and thus require some dedicated mechanical modeling. The accompanying mechanical modeling proposed herein is intended to represent the chemical part......The development of full displacement field measurements as an alternative to the optical lever technique to measure the mechanical response for microelectro-mechanical systems components in their environment calls for a modeling of chemically-induced mechanical fields (stress, strain...

  20. Oral dosing of chemical indicators for in vivo monitoring of Ca2+ dynamics in insect muscle.

    Science.gov (United States)

    Ferdinandus; Arai, Satoshi; Ishiwata, Shin'ichi; Suzuki, Madoka; Sato, Hirotaka

    2015-01-01

    This paper proposes a remarkably facile staining protocol to visually investigate dynamic physiological events in insect tissues. We attempted to monitor Ca2+ dynamics during contraction of electrically stimulated living muscle. Advances in circuit miniaturization and insect neuromuscular physiology have enabled the hybridization of living insects and man-made electronic components, such as microcomputers, the result of which has been often referred as a Living Machine, Biohybrid, or Cyborg Insect. In order for Cyborg Insects to be of practical use, electrical stimulation parameters need to be optimized to induce desired muscle response (motor action) and minimize the damage in the muscle due to the electrical stimuli. Staining tissues and organs as well as measuring the dynamics of chemicals of interest in muscle should be conducted to quantitatively and systematically evaluate the effect of various stimulation parameters on the muscle response. However, existing staining processes require invasive surgery and/or arduous procedures using genetically encoded sensors. In this study, we developed a non-invasive and remarkably facile method for staining, in which chemical indicators can be orally administered (oral dosing). A chemical Ca2+ indicator was orally introduced into an insect of interest via food containing the chemical indicator and the indicator diffused from the insect digestion system to the target muscle tissue. We found that there was a positive relationship between the fluorescence intensity of the indicator and the frequency of electrical stimulation which indicates the orally dosed indicator successfully monitored Ca2+ dynamics in the muscle tissue. This oral dosing method has a potential to globally stain tissues including neurons, and investigating various physiological events in insects.

  1. Protective effect of silymarin against chemical-induced cardiotoxicity

    Directory of Open Access Journals (Sweden)

    Bibi Marjan Razavi

    2016-09-01

    Full Text Available Cardiac disorders remain one of the most important causes of death in the world. Oxidative stress has been suggested as one of the molecular mechanisms involved in drug-induced cardiac toxicity. Recently, several natural products have been utilized in different studies with the aim to protect the progression of oxidative stress-induced cardiac disorders. There is a large body of evidence that administration of antioxidants may be useful in ameliorating cardiac toxicity. Silymarin, a polyphenolic flavonoid has been shown to have utility in several cardiovascular disorders. In this review, various studies in scientific databases regarding the preventive effects of silymarin against cardiotoxicity induced by chemicals were introduced. Although there are many studies representing the valuable effects of silymarin in different diseases, the number of researches relating to the possible cardiac protective effects of silymarin against drugs induced toxicity is rather limited. Results of these studies show that silymarin has a broad spectrum of cardiac protective activity against toxicity induced by some chemicals including metals, environmental pollutants, oxidative agents and anticancer drugs. Further studies are needed to establish the utility of silymarin in protection against cardiac toxicity.

  2. Nonequilibrium dynamics in chemical systems A brief account

    Science.gov (United States)

    Nicolis, G.; Baras, F.

    1985-12-01

    During the period of September 3 to 7, 1984 a symposium on “Nonequilibrium Dynamics in Chemical Systems” was organized by the Centre de Recherche Paul Pascal in Bordeaux, France. It was supported, primarily, by the French Centre National de la Recherche Scientifique and attended by about 90 participants from Australia, Belgium, Canada, Denmark, France, Germany, Hungary, Israël, Italy, Japan, The Netherlands, Poland, Tchekoslovakia, Spain, United Kingdom, United States and Zimbabwe. A list of topics and speakers is found in the table below. Two highly successful conferences centered on nonlinear phenomena in chemical systems far from equilibrium had already been organized by the Bordeaux group in the past. The first of them [1], held in September 1978, was dominated by the theme that nonequilibrium can act as a source of order. Sustained oscillations and bistability were the two principal phenomena studied from this point of view. Thanks to the systematic utilization of the continuous stirred tank reactor (CSTR) the study of open systems could finally be realized. Reliable state diagrams were thus produced, notably by the Bordeaux group, in which one could identify the transition points to new states. The Belousov-Zhabotinskii (BZ) reaction and its variants were the main vehicle on which these new ideas could be illustrated. The second Bordeaux conference [2], held in September 1981, was largely dominated by the major progress that had just marked two vital areas of this field: the discovery of new classes of chemical oscillators; and the invasion of chaotic dynamics in chemistry. These themes also dominated the first Gordon Conference on Chemical Oscillations held in New Hampshire in July 1982. In contrast to its two predecessors, the third Bordeaux conference held in September 1984 was not dominated by a single central theme. New questions were raised in situations in which until very recently things were considered to be perfectly clear. Simple,

  3. Optimizing chemically induced resistance in tomato against Botrytis cinerea

    DEFF Research Database (Denmark)

    Luna, Estrella; Beardon, Emily G; Ravnskov, Sabine

    2016-01-01

    Resistance-inducing chemicals can offer broad-spectrum disease protection in crops, but can also affect plant growth and interactions with plant-beneficial microbes. We have evaluated different application methods of ß-aminobutyric acid (BABA) and jasmonic acid (JA) for long-lasting induced...... resistance in tomato against Botrytis cinerea. In addition, we have studied non-target effects on plant growth and root colonization by arbuscular mycorrhizal fungi (AMF). Germinating seeds for one week in BABA- or JA-containing solutions promoted seed germination efficiency, did not affect plant growth...... repressed plant growth at higher concentrations of the chemicals, which was particularly pronounced in hydroponically grown plants after BABA treatment. Both seed coating with BABA, and seedling treatments with BABA or JA, did not affect AMF root colonization in soil-grown tomato. Our study has identified...

  4. Wave-induced dynamics of flexible blades

    CERN Document Server

    Luhar, M

    2015-01-01

    We present an experimental and numerical study that describes the motion of flexible blades, scaled to be dynamically similar to natural aquatic vegetation, forced by wave-induced oscillatory flows. For the conditions tested, blade motion is governed primarily by two dimensionless variables: (i) the Cauchy number, $Ca$, which represents the ratio of the hydrodynamic forcing to the restoring force due to blade stiffness, and (ii) the ratio of the blade length to the wave orbital excursion, $L$. For flexible blades with $Ca \\gg 1$, the relationship between drag and velocity can be described by two different scaling laws at the large- and small-excursion limits. For large excursions ($L \\ll 1$), the flow resembles a unidirectional current and the scaling laws developed for steady-flow reconfiguration studies hold. For small excursions ($L \\gg 1$), the beam equations may be linearized and a different scaling law for drag applies. The experimental force measurements suggest that the small-excursion scaling applies...

  5. Chemically induced electric field: flat band potential engineering

    Science.gov (United States)

    Bak, T.; Guo, Z.; Li, W.; Atanacio, A. J.; Nowotny, J.

    2012-10-01

    The present work considers engineering of the flat band potential, FBP, of metal oxides in a controlled manner. The aim is to minimise the energy losses related to recombination. The related experimental approaches include imposition of a chemically-induced electric field using the phenomena of segregation, diffusion and the formation of multilayer systems. This paper considers several basic phenomena that allow the modification of the surface charge and the space charge at the gas/solid and solid/liquid interfaces.

  6. Transient Substrate-Induced Catalyst Formation in a Dynamic Molecular Network

    NARCIS (Netherlands)

    Fanlo-Virgos, Hugo; Alba, Andrea-Nekane R.; Hamieh, Saleh; Colomb-Delsuc, Mathieu; Otto, Sijbren

    2014-01-01

    In biology enzyme concentrations are continuously regulated, yet for synthetic catalytic systems such regulatory mechanisms are underdeveloped. We now report how a substrate of a chemical reaction induces the formation of its own catalyst from a dynamic molecular network. After complete conversion

  7. Determination of Reference Chemical Potential Using Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Krishnadeo Jatkar

    2010-01-01

    Full Text Available A new method implementing molecular dynamics (MD simulations for calculating the reference properties of simple gas hydrates has been proposed. The guest molecules affect interaction between adjacent water molecules distorting the hydrate lattice, which requires diverse values of reference properties for different gas hydrates. We performed simulations to validate the experimental data for determining Δ0, the chemical potential difference between water and theoretical empty cavity at the reference state, for structure II type gas hydrates. Simulations have also been used to observe the variation of the hydrate unit cell volume with temperature. All simulations were performed using TIP4P water molecules at the reference temperature and pressure conditions. The values were close to the experimental values obtained by the Lee-Holder model, considering lattice distortion.

  8. Contemporary research of dynamically induced phase transitions

    Science.gov (United States)

    Hull, L. M.

    2017-01-01

    Dynamically induced phase transitions in metals, within the present discussion, are those that take place within a time scale characteristic of the shock waves and any reflections or rarefactions involved in the loading structure along with associated plastic flow. Contemporary topics of interest include the influence of loading wave shape, the effect of shear produced by directionality of the loading relative to the sample dimensions and initial velocity field, and the loading duration (kinetic effects, hysteresis) on the appearance and longevity of a transformed phase. These topics often arise while considering the loading of parts of various shapes with high explosives, are typically two or three-dimensional, and are often selected because of the potential of the transformed phase to significantly modify the motion. In this paper, we look at current work on phase transitions in metals influenced by shear reported in the literature, and relate recent work conducted at Los Alamos on iron's epsilon phase transition that indicates a significant response to shear produced by reflected elastic waves. A brief discussion of criteria for the occurrence of stress induced phase transitions is provided. Closing remarks regard certain physical processes, such as fragmentation and jet formation, which may be strongly influenced by phase transitions.

  9. Consequences of an unstable chemical stratification on mantle dynamics

    Science.gov (United States)

    Plesa, Ana-Catalina; Tosi, Nicola; Breuer, Doris

    2013-04-01

    Early in the history of terrestrial planets, the fractional crystallization of primordial magma oceans may have led to the formation of large scale chemical heterogeneities. These may have been preserved over the entire planetary evolution as suggested for Mars by the isotopic analysis of the so-called SNC meteorites. The fractional crystallization of a magma ocean leads to a chemical stratification characterized by a progressive enrichment in heavy elements from the core-mantle boundary to the surface. This results in an unstable configuration that causes the overturn of the mantle and the subsequent formation of a stable chemical layering. Assuming scaling parameters appropriate for Mars, we first performed simulations of 2D thermo-chemical convection in Cartesian geometry with the numerical code YACC [1]. We investigated systems heated either solely from below or from within by varying systematically the buoyancy ratio B, which measures the relative importance of chemical to thermal buoyancy, and the mantle rheology, by considering systems with constant, strongly temperature-dependent and plastic viscosity. We ran a large set of simulations spanning a wide parameter space in order to understand the basic physics governing the magma ocean cumulate overturn and its consequence on mantle dynamics. Moreover, we derived scaling laws that relate the time over which chemical heterogeneities can be preserved (mixing time) and the critical yield stress (maximal yield stress that allows the lithosphere to undergo brittle failure) to the buoyancy ratio. We have found that the mixing time increases exponentially with B, while the critical yield stress shows a linear dependence. We investigated then Mars' early thermo-chemical evolution using the code GAIA in a 2D cylindrical geometry [2] and assuming a detailed magma ocean crystallization sequence as obtained from geochemical modeling [3]. We used an initial composition profile adapted from [3], accounted for an exothermic

  10. Modelling biological and chemically induced precipitation of calcium phosphate in enhanced biological phosphorus removal systems.

    Science.gov (United States)

    Barat, R; Montoya, T; Seco, A; Ferrer, J

    2011-06-01

    The biologically induced precipitation processes can be important in wastewater treatment, in particular treating raw wastewater with high calcium concentration combined with Enhanced Biological Phosphorus Removal. Currently, there is little information and experience in modelling jointly biological and chemical processes. This paper presents a calcium phosphate precipitation model and its inclusion in the Activated Sludge Model No 2d (ASM2d). The proposed precipitation model considers that aqueous phase reactions quickly achieve the chemical equilibrium and that aqueous-solid change is kinetically governed. The model was calibrated using data from four experiments in a Sequencing Batch Reactor (SBR) operated for EBPR and finally validated with two experiments. The precipitation model proposed was able to reproduce the dynamics of amorphous calcium phosphate (ACP) formation and later crystallization to hydroxyapatite (HAP) under different scenarios. The model successfully characterised the EBPR performance of the SBR, including the biological, physical and chemical processes.

  11. Dynamic Chemically Driven Dewetting, Spreading, and Self-Running of Sessile Droplets on Crystalline Silicon.

    Science.gov (United States)

    Arscott, Steve

    2016-12-06

    A chemically driven dewetting effect is demonstrated using sessile droplets of dilute hydrofluoric acid on chemically oxidized silicon wafers. The dewetting occurs as the thin oxide is slowly etched by the droplet and replaced by a hydrogen-terminated surface; the result of this is a gradual increase in the contact angle of the droplet with time. The time-varying work of adhesion is calculated from the time-varying contact angle; this corresponds to the changing chemical nature of the surface during dewetting and can be modeled by the well-known logistic (sigmoid) function often used for the modeling of restricted growth, in this case, the transition from an oxidized surface to a hydrogen-terminated silicon surface. The observation of the time-varying contact angle allows one to both measure the etch rate of the silicon oxide and estimate the hydrogenation rate as a function of HF concentration and wafer type. In addition to this, at a certain HF concentration, a self-running droplet effect is observed. In contrast, on hydrogen-terminated silicon wafers, a chemically induced spreading effect is observed using sessile droplets of nitric acid. The droplet spreading can also be modeled using a logistical function, where the restricted growth is the transition from hydrogen-terminated to a chemically induced oxidized silicon surface. The chemically driven dewetting and spreading observed here add to the methods available to study dynamic wetting (e.g., the moving three-phase contact line) of sessile droplets on surfaces. By slowing down chemical kinetics of the wetting, one is able to record the changing profile of the sessile droplet with time and gather information concerning the time-varying surface chemistry. The data also indicates a chemical interface hysteresis (CIH) that is compared to contact angle hysteresis (CAH). The approach can also be used to study the chemical etching and deposition behavior of thin films using liquids by monitoring the macroscopic

  12. In situ analysis of chemical components induced by steaming between fresh ginseng, steamed ginseng, and red ginseng

    Directory of Open Access Journals (Sweden)

    Gyo In

    2017-07-01

    Conclusion: This study elucidates the dynamic changes in the chemical components of P. ginseng when the steaming process was induced. These results are thought to be helpful for quality control and standardization of herbal drugs using P. ginseng and they also provide a scientific basis for pharmacological research of processed ginseng (Red ginseng.

  13. Dynamic behavior of chemical reactivity indices in density functional theory: A Bohn-Oppenheimer quantum molecular dynamics study

    Indian Academy of Sciences (India)

    Shubin Liu

    2005-09-01

    Dynamic behaviors of chemical concepts in density functional theory such as frontier orbitals (HOMO/LUMO), chemical potential, hardness, and electrophilicity index have been investigated in this work in the context of Bohn-Oppenheimer quantum molecular dynamics in association with molecular conformation changes. Exemplary molecular systems like CH$^{+}_{5}$ , Cl- (H2O)30 and Ca2+ (H2O)15 are studied at 300 K in the gas phase, demonstrating that HOMO is more dynamic than LUMO, chemical potential and hardness often fluctuate concurrently. It is argued that DFT concepts and indices may serve as a good framework to understand molecular conformation changes as well as other dynamic phenomena.

  14. From dynamic self-assembly to networked chemical systems.

    Science.gov (United States)

    Grzybowski, Bartosz A; Fitzner, Krzysztof; Paczesny, Jan; Granick, Steve

    2017-07-13

    Although dynamic self-assembly, DySA, is a relatively new area of research, the past decade has brought numerous demonstrations of how various types of components - on scales from (macro)molecular to macroscopic - can be arranged into ordered structures thriving in non-equilibrium, steady states. At the same time, none of these dynamic assemblies has so far proven practically relevant, prompting questions about the field's prospects and ultimate objectives. The main thesis of this Review is that formation of dynamic assemblies cannot be an end in itself - instead, we should think more ambitiously of using such assemblies as control elements (reconfigurable catalysts, nanomachines, etc.) of larger, networked systems directing sequences of chemical reactions or assembly tasks. Such networked systems would be inspired by biology but intended to operate in environments and conditions incompatible with living matter (e.g., in organic solvents, elevated temperatures, etc.). To realize this vision, we need to start considering not only the interactions mediating dynamic self-assembly of individual components, but also how components of different types could coexist and communicate within larger, multicomponent ensembles. Along these lines, the review starts with the discussion of the conceptual foundations of self-assembly in equilibrium and non-equilibrium regimes. It discusses key examples of interactions and phenomena that can provide the basis for various DySA modalities (e.g., those driven by light, magnetic fields, flows, etc.). It then focuses on the recent examples where organization of components in steady states is coupled to other processes taking place in the system (catalysis, formation of dynamic supramolecular materials, control of chirality, etc.). With these examples of functional DySA, we then look forward and consider conditions that must be fulfilled to allow components of multiple types to coexist, function, and communicate with one another within the

  15. Precise excision of transposons and point mutations induced by chemicals.

    Science.gov (United States)

    Rusina OYu; Mirskaya, E E; Andreeva, I V; Skavronskaya, A G

    1992-11-01

    The ability of 23 chemicals (carcinogens and non-carcinogens) to induce precise excision of Tn10 and point mutations was studied in experiments with a single strain. The mutation assay was shown to detect a wider spectrum of genotoxic agents than the assay of Tn10 precise excision. The latter was induced only by potent SOS mutagens, which is in accordance with data on the SOS dependence of the induction of precise excision of Tn10. The precise excision assay as an additional test contributing to the knowledge of particular features of the action of a tested mutagen is discussed. The induction of precise excision of Tn10 by pyrene (and its failure to induce point mutations in this strain) demonstrates the value of using the transposon excision assay in cases of 'problem' mutagens.

  16. Comparative sensitivity of human and rat neural cultures to chemical-induced inhibition of neurite outgrowth

    Energy Technology Data Exchange (ETDEWEB)

    Harrill, Joshua A.; Freudenrich, Theresa M.; Robinette, Brian L.; Mundy, William R., E-mail: mundy.william@epa.gov

    2011-11-15

    cultures were more sensitive to neurite outgrowth inhibitors, they also had a lower dynamic range for detecting chemical-induced neurite outgrowth inhibition and greater variability from culture-to-culture as compared to rat primary cortical cultures.

  17. Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology

    CERN Document Server

    Sushko, Gennady B; Verkhovtsev, Alexey V; Volkov, Sergey N; Solov'yov, Andrey V

    2015-01-01

    The concept of molecular mechanics force field has nowadays been widely accepted for studying various processes in biomolecular systems. In this paper we suggest a modification for the standard CHARMM force field, that permits simulations of systems with dynamically changing molecular topologies. The implementation of the modified force field was carried out in the popular program MBN Explorer, and, to support the development, in this paper we provide several case studies where dynamical topology is necessary. In particular, it is shown, that the modified molecular mechanics force field can be applied for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation or collision induced damage, transformation and fragmentation processes involving biomolecular systems.

  18. Moisture-induced solid state instabilities in α-chymotrypsin and their reduction through chemical glycosylation

    Directory of Open Access Journals (Sweden)

    Solá Ricardo J

    2010-08-01

    Full Text Available Abstract Background Protein instability remains the main factor limiting the development of protein therapeutics. The fragile nature (structurally and chemically of proteins makes them susceptible to detrimental events during processing, storage, and delivery. To overcome this, proteins are often formulated in the solid-state which combines superior stability properties with reduced operational costs. Nevertheless, solid protein pharmaceuticals can also suffer from instability problems due to moisture sorption. Chemical protein glycosylation has evolved into an important tool to overcome several instability issues associated with proteins. Herein, we employed chemical glycosylation to stabilize a solid-state protein formulation against moisture-induced deterioration in the lyophilized state. Results First, we investigated the consequences of moisture sorption on the stability and structural conformation of the model enzyme α-chymotrypsin (α-CT under controlled humidity conditions. Results showed that α-CT aggregates and inactivates as a function of increased relative humidity (RH. Furthermore, α-CT loses its native secondary and tertiary structure rapidly at increasing RH. In addition, H/D exchange studies revealed that α-CT structural dynamics increased at increasing RH. The magnitude of the structural changes in tendency parallels the solid-state instability data (i.e., formation of buffer-insoluble aggregates, inactivation, and loss of native conformation upon reconstitution. To determine if these moisture-induced instability issues could be ameliorated by chemical glycosylation we proceeded to modify our model protein with chemically activated glycans of differing lengths (lactose and dextran (10 kDa. The various glycoconjugates showed a marked decrease in aggregation and an increase in residual activity after incubation. These stabilization effects were found to be independent of the glycan size. Conclusion Water sorption leads to

  19. Analysis of forward and inverse problems in chemical dynamics and spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Rabitz, H. [Princeton Univ., NJ (United States)

    1993-12-01

    The overall scope of this research concerns the development and application of forward and inverse analysis tools for problems in chemical dynamics and chemical kinetics. The chemical dynamics work is specifically associated with relating features in potential surfaces and resultant dynamical behavior. The analogous inverse research aims to provide stable algorithms for extracting potential surfaces from laboratory data. In the case of chemical kinetics, the focus is on the development of systematic means to reduce the complexity of chemical kinetic models. Recent progress in these directions is summarized below.

  20. Thermally induced dynamics in ultrathin magnetic tunnel junctions

    NARCIS (Netherlands)

    Ogrodnik, P.; Bauer, G.E.W.; Xia, K.

    2013-01-01

    We consider the magnetization dynamics induced by thermally induced spin transfer torques in thin Fe|MgO|Fe tunnel junctions. The magnetization dynamics is described by the Landau-Lifshitz-Gilbert equation, including the thermal torques as computed from first principles. We show that the angular ske

  1. The herbicide atrazine induces hyperactivity and compromises tadpole detection of predator chemical cues.

    Science.gov (United States)

    Ehrsam, Mackenzie; Knutie, Sarah A; Rohr, Jason R

    2016-09-01

    The ability to detect chemical cues is often critical for freshwater organisms to avoid predation and find food and mates. In particular, reduced activity and avoidance of chemical cues signaling predation risk are generally adaptive behaviors that reduce prey encounter rates with predators. The present study examined the effects of the common herbicide atrazine on the ability of Cuban tree frog (Osteopilus septentrionalis) tadpoles to detect and respond to chemical cues from larval dragonfly (Libellulidae sp.) predators. Tadpoles exposed to an estimated environmental concentration of atrazine (calculated using US Environmental Protection Agency software; measured concentration, 178 μg/L) were significantly hyperactive relative to those exposed to solvent control. In addition, control tadpoles significantly avoided predator chemical cues, but tadpoles exposed to atrazine did not. These results are consistent with previous studies that have demonstrated that ecologically relevant concentrations of atrazine can induce hyperactivity and impair the olfactory abilities of other freshwater vertebrates. The authors call for additional studies examining the role of chemical contaminants in disrupting chemical communication and the quantification of subsequent impacts on the fitness and population dynamics of wildlife. Environ Toxicol Chem 2016;35:2239-2244. © 2016 SETAC.

  2. Shock-Induced Chemical Reactions in Structural Energetic Materials

    Science.gov (United States)

    Narayanan, V.; Lu, X.; Hanagud, S.

    2006-07-01

    Various powder mixtures like intermetallic mixtures and mixtures of metals and metal oxides have potential applications as structural energetic materials (SEMs). Technologies of varying the compositions and the powder sizes and their synthesis are being investigated to provide multiple desirable characteristics, like high strength and high energy content. In this paper, we formulate a model for SEMs for their application in shock conditions, in the framework of nonequilibrium thermodynamics and continuum mechanics. A mixture of Al and KClO4 is selected as the example for SEMs. A mixture, pore collapse and chemical reaction model are included. By adapting energy barriers for reaction as a function of temperature, particle size and pressure and introducing a relaxation mechanism in the reaction model, a shock-induced chemical reaction model is developed. The variation of the relaxation mechanism is also modeled. The initiation and propagation of chemical reactions are studied. The time and spatial dependency of chemical reaction on the shock wave conditions are investigated.

  3. On the study of nonlinear dynamics of complex chemical reaction systems

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    With ever-increasing attentions being paid to complex systems such as the life system, soft matter, and nano-systems, theoretical studies of non-equilibrium nonlinear problems involved in chemical dynamics are now of general interest. In this mini-review, we mainly give a brief introduction to some frontier topics in this field, namely, nonlinear state-state dynamics, nonlinear chemical dynamics on complex networks, and nonlinear dynamics in mesoscopic chemical reaction systems. Deep study of these topics will make great contribution to discovering new laws of chemical dynamics, to exploring new control methods of complex chemical processes, to figuring out the very roles of chemical processes in the life system, and to crosslinking the scientific study of chemistry, physics and biology.

  4. Characterization of mu s-ms dynamics of proteins using a combined analysis of N-15 NMR relaxation and chemical shift: Conformational exchange in plastocyanin induced by histidine protonations

    DEFF Research Database (Denmark)

    Hass, M. A. S.; Thuesen, Marianne Hallberg; Christensen, Hans Erik Mølager

    2004-01-01

    An approach is presented that allows a detailed, quantitative characterization of conformational exchange processes in proteins on the mus-ms time scale. The approach relies on a combined analysis of NMR relaxation rates and chemical shift changes and requires that the chemical shift...... of the exchanging species can be determined independently of the relaxation rates. The applicability of the approach is demonstrated by a detailed analysis of the conformational exchange processes previously observed in the reduced form of the blue copper protein, plastocyanin from the cyanobacteria Anabaena...... quantitatively by the correlation between the R-ex terms and the corresponding chemical shift differences of the exchanging species. By this approach, the R-ex terms of N-15 nuclei belonging to contiguous regions in the protein could be assigned to the same exchange process. Furthermore, the analysis...

  5. The quantum dynamics of electronically nonadiabatic chemical reactions

    Science.gov (United States)

    Truhlar, Donald G.

    1993-01-01

    Considerable progress was achieved on the quantum mechanical treatment of electronically nonadiabatic collisions involving energy transfer and chemical reaction in the collision of an electronically excited atom with a molecule. In the first step, a new diabatic representation for the coupled potential energy surfaces was created. A two-state diabatic representation was developed which was designed to realistically reproduce the two lowest adiabatic states of the valence bond model and also to have the following three desirable features: (1) it is more economical to evaluate; (2) it is more portable; and (3) all spline fits are replaced by analytic functions. The new representation consists of a set of two coupled diabatic potential energy surfaces plus a coupling surface. It is suitable for dynamics calculations on both the electronic quenching and reaction processes in collisions of Na(3p2p) with H2. The new two-state representation was obtained by a three-step process from a modified eight-state diatomics-in-molecules (DIM) representation of Blais. The second step required the development of new dynamical methods. A formalism was developed for treating reactions with very general basis functions including electronically excited states. Our formalism is based on the generalized Newton, scattered wave, and outgoing wave variational principles that were used previously for reactive collisions on a single potential energy surface, and it incorporates three new features: (1) the basis functions include electronic degrees of freedom, as required to treat reactions involving electronic excitation and two or more coupled potential energy surfaces; (2) the primitive electronic basis is assumed to be diabatic, and it is not assumed that it diagonalizes the electronic Hamiltonian even asymptotically; and (3) contracted basis functions for vibrational-rotational-orbital degrees of freedom are included in a very general way, similar to previous prescriptions for locally

  6. A chemical chaperone induces inhomogeneous conformational changes in flexible proteins.

    Science.gov (United States)

    Hamdane, Djemel; Velours, Christophe; Cornu, David; Nicaise, Magali; Lombard, Murielle; Fontecave, Marc

    2016-07-27

    Organic osmolytes also known as chemical chaperones are major cellular compounds that favor, by an unclear mechanism, protein's compaction and stabilization of the native state. Here, we have examined the chaperone effect of the naturally occurring trimethylamine N-oxide (TMAO) osmolyte on a loosely packed protein (LPP), known to be a highly flexible form, using an apoprotein mutant of the flavin-dependent RNA methyltransferase as a model. Thermal and chemical denaturation experiments showed that TMAO stabilizes the structural integrity of the apoprotein dramatically. The denaturation reaction is irreversible indicating that the stability of the apoprotein is under kinetic control. This result implies that the stabilization is due to a TMAO-induced reconfiguration of the flexible LPP state, which leads to conformational limitations of the apoprotein likely driven by favorable entropic contribution. Evidence for the conformational perturbation of the apoprotein had been obtained through several biophysical approaches notably analytical ultracentrifugation, circular dichroism, fluorescence spectroscopy, labelling experiments and proteolysis coupled to mass spectrometry. Unexpectedly, TMAO promotes an overall elongation or asymmetrical changes of the hydrodynamic shape of the apoprotein without alteration of the secondary structure. The modulation of the hydrodynamic properties of the protein is associated with diverse inhomogenous conformational changes: loss of the solvent accessible cavities resulting in a dried protein matrix; some side-chain residues initially buried become solvent exposed while some others become hidden. Consequently, the TMAO-induced protein state exhibits impaired capability in the flavin binding process. Our study suggests that the nature of protein conformational changes induced by the chemical chaperones may be specific to protein packing and plasticity. This could be an efficient mechanism by which the cell controls and finely tunes the

  7. Chemically induced magnetism in atomically precise gold clusters.

    Science.gov (United States)

    Krishna, Katla Sai; Tarakeshwar, Pilarisetty; Mujica, Vladimiro; Kumar, Challa S S R

    2014-03-12

    Comparative theoretical and experimental investigations are reported into chemically induced magnetism in atomically-precise, ligand-stabilized gold clusters Au25 , Au38 and Au55 . The results indicate that [Au25 (PPh3 )10 (SC12 H25 )5 Cl2 ](2+) and Au38 (SC12 H25 )24 are diamagnetic, Au25 (SC2 H4 Ph)18 is paramagnetic, and Au55 (PPh3 )12 Cl6 , is ferromagnetic at room temperature. Understanding the magnetic properties resulting from quantum size effects in such atomically precise gold clusters could lead to new fundamental discoveries and applications.

  8. Dynamic Adsorptive Removal of Toxic Chemicals for Purification of Water

    Directory of Open Access Journals (Sweden)

    Amit Saxena

    2005-04-01

    Full Text Available To determine the efficiency of carbon column for the removal of toxic chemicals from water, the adsorption of phenol in concentration range from 0.600 glt to 1.475 gll was studied on activecarbon of 80 CTC grade, 12 X 30 BSS particle size, 1280 m2/g surface area, and of coconut shell origin, under dynamic conditions at space velocity from 0.318 min-' to 4.24 min-' at 25 'C. The carbon column of 100 cm length and 2 cm diameter was found to be removing phenol from the aqueous solution of concentration 1.475 gll up to 84 min at 0.678 min-' space velocity at 5.0 ppm phenol breakthrough concentration. However, no phenol was observed in carbon-treated water after 80 min. The service life of carbon column (100 cm lengthX25 cm diameter was assessed through the water purification system developed at the Defence Laboratory, Jodhpur and was determined to be 4.095 days with twoas factor of safety for 10 ppm initial concentration of phenol at 0.678 min-' space velocity (corresponding to water flow rate. Effects of carbon bed length, water flow rate, and the phenol concentration were also studied.

  9. Spatially organized dynamical states in chemical oscillator networks: synchronization, dynamical differentiation, and chimera patterns.

    Directory of Open Access Journals (Sweden)

    Mahesh Wickramasinghe

    Full Text Available Dynamical processes in many engineered and living systems take place on complex networks of discrete dynamical units. We present laboratory experiments with a networked chemical system of nickel electrodissolution in which synchronization patterns are recorded in systems with smooth periodic, relaxation periodic, and chaotic oscillators organized in networks composed of up to twenty dynamical units and 140 connections. The reaction system formed domains of synchronization patterns that are strongly affected by the architecture of the network. Spatially organized partial synchronization could be observed either due to densely connected network nodes or through the 'chimera' symmetry breaking mechanism. Relaxation periodic and chaotic oscillators formed structures by dynamical differentiation. We have identified effects of network structure on pattern selection (through permutation symmetry and coupling directness and on formation of hierarchical and 'fuzzy' clusters. With chaotic oscillators we provide experimental evidence that critical coupling strengths at which transition to identical synchronization occurs can be interpreted by experiments with a pair of oscillators and analysis of the eigenvalues of the Laplacian connectivity matrix. The experiments thus provide an insight into the extent of the impact of the architecture of a network on self-organized synchronization patterns.

  10. Exploitation of Chemical Signaling by Parasitoids: Impact on Host Population Dynamics

    NARCIS (Netherlands)

    Lof, M.E.; Gee, de M.; Dicke, M.; Gort, G.; Hemerik, L.

    2013-01-01

    Chemical information mediates species interactions in a wide range of organisms. Yet, the effect of chemical information on population dynamics is rarely addressed. We designed a spatio-temporal parasitoid—host model to investigate the population dynamics when both the insect host and the parasitic

  11. Shock initiated thermal and chemical responses of HMX crystal from ReaxFF molecular dynamics simulation.

    Science.gov (United States)

    Zhou, Tingting; Song, Huajie; Liu, Yi; Huang, Fenglei

    2014-07-21

    To gain an atomistic-level understanding of the thermal and chemical responses of condensed energetic materials under thermal shock, we developed a thermal shock reactive dynamics (TS-RD) computational protocol using molecular dynamics simulation coupled with ReaxFF force field. β-Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX) was selected as a a target explosive due to its wide usage in the military and industry. The results show that a thermal shock initiated by a large temperature gradient between the "hot" region and the "cold" region results in thermal expansion of the particles and induces a thermal-mechanical wave propagating back and forth in the system with an averaged velocity of 3.32 km s(-1). Heat propagating along the direction of thermal shock leads to a temperature increment of the system and thus chemical reaction initiation. Applying a continuum reactive heat conduction model combined with the temperature distribution obtained from the RD simulation, a heat conduction coefficient is derived as 0.80 W m(-1) K(-1). The chemical reaction mechanisms during thermal shock were analyzed, showing that the reaction is triggered by N-NO2 bond breaking followed by HONO elimination and ring fission. The propagation rates of the reaction front and reaction center are obtained to be 0.069 and 0.038 km s(-1), based on the time and spatial distribution of NO2. The pressure effect on the thermal shock was also investigated by employing uniaxial compression before the thermal shock. We find that compression significantly accelerates thermal-mechanical wave propagation and heat conduction, resulting in higher temperature and more excited molecules and thus earlier initiation and faster propagation of chemical reactions.

  12. Molecular Dynamics Simulations of Chemical Reactions for Use in Education

    Science.gov (United States)

    Qian Xie; Tinker, Robert

    2006-01-01

    One of the simulation engines of an open-source program called the Molecular Workbench, which can simulate thermodynamics of chemical reactions, is described. This type of real-time, interactive simulation and visualization of chemical reactions at the atomic scale could help students understand the connections between chemical reaction equations…

  13. Molecular Dynamics Simulations of Chemical Reactions for Use in Education

    Science.gov (United States)

    Qian Xie; Tinker, Robert

    2006-01-01

    One of the simulation engines of an open-source program called the Molecular Workbench, which can simulate thermodynamics of chemical reactions, is described. This type of real-time, interactive simulation and visualization of chemical reactions at the atomic scale could help students understand the connections between chemical reaction equations…

  14. A high-throughput chemically induced inflammation assay in zebrafish

    Directory of Open Access Journals (Sweden)

    Liebel Urban

    2010-12-01

    Full Text Available Abstract Background Studies on innate immunity have benefited from the introduction of zebrafish as a model system. Transgenic fish expressing fluorescent proteins in leukocyte populations allow direct, quantitative visualization of an inflammatory response in vivo. It has been proposed that this animal model can be used for high-throughput screens aimed at the identification of novel immunomodulatory lead compounds. However, current assays require invasive manipulation of fish individually, thus preventing high-content screening. Results Here we show that specific, noninvasive damage to lateral line neuromast cells can induce a robust acute inflammatory response. Exposure of fish larvae to sublethal concentrations of copper sulfate selectively damages the sensory hair cell population inducing infiltration of leukocytes to neuromasts within 20 minutes. Inflammation can be assayed in real time using transgenic fish expressing fluorescent proteins in leukocytes or by histochemical assays in fixed larvae. We demonstrate the usefulness of this method for chemical and genetic screens to detect the effect of immunomodulatory compounds and mutations affecting the leukocyte response. Moreover, we transformed the assay into a high-throughput screening method by using a customized automated imaging and processing system that quantifies the magnitude of the inflammatory reaction. Conclusions This approach allows rapid screening of thousands of compounds or mutagenized zebrafish for effects on inflammation and enables the identification of novel players in the regulation of innate immunity and potential lead compounds toward new immunomodulatory therapies. We have called this method the chemically induced inflammation assay, or ChIn assay. See Commentary article: http://www.biomedcentral.com/1741-7007/8/148.

  15. Modeling drug- and chemical- induced hepatotoxicity with systems biology approaches

    Directory of Open Access Journals (Sweden)

    Sudin eBhattacharya

    2012-12-01

    Full Text Available We provide an overview of computational systems biology approaches as applied to the study of chemical- and drug-induced toxicity. The concept of ‘toxicity pathways’ is described in the context of the 2007 US National Academies of Science report, Toxicity testing in the 21st Century: A Vision and A Strategy. Pathway mapping and modeling based on network biology concepts are a key component of the vision laid out in this report for a more biologically-based analysis of dose-response behavior and the safety of chemicals and drugs. We focus on toxicity of the liver (hepatotoxicity – a complex phenotypic response with contributions from a number of different cell types and biological processes. We describe three case studies of complementary multi-scale computational modeling approaches to understand perturbation of toxicity pathways in the human liver as a result of exposure to environmental contaminants and specific drugs. One approach involves development of a spatial, multicellular virtual tissue model of the liver lobule that combines molecular circuits in individual hepatocytes with cell-cell interactions and blood-mediated transport of toxicants through hepatic sinusoids, to enable quantitative, mechanistic prediction of hepatic dose-response for activation of the AhR toxicity pathway. Simultaneously, methods are being developing to extract quantitative maps of intracellular signaling and transcriptional regulatory networks perturbed by environmental contaminants, using a combination of gene expression and genome-wide protein-DNA interaction data. A predictive physiological model (DILIsymTM to understand drug-induced liver injury (DILI, the most common adverse event leading to termination of clinical development programs and regulatory actions on drugs, is also described. The model initially focuses on reactive metabolite-induced DILI in response to administration of acetaminophen, and spans multiple biological scales.

  16. Shock-induced hotspot formation and chemical reaction initiation in PETN containing a spherical void

    Science.gov (United States)

    Shan, Tzu-Ray; Thompson, Aidan P.

    2014-05-01

    We present results of reactive molecular dynamics simulations of hotspot formation and chemical reaction initiation in shock-induced compression of pentaerythritol tetranitrate (PETN) with the ReaxFF reactive force field. A supported shockwave is driven through a PETN crystal containing a 20 nm spherical void at a sub-threshold impact velocity of 2 km/s. Formation of a hotspot due to shock-induced void collapse is observed. During void collapse, NO2 is the dominant species ejected from the upstream void surface. Once the ejecta collide with the downstream void surface and the hotspot develops, formation of final products such as N2 and H2O is observed. The simulation provides a detailed picture of how void collapse and hotspot formation leads to initiation at sub-threshold impact velocities.

  17. Shock induced chemical reactions in energetic structural materials

    Science.gov (United States)

    Reding, Derek J.

    Energetic structural materials (ESMs) constitute a new class of materials that provide dual functions of strength and energetic characteristics. ESMs are typically composed of micron-scale or nano-scale intermetallic mixtures or mixtures of metals and metal oxides, polymer binders, and structural reinforcements. Voids are included to produce a composite with favorable chemical reaction characteristics. In this thesis, a continuum approach is used to simulate gas-gun or explosive loading experiments where a strong shock is induced in the ESM by an impacting plate. Algorithms are developed to obtain equations of state of mixtures. It is usually assumed that the shock loading increases the energy of the ESM and causes the ESM to reach the transition state. It is also assumed that the activation energy needed to reach the transition state is a function of the temperature of the mixture. In this thesis, it is proposed that the activation energy is a function of temperature and the stress state of the mixture. The incorporation of such an activation energy is selected in this thesis. Then, a multi-scale chemical reaction model for a heterogeneous mixture is introduced. This model incorporates reaction initiation, propagation, and extent of completed reaction in spatially heterogeneous distributions of reactants. A new model is proposed for the pore collapse of mixtures. This model is formulated by modifying the Carol, Holt, and Nesterenko spherically symmetric model to include mixtures and compressibility effects. Uncertainties in the model result from assumptions in formulating the models for continuum relationships and chemical reactions in mixtures that are distributed heterogeneously in space and in numerical integration of the resulting equations. It is important to quantify these uncertainties. In this thesis, such an uncertainty quantification is investigated by systematically identifying the physical processes that occur during shock compression of ESMs which are

  18. Laser-induced vibrational dynamics of ozone in solid argon

    DEFF Research Database (Denmark)

    Hansen, Flemming Yssing; Amstrup, B.; Henriksen, Niels Engholm

    1997-01-01

    We consider the vibrational dynamics, induced by an intense infrared laser pulse, in an ozone molecule with isotopic substitution, that is, (OOO)-O-16-O-16-O-18 and compare the dynamics in the gas phase and in solid ar on. not perturbed by argon on a time-scale of a few picoseconds and selective...

  19. Chemical reaction dynamics of PeCB and TCDD decomposition: A tight-binding quantum chemical molecular dynamics study with first-principles parameterization

    Science.gov (United States)

    Suzuki, Ai; Selvam, Parasuraman; Kusagaya, Tomonori; Takami, Seiichi; Kubo, Momoji; Imamura, Akira; Miyamoto, Akira

    The decomposition reaction dynamics of 2,3,4,4',5-penta-chlorinated biphenyl (2,3,4,4',5-PeCB), 3,3',4,4',5-penta-chlorinated biphenyl (3,3',4,4',5-PeCB), and 2,3,7,8-tetra-chlorinated dibenzo-p-dioxin (2,3,7,8-TCDD) was clarified for the first time at atomic and electronic levels, using our novel tight-binding quantum chemical molecular dynamics method with first-principles parameterization. The calculation speed of our new method is over 5000 times faster than that of the conventional first-principles molecular dynamics method. We confirmed that the structure, energy, and electronic states of the above molecules calculated by our new method are quantitatively consistent with those by first-principles calculations. After the confirmation of our methodology, we investigated the decomposition reaction dynamics of the above molecules and the calculated dynamic behaviors indicate that the oxidation of the 2,3,4,4',5-PeCB, 3,3',4,4',5-PeCB, and 2,3,7,8-TCDD proceeds through an epoxide intermediate, which is in good agreement with the previous experimental reports and consistent with our static density functional theory calculations. These results proved that our new tight-binding quantum chemical molecular dynamics method with first-principles parameterization is an effective tool to clarify the chemical reaction dynamics at reaction temperatures.

  20. Protein's native state stability in a chemically induced denaturation mechanism.

    Science.gov (United States)

    Olivares-Quiroz, L; Garcia-Colin, L S

    2007-05-21

    In this work, we present a generalization of Zwanzig's protein unfolding analysis [Zwanzig, R., 1997. Two-state models of protein folding kinetics. Proc. Natl Acad. Sci. USA 94, 148-150; Zwanzig, R., 1995. Simple model of protein folding kinetics. Proc. Natl Acad. Sci. USA 92, 9801], in order to calculate the free energy change Delta(N)(D)F between the protein's native state N and its unfolded state D in a chemically induced denaturation. This Extended Zwanzig Model (EZM) is both based on an equilibrium statistical mechanics approach and the inclusion of experimental denaturation curves. It enables us to construct a suitable partition function Z and to derive an analytical formula for Delta(N)(D)F in terms of the number K of residues of the macromolecule, the average number nu of accessible states for each single amino acid and the concentration C(1/2) where the midpoint of the ND transition occurs. The results of the EZM for proteins where chemical denaturation follows a sigmoidal-type profile, as it occurs for the case of the T70N human variant of lysozyme (PDB code: T70N) [Esposito, G., et al., 2003. J. Biol. Chem. 278, 25910-25918], can be splitted into two lines. First, EZM shows that for sigmoidal denaturation profiles, the internal degrees of freedom of the chain play an outstanding role in the stability of the native state. On the other hand, that under certain conditions DeltaF can be written as a quadratic polynomial on concentration C(1/2), i.e., DeltaF approximately aC(1/2)(2)+bC(1/2)+c, where a,b,c are constant coefficients directly linked to protein's size K and the averaged number of non-native conformations nu. Such functional form for DeltaF has been widely known to fit experimental measures in chemically induced protein denaturation [Yagi, M., et al., 2003. J. Biol. Chem. 278, 47009-47015; Asgeirsson, B., Guojonsdottir, K., 2006. Biochim. Biophys. Acta 1764, 190-198; Sharma, S., et al., 2006. Protein Pept. Lett. 13(4), 323-329; Salem, M., et al

  1. Vacuum Ultraviolet Laser Probe of Chemical Dynamics of Aerospace Relevance

    Science.gov (United States)

    2012-09-12

    valuable for modeling aerospace environments using the Direct Simulation Monte Carlo and Particles in Cell methods. Environments of interest to the...School of Chemical Biology and Biotechnology”, Shenzhen , China, Nov. 21, 2010. 29. C. Y. Ng, “The Role of Basic (Chemical) Research in Modern

  2. Charged impurity-induced scatterings in chemical vapor deposited graphene

    Energy Technology Data Exchange (ETDEWEB)

    Li, Ming-Yang; Tang, Chiu-Chun [Department of Physics, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Ling, D. C. [Department of Physics, Tamkang University, Tamsui Dist., New Taipei 25137, Taiwan (China); Li, L. J. [Department of Physics, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 11529, Taiwan (China); Chi, C. C.; Chen, Jeng-Chung [Department of Physics, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan (China)

    2013-12-21

    We investigate the effects of defect scatterings on the electric transport properties of chemical vapor deposited (CVD) graphene by measuring the carrier density dependence of the magneto-conductivity. To clarify the dominant scattering mechanism, we perform extensive measurements on large-area samples with different mobility to exclude the edge effect. We analyze our data with the major scattering mechanisms such as short-range static scatters, short-range screened Coulomb disorders, and weak-localization (WL). We establish that the charged impurities are the predominant scatters because there is a strong correlation between the mobility and the charge impurity density. Near the charge neutral point (CNP), the electron-hole puddles that are induced by the charged impurities enhance the inter-valley scattering, which is favorable for WL observations. Away from the CNP, the charged-impurity-induced scattering is weak because of the effective screening by the charge carriers. As a result, the local static structural defects govern the charge transport. Our findings provide compelling evidence for understanding the scattering mechanisms in graphene and pave the way for the improvement of fabrication techniques to achieve high-quality CVD graphene.

  3. Modeling and dynamic simulation of ultraviolet induced growing interfaces

    Science.gov (United States)

    Flicstein, J.; Guillonneau, E.; Pata, S.; Kee Chun, L. S.; Palmier, J. F.; Daguet, C.; Courant, J. L.

    1999-01-01

    A solid-on-solid (SOS) model to simulate SiN:H dynamic surface characteristics in ultraviolet chemical vapor deposition (CVD) onto indium phosphide is presented. It is recognized that the nucleation process occurs at an UV induced active charged center on the surface of the substrate. Photolysis rates are determined using bond dissociation energies for molecular processes to generate active adsorbed species. The microscopic activation energy in elementary processes depends on the configuration of neighbouring atoms. Monte Carlo-Metropolis method using microscopic activation energy barriers is taken into account in molecular processes by a three-dimensional algorithm. The model includes lattice coordination and atom-atom interactions out to third-nearest neighbours. The molecular events are chosen with a probability of occurrence that depends on the kinetic rates at each atomic site. Stable incorporation of main species is enabled. Three-dimensional simulation of a growing interface indicates validation of a thermally activated rough-smooth transition for submicronic thick layers in the Kardar-Parisi-Zhang model.

  4. Lattice dynamics and disorder-induced contraction in functionalized graphene

    Science.gov (United States)

    Feng Huang, Liang; Zeng, Zhi

    2013-02-01

    The lattice dynamics and disorder-induced contraction in hydrogenated, fluorinated, and chlorinated graphene are studied by first-principles simulation. The effects of the functionalization on the phonon dispersions, Grüneissen constants, vibrational thermodynamic functions (free energy, internal energy, entropy, and heat capacity), thermal-expansion coefficients, and bulk moduli are systematically investigated. Functionalization changes the chemical-bond length, mass, thickness, vibrational-mode symmetry, and mode number, and subsequently has significant effects on the phonon dispersions and Grüneissen constants. Functionalization generally increases the vibrational thermodynamic functions, and their temperature dependences all present conventional isotope effects. Functionalization suppresses (enhances) the thermal contraction (expansion) of the lattice, due to the increases in the system mass, membrane thickness, and the compressibility of the phonons. Both the lattice-constant variation and the phonon thermalization contribute to the temperature dependence of the bulk modulus. Both pristine and hydrogenated graphene can be viewed as two kinds of materials having the Invar and Elinvar properties. The contribution to the lattice contraction in functionalized graphene from the conformation disorder (about 2.0%) is much larger than that by thermalization (<0.1% at 300 K), which explains the mismatch between the experimental and theoretical lattice constants.

  5. CD-REST: a system for extracting chemical-induced disease relation in literature

    OpenAIRE

    Xu, Jun; Wu, Yonghui; Zhang, Yaoyun; Wang, Jingqi; Lee, Hee-jin; Xu, Hua

    2016-01-01

    Mining chemical-induced disease relations embedded in the vast biomedical literature could facilitate a wide range of computational biomedical applications, such as pharmacovigilance. The BioCreative V organized a Chemical Disease Relation (CDR) Track regarding chemical-induced disease relation extraction from biomedical literature in 2015. We participated in all subtasks of this challenge. In this article, we present our participation system Chemical Disease Relation Extraction SysTem (CD-RE...

  6. Correlation between dynamic wetting behavior and chemical components of thermally modified wood

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Wang; Zhu, Yuan; Cao, Jinzhen, E-mail: caoj@bjfu.edu.cn; Sun, Wenjing

    2015-01-01

    Highlights: • We studied the dynamic wetting behavior of thermally modified wood by wetting models. • We found lower wetting speed of water droplets on thermally modified wood surface. • Dynamic wetting behavior and surface chemical components show a strong correlation. - Abstract: In order to investigate the dynamic wetting behavior of thermally modified wood, Cathay poplar (Populus cathayana Rehd.) and Scots pine (Pinus sylvestris L.) samples were thermally modified in an oven at 160, 180, 200, 220 or 240 °C for 4 h in this study. The dynamic contact angles and droplet volumes of water droplets on modified and unmodified wood surfaces were measured by sessile drop method, and their changing rates (expression index: K value and wetting slope) calculated by wetting models were illustrated for mapping the dynamic wetting process. The surface chemical components were also measured by X-ray photoelectron spectroscopy analysis (XPS), thus the relationship between dynamic wetting behavior and chemical components of thermally modified wood were determined. The results indicated that thermal modification was capable of decreasing the dynamic wettability of wood, expressed in lowing spread and penetration speed of water droplets on wood surfaces. This change was more obvious with the increased heating temperature. The K values varied linearly with the chemical components parameter (mass loss, O/C ratio, and C{sub 1}/C{sub 2} ratio), indicating a strong correlation between dynamic wetting behavior and chemical components of thermally modified wood.

  7. (--Pentazocine induces visceral chemical antinociception, but not thermal, mechanical, or somatic chemical antinociception, in μ-opioid receptor knockout mice

    Directory of Open Access Journals (Sweden)

    Satoh Masamichi

    2011-04-01

    Full Text Available Abstract Background (--Pentazocine has been hypothesized to induce analgesia via the κ-opioid (KOP receptor, although the involvement of other opioid receptor subtypes in the effects of pentazocine remains unknown. In this study, we investigated the role of the μ-opioid (MOP receptor in thermal, mechanical, and chemical antinociception induced by (--pentazocine using MOP receptor knockout (MOP-KO mice. Results (--Pentazocine-induced thermal antinociception, assessed by the hot-plate and tail-flick tests, was significantly reduced in heterozygous and abolished in homozygous MOP-KO mice compared with wildtype mice. The results obtained from the (--pentazocine-induced mechanical and somatic chemical antinociception experiments, which used the hind-paw pressure and formalin tests, were similar to the results obtained from the thermal antinociception experiments in these mice. However, (--pentazocine retained its ability to induce significant visceral chemical antinociception, assessed by the writhing test, in homozygous MOP-KO mice, an effect that was completely blocked by pretreatment with nor-binaltorphimine, a KOP receptor antagonist. In vitro binding and cyclic adenosine monophosphate assays showed that (--pentazocine possessed higher affinity for KOP and MOP receptors than for δ-opioid receptors. Conclusions The present study demonstrated the abolition of the thermal, mechanical, and somatic chemical antinociceptive effects of (--pentazocine and retention of the visceral chemical antinociceptive effects of (--pentazocine in MOP-KO mice. These results suggest that the MOP receptor plays a pivotal role in thermal, mechanical, and somatic chemical antinociception induced by (--pentazocine, whereas the KOP receptor is involved in visceral chemical antinociception induced by (--pentazocine.

  8. Flow-Induced Control of Pattern Formation in Chemical Systems

    Science.gov (United States)

    Berenstein, Igal; Beta, Carsten

    Since Alan Turing's seminal paper in 1952, the study of spatio-temporal patterns that arise in systems of reacting and diffusing components has grown into an immense and vibrant realm of scientific research. This field includes not only chemical systems but spans many areas of science as diverse as cell and developmental biology, ecology, geosciences, or semiconductor physics. For several decades research in this field has concentrated on the vast variety of patterns that can emerge in reaction-diffusion systems and on the underlying instabilities. In the 1990s, stimulated by the pioneering work of Ott, Grebogi and Yorke, control of pattern formation arose as a new topical focus and gradually developed into an entire new field of research. On the one hand, research interests concentrated on control and suppression of undesired dynamical states, in particular on control of chaos. On the other hand, the design and engineering of particular space-time patterns became a major focus in this field that motivates ongoing scientific effort until today...

  9. Radiation induced dynamic mutations and transgenerational effects.

    Science.gov (United States)

    Niwa, Ohtsura

    2006-01-01

    Many studies have confirmed that radiation can induce genomic instability in whole body systems. Although the molecular mechanisms underlying induced genomic instability are not known at present, this interesting phenomenon could be the manifestation of a cellular fail-safe system in which fidelity of repair and replication is down-regulated to tolerate DNA damage. Two features of genomic instability namely, delayed mutation and untargeted mutation, require two mechanisms of ;damage memory' and ;damage sensing, signal transduction and execution' to induce mutations at a non damaged-site. In this report, the phenomenon of transgenerational genomic instability and possible mechanisms are discussed using mouse data collected in our laboratory as the main bases.

  10. Dissipative particle dynamics simulation of wettability alternation phenomena in the chemical flooding process

    Institute of Scientific and Technical Information of China (English)

    Xiaobo Li; Yuewu Liu; Jianfei Tang; Shujiao Li

    2009-01-01

    Wettability alternation phenomena is considered one of the most important enhanced oil recovery (EOR) mechanisms in the chemical flooding process and induced by the adsorption of surfactant on the rock surface. These phenomena are studied by a mesoscopic method named as dissipative particle dynamics (DPD). Both the alteration phenomena of water-wet to oil-wet and that of oil-wet to waterwet are simulated based on reasonable definition of interaction parameters between beads. The wetting hysteresis phenomenon and the process of oil-drops detachment from rock surfaces with different wettability are simulated by adding long-range external forces on the fluid particles. The simulation results show that, the oil drop is liable to spread on the oil-wetting surface and move in the form of liquid film flow, whereas it is likely to move as a whole on the waterwetting surface. There are the same phenomena occuring in wettability-alternated cases. The results also show that DPD method provides a feasible approach to the problems of seepage flow with physicochemical phenomena and can be used to study the mechanism of EOR of chemical flooding.

  11. Compositeness Condition for Dynamically Induced Gauge Theories

    CERN Document Server

    Akama, K; Akama, Keiichi; Hattori, Takashi

    1997-01-01

    We show that the compositeness condition for the induced gauge boson in the four-fermion interaction theory actually works beyond the one-loop approximation. The next-to-leading contributions are calculated, and turn out to be reasonably suppressed, so that the leading-order approximation is justified.

  12. Dynamic optically induced planar terahertz quasioptics

    DEFF Research Database (Denmark)

    Cooke, David; Jepsen, Peter Uhd

    2009-01-01

    that photoexcitations with sufficient conductivity can induce a partial reflection, capable of steering the pulse inside the two-dimensional waveguide. A beamsplitter is demonstrated as proof of principle and is used to delay the arrival of the reflected terahertz pulse at the detector by several picoseconds by moving...

  13. Chemical Kinetics, Heat Transfer, and Sensor Dynamics Revisited in a Simple Experiment

    Science.gov (United States)

    Sad, Maria E.; Sad, Mario R.; Castro, Alberto A.; Garetto, Teresita F.

    2008-01-01

    A simple experiment about thermal effects in chemical reactors is described, which can be used to illustrate chemical reactor models, the determination and validation of their parameters, and some simple principles of heat transfer and sensor dynamics. It is based in the exothermic reaction between aqueous solutions of sodium thiosulfate and…

  14. Chemical Kinetics, Heat Transfer, and Sensor Dynamics Revisited in a Simple Experiment

    Science.gov (United States)

    Sad, Maria E.; Sad, Mario R.; Castro, Alberto A.; Garetto, Teresita F.

    2008-01-01

    A simple experiment about thermal effects in chemical reactors is described, which can be used to illustrate chemical reactor models, the determination and validation of their parameters, and some simple principles of heat transfer and sensor dynamics. It is based in the exothermic reaction between aqueous solutions of sodium thiosulfate and…

  15. Modeling of glutamate-induced dynamical patterns

    DEFF Research Database (Denmark)

    Faurby-Bentzen, Christian Krefeld; Zhabotinsky, A.M.; Laugesen, Jakob Lund

    2009-01-01

    Based on established physiological mechanisms, the paper presents a detailed computer model, which supports the hypothesis that temporal lobe epilepsy may be caused by failure of glutamate reuptake from the extracellular space. The elevated glutamate concentration causes an increased activation o...... of NMDA receptors in pyramidal neurons, which in turn leads to neuronal dynamics that is qualitatively identical to epileptiform activity. We identify by chaos analysis a surprising possibility that muscarinergic receptors can help the system out of a chaotic regime....

  16. Photo-induced chemical reaction of trans-resveratrol.

    Science.gov (United States)

    Zhao, Yue; Shi, Meng; Ye, Jian-Hui; Zheng, Xin-Qiang; Lu, Jian-Liang; Liang, Yue-Rong

    2015-03-15

    Photo-induced chemical reaction of trans-resveratrol has been studied. UV B, liquid state and sufficient exposure time are essential conditions to the photochemical change of trans-resveratrol. Three principal compounds, cis-resveratrol, 2,4,6-phenanthrenetriol and 2-(4-hydroxyphenyl)-5,6-benzofurandione, were successively generated in the reaction solution of trans-resveratrol (0.25 mM, 100% ethanol) under 100 μW cm(-2) UV B radiation for 4h. cis-Resveratrol, originated from isomerization of trans-resveratrol, resulted in 2,4,6-phenanthrenetriol through photocyclisation reaction meanwhile loss of 2 H. 2,4,6-Phenanthrenetriol played a role of photosensitizer producing singlet oxygen in the reaction pathway. The singlet oxygen triggered [4+2] cycloaddition reaction of trans-resveratrol, and then resulted in the generation of 2-(4-hydroxyphenyl)-5,6-benzofurandione through photorearrangement and oxidation reaction. The singlet oxygen reaction was closely related to the substrate concentration of trans-resveratrol in solution.

  17. Crossed Molecular Beam Studies and Dynamics of Decomposition of Chemically Activated Radicals

    Science.gov (United States)

    Lee, Y. T.

    1973-09-01

    The power of the crossed molecular beams method in the investigation of the dynamics of chemical reactions lies mainly in the direct observation of the consequences of single collisions of well controlled reactant molecules. The primary experimental observations which provide information on reaction dynamics are the measurements of angular and velocity distributions of reaction products.

  18. Design of multi-phase dynamic chemical networks

    Science.gov (United States)

    Chen, Chenrui; Tan, Junjun; Hsieh, Ming-Chien; Pan, Ting; Goodwin, Jay T.; Mehta, Anil K.; Grover, Martha A.; Lynn, David G.

    2017-08-01

    Template-directed polymerization reactions enable the accurate storage and processing of nature's biopolymer information. This mutualistic relationship of nucleic acids and proteins, a network known as life's central dogma, is now marvellously complex, and the progressive steps necessary for creating the initial sequence and chain-length-specific polymer templates are lost to time. Here we design and construct dynamic polymerization networks that exploit metastable prion cross-β phases. Mixed-phase environments have been used for constructing synthetic polymers, but these dynamic phases emerge naturally from the growing peptide oligomers and create environments suitable both to nucleate assembly and select for ordered templates. The resulting templates direct the amplification of a phase containing only chain-length-specific peptide-like oligomers. Such multi-phase biopolymer dynamics reveal pathways for the emergence, self-selection and amplification of chain-length- and possibly sequence-specific biopolymers.

  19. Advances in chemical physics dynamical processes in condensed matter

    CERN Document Server

    Evans, Myron W

    2009-01-01

    Transport Properties and Soliton Models for Polyacetylene (M. Andretta, et al.). Development and Application of the Theory of Brownian Motion (W. Coffey). The Fading of Memory During the Regression of Structural Fluctuations (L. Dissado, et al.). Cooperative Molecular Behavior and Field Effects on Liquids: Experimental Considerations (G. Evans). A Review and Computer Simulation of the Molecular Dynamics of a Series of Specific Molecular Liquids (M. Evans and G. Evans). Recent Advances in Molecular-Dynamics Computer Simulation (D. Fincham and D. Heyes). Nonadiabatic Scattering Probl

  20. Agent-Based Chemical Plume Tracing Using Fluid Dynamics

    Science.gov (United States)

    Zarzhitsky, Dimitri; Spears, Diana; Thayer, David; Spears, William

    2004-01-01

    This paper presents a rigorous evaluation of a novel, distributed chemical plume tracing algorithm. The algorithm is a combination of the best aspects of the two most popular predecessors for this task. Furthermore, it is based on solid, formal principles from the field of fluid mechanics. The algorithm is applied by a network of mobile sensing agents (e.g., robots or micro-air vehicles) that sense the ambient fluid velocity and chemical concentration, and calculate derivatives. The algorithm drives the robotic network to the source of the toxic plume, where measures can be taken to disable the source emitter. This work is part of a much larger effort in research and development of a physics-based approach to developing networks of mobile sensing agents for monitoring, tracking, reporting and responding to hazardous conditions.

  1. Differential Gene Expression in Chemically Induced Mouse Lung Adenomas

    Directory of Open Access Journals (Sweden)

    Ruisheng Yao

    2003-01-01

    Full Text Available Because of similarities in histopathology and tumor progression stages between mouse and human lung adenocarcinomas, the mouse lung tumor model with lung adenomas as the endpoint has been used extensively to evaluate the efficacy of putative lung cancer chemopreventive agents. In this study, a competitive cDNA library screening (CCLS was employed to determine changes in the expression of mRNA in chemically induced lung adenomas compared with paired normal lung tissues. A total of 2555 clones having altered expression in tumors were observed following competitive hybridization between normal lung and lung adenomas after primary screening of over 160,000 clones from a mouse lung cDNA library. Among the 755 clones confirmed by dot blot hybridization, 240 clones were underexpressed, whereas 515 clones were overexpressed in tumors. Sixty-five clones with the most frequently altered expression in six individual tumors were confirmed by semiquantitative RT-PCR. When examining the 58 known genes, 39 clones had increased expression and 19 had decreased expression, whereas the 7 novel genes showed overexpression. A high percentage (>60% of overexpressed or underexpressed genes was observed in at least two or three of the lesions. Reproducibly overexpressed genes included ERK-1, JAK-1, surfactant proteins A, B, and C, NFAT1, α-1 protease inhibitor, helix-loop-helix ubiquitous kinase (CHUK, α-adaptin, α-1 PI2, thioether S-methyltransferase, and CYP2C40. Reproducibly underexpressed genes included paroxanase, ALDH II, CC10, von Ebner salivary gland protein, and α- and β-globin. In addition, CCLS identified several novel genes or genes not previously associated with lung carcinogenesis, including a hypothetical protein (FLJ11240 and a guanine nucleotide exchange factor homologue. This study shows the efficacy of this methodology for identifying genes with altered expression. These genes may prove to be helpful in our understanding of the genetic basis of

  2. RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics

    KAUST Repository

    Suleimanov, Yu.V.

    2013-03-01

    We present RPMDrate, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any complexity in their full dimensionality. The program has been tested for the H+H2, H+CH 4, OH+CH4 and H+C2H6 reactions. © 2012 Elsevier B.V. All rights reserved.

  3. Effect of Coriolis coupling in chemical reaction dynamics.

    Science.gov (United States)

    Chu, Tian-Shu; Han, Ke-Li

    2008-05-14

    It is essential to evaluate the role of Coriolis coupling effect in molecular reaction dynamics. Here we consider Coriolis coupling effect in quantum reactive scattering calculations in the context of both adiabaticity and nonadiabaticity, with particular emphasis on examining the role of Coriolis coupling effect in reaction dynamics of triatomic molecular systems. We present the results of our own calculations by the time-dependent quantum wave packet approach for H + D2 and F(2P3/2,2P1/2) + H2 as well as for the ion-molecule collisions of He + H2 +, D(-) + H2, H(-) + D2, and D+ + H2, after reviewing in detail other related research efforts on this issue.

  4. Wide Dynamic Range CMOS Potentiostat for Amperometric Chemical Sensor

    Directory of Open Access Journals (Sweden)

    Wei-Song Wang

    2010-03-01

    Full Text Available Presented is a single-ended potentiostat topology with a new interface connection between sensor electrodes and potentiostat circuit to avoid deviation of cell voltage and linearly convert the cell current into voltage signal. Additionally, due to the increased harmonic distortion quantity when detecting low-level sensor current, the performance of potentiostat linearity which causes the detectable current and dynamic range to be limited is relatively decreased. Thus, to alleviate these irregularities, a fully-differential potentiostat is designed with a wide output voltage swing compared to single-ended potentiostat. Two proposed potentiostats were implemented using TSMC 0.18-μm CMOS process for biomedical application. Measurement results show that the fully differential potentiostat performs relatively better in terms of linearity when measuring current from 500 ºpA to 10 uA. Besides, the dynamic range value can reach a value of 86 dB.

  5. Wide Dynamic Range CMOS Potentiostat for Amperometric Chemical Sensor

    OpenAIRE

    Wei-Song Wang; Wei-Ting Kuo; Hong-Yi Huang; Ching-Hsing Luo

    2010-01-01

    Presented is a single-ended potentiostat topology with a new interface connection between sensor electrodes and potentiostat circuit to avoid deviation of cell voltage and linearly convert the cell current into voltage signal. Additionally, due to the increased harmonic distortion quantity when detecting low-level sensor current, the performance of potentiostat linearity which causes the detectable current and dynamic range to be limited is relatively decreased. Thus, to alleviate these irreg...

  6. Time-resolved imaging of purely valence-electron dynamics during a chemical reaction

    DEFF Research Database (Denmark)

    Hockett, Paul; Bisgaard, Christer Z.; Clarkin, Owen J.

    2011-01-01

    Chemical reactions are manifestations of the dynamics of molecular valence electrons and their couplings to atomic motions. Emerging methods in attosecond science can probe purely electronic dynamics in atomic and molecular systems(1-6). By contrast, time-resolved structural-dynamics methods......,17): in both cases, this sensitivity derives from the ionization-matrix element(18,19). Here we demonstrate a time-resolved molecular-frame photoelectron-angular-distribution (TRMFPAD) method for imaging the purely valence-electron dynamics during a chemical reaction. Specifically, the TRMFPADs measured during...... the non-adiabatic photodissociation of carbon disulphide demonstrate how the purely electronic rearrangements of the valence electrons can be projected from inherently coupled electronic-vibrational dynamics. Combined with ongoing efforts in molecular frame alignment(20) and orientation(21,22), TRMFPADs...

  7. Dynamics of the chemical composition of rainwater throughout Hurricane Irene

    Directory of Open Access Journals (Sweden)

    K. M. Mullaugh

    2013-03-01

    Full Text Available Sequential sampling of rainwater from Hurricane Irene was carried out in Wilmington, NC, USA on 26 and 27 August 2011. Eleven samples were analyzed for pH, major ions (Cl−, NO3−, SO42−, Na+, K+, Mg2+, Ca2+, NH4+, dissolved organic carbon (DOC and hydrogen peroxide (H2O2. Hurricane Irene contributed 16% of the total rainwater and 18% of the total chloride wet deposition received in Wilmington NC during all of 2011. This work highlights the main physical factors influencing the chemical composition of tropical storm rainwater: wind speed, wind direction, back trajectory and vertical mixing, time of day and total rain volume. Samples collected early in the storm, when winds blew out of the east, contained dissolved components indicative of marine sources (salts from sea spray and low DOC. The sea-salt components in the samples had two maxima in concentration during the storm the first of which occurred before the volume of rain had sufficiently washed out sea salt from the atmosphere and the second when back trajectories showed large volumes of marine surface air were lifted. As the storm progressed and winds shifted to a westerly direction, the chemical composition of the rainwater became characteristic of terrestrial storms (high DOC and NH4+ and low sea salt. This work demonstrates that tropical storms are not only responsible for significant wet deposition of marine components to land, but terrestrial components can also become entrained in rainwater, which can then be delivered to coastal waters via wet deposition. This study also underscores why analysis of one composite sample can lead to an incomplete interpretation of the factors that influence the chemically divergent analytes in rainwater during extreme weather events.

  8. Dynamically Induced Planck Scale and Inflation

    CERN Document Server

    Kannike, Kristjan; Pizza, Liberato; Racioppi, Antonio; Raidal, Martti; Salvio, Alberto; Strumia, Alessandro

    2015-01-01

    Theories where the Planck scale is dynamically generated from dimensionless interactions provide predictive inflationary potentials and super-Planckian field variations. We first study the minimal single-field realisation in the low-energy effective field theory limit, finding the predictions $n_s \\approx 0.96$ for the spectral index and $r \\approx 0.13$ for the tensor-to-scalar ratio, close to those of a quadratic potential. Next we consider agravity as a dimensionless quantum gravity theory finding a multi-field inflation that converges towards an attractor trajectory that predicts $n_s\\approx 0.96$ and $0.003

  9. Dissipative Particle Dynamics of tension-induced membrane fusion

    DEFF Research Database (Denmark)

    Shillcock, Julian C.

    2009-01-01

    Recent studies of tension-induced membrane fusion using dissipative particle dynamics (DPD) simulations are briefly reviewed. The stochastic nature of the fusion process makes it necessary to simulate a large number of fusion attempts in order to obtain reliable fusion statistics and to extract...

  10. Correlation between dynamic wetting behavior and chemical components of thermally modified wood

    Science.gov (United States)

    Wang, Wang; Zhu, Yuan; Cao, Jinzhen; Sun, Wenjing

    2015-01-01

    In order to investigate the dynamic wetting behavior of thermally modified wood, Cathay poplar (Populus cathayana Rehd.) and Scots pine (Pinus sylvestris L.) samples were thermally modified in an oven at 160, 180, 200, 220 or 240 °C for 4 h in this study. The dynamic contact angles and droplet volumes of water droplets on modified and unmodified wood surfaces were measured by sessile drop method, and their changing rates (expression index: K value and wetting slope) calculated by wetting models were illustrated for mapping the dynamic wetting process. The surface chemical components were also measured by X-ray photoelectron spectroscopy analysis (XPS), thus the relationship between dynamic wetting behavior and chemical components of thermally modified wood were determined. The results indicated that thermal modification was capable of decreasing the dynamic wettability of wood, expressed in lowing spread and penetration speed of water droplets on wood surfaces. This change was more obvious with the increased heating temperature. The K values varied linearly with the chemical components parameter (mass loss, O/C ratio, and C1/C2 ratio), indicating a strong correlation between dynamic wetting behavior and chemical components of thermally modified wood.

  11. Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins

    Energy Technology Data Exchange (ETDEWEB)

    Karp, Jerome M.; Erylimaz, Ertan; Cowburn, David, E-mail: cowburn@cowburnlab.org, E-mail: David.cowburn@einstein.yu.edu [Albert Einstein College of Medicine of Yeshiva University, Department of Biochemistry (United States)

    2015-01-15

    There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We find that using MD simulation data as input for chemical shift prediction does not consistently improve prediction accuracy over use of a static X-ray crystal structure. This appears to result from the complex conformational ensemble of the disordered protein segments. We show that using accelerated molecular dynamics (aMD) simulations improves chemical shift prediction, suggesting that methods which better sample the conformational ensemble like aMD are more appropriate tools for use in chemical shift prediction for proteins with disordered regions. Moreover, our study suggests that data accurately reflecting protein dynamics must be used as input for chemical shift prediction in order to correctly predict chemical shifts in systems with disorder.

  12. Competition induces allelopathy but suppresses growth and anti-herbivore defence in a chemically rich seaweed.

    Science.gov (United States)

    Rasher, Douglas B; Hay, Mark E

    2014-02-22

    Many seaweeds and terrestrial plants induce chemical defences in response to herbivory, but whether they induce chemical defences against competitors (allelopathy) remains poorly understood. We evaluated whether two tropical seaweeds induce allelopathy in response to competition with a reef-building coral. We also assessed the effects of competition on seaweed growth and seaweed chemical defence against herbivores. Following 8 days of competition with the coral Porites cylindrica, the chemically rich seaweed Galaxaura filamentosa induced increased allelochemicals and became nearly twice as damaging to the coral. However, it also experienced significantly reduced growth and increased palatability to herbivores (because of reduced chemical defences). Under the same conditions, the seaweed Sargassum polycystum did not induce allelopathy and did not experience a change in growth or palatability. This is the first demonstration of induced allelopathy in a seaweed, or of competitors reducing seaweed chemical defences against herbivores. Our results suggest that the chemical ecology of coral-seaweed-herbivore interactions can be complex and nuanced, highlighting the need to incorporate greater ecological complexity into the study of chemical defence.

  13. Chemical -induced apoptotic cell death in tomato cells : involvement of caspase-like proteases

    NARCIS (Netherlands)

    Jong, de A.J.; Hoeberichts, F.A.; Yakimova, E.T.; Maximova, E.; Woltering, E.J.

    2000-01-01

    A new system to study programmed cell death in plants is described. Tomato (Lycopersicon esculentum Mill.) suspension cells were induced to undergo programmed cell death by treatment with known inducers of apoptosis in mammalian cells. This chemical-induced cell death was accompanied by the characte

  14. Current-induced dynamics in carbon atomic contacts

    DEFF Research Database (Denmark)

    Lu, Jing Tao; Gunst, Tue; Brandbyge, Mads

    2011-01-01

    voltage, which can be used to explore current-induced vibrational instabilities due the NC/BP forces. Furthermore, using tight-binding and the Brenner potential we illustrate how Langevin-type molecular-dynamics calculations including the Joule heating effect for the carbon-chain systems can be performed...... of molecular-scale contacts. Systems based on molecules bridging electrically gated graphene electrodes may offer an interesting test-bed for these effects. Results: We employ a semi-classical Langevin approach in combination with DFT calculations to study the current-induced vibrational dynamics of an atomic...... carbon chain connecting electrically gated graphene electrodes. This illustrates how the device stability can be predicted solely from the modes obtained from the Langevin equation, including the current-induced forces. We point out that the gate offers control of the current, independent of the bias...

  15. Current-induced dynamics in carbon atomic contacts

    Directory of Open Access Journals (Sweden)

    Jing-Tao Lü

    2011-12-01

    Full Text Available Background: The effect of electric current on the motion of atoms still poses many questions, and several mechanisms are at play. Recently there has been focus on the importance of the current-induced nonconservative forces (NC and Berry-phase derived forces (BP with respect to the stability of molecular-scale contacts. Systems based on molecules bridging electrically gated graphene electrodes may offer an interesting test-bed for these effects.Results: We employ a semi-classical Langevin approach in combination with DFT calculations to study the current-induced vibrational dynamics of an atomic carbon chain connecting electrically gated graphene electrodes. This illustrates how the device stability can be predicted solely from the modes obtained from the Langevin equation, including the current-induced forces. We point out that the gate offers control of the current, independent of the bias voltage, which can be used to explore current-induced vibrational instabilities due the NC/BP forces. Furthermore, using tight-binding and the Brenner potential we illustrate how Langevin-type molecular-dynamics calculations including the Joule heating effect for the carbon-chain systems can be performed. Molecular dynamics including current-induced forces enables an energy redistribution mechanism among the modes, mediated by anharmonic interactions, which is found to be vital in the description of the electrical heating.Conclusion: We have developed a semiclassical Langevin equation approach that can be used to explore current-induced dynamics and instabilities. We find instabilities at experimentally relevant bias and gate voltages for the carbon-chain system.

  16. Coupled molecular dynamics-Monte Carlo model to study the role of chemical processes during laser ablation of polymeric materials.

    Science.gov (United States)

    Prasad, Manish; Conforti, Patrick F; Garrison, Barbara J

    2007-08-28

    The coarse grained chemical reaction model is enhanced to build a molecular dynamics (MD) simulation framework with an embedded Monte Carlo (MC) based reaction scheme. The MC scheme utilizes predetermined reaction chemistry, energetics, and rate kinetics of materials to incorporate chemical reactions occurring in a substrate into the MD simulation. The kinetics information is utilized to set the probabilities for the types of reactions to perform based on radical survival times and reaction rates. Implementing a reaction involves changing the reactants species types which alters their interaction potentials and thus produces the required energy change. We discuss the application of this method to study the initiation of ultraviolet laser ablation in poly(methyl methacrylate). The use of this scheme enables the modeling of all possible photoexcitation pathways in the polymer. It also permits a direct study of the role of thermal, mechanical, and chemical processes that can set off ablation. We demonstrate that the role of laser induced heating, thermomechanical stresses, pressure wave formation and relaxation, and thermochemical decomposition of the polymer substrate can be investigated directly by suitably choosing the potential energy and chemical reaction energy landscape. The results highlight the usefulness of such a modeling approach by showing that various processes in polymer ablation are intricately linked leading to the transformation of the substrate and its ejection. The method, in principle, can be utilized to study systems where chemical reactions are expected to play a dominant role or interact strongly with other physical processes.

  17. Dynamical resonance in F+H2 chemical reaction and rotational excitation effect

    Institute of Scientific and Technical Information of China (English)

    YANG XueMing; XIE DaiQian; ZHANG DongHui

    2007-01-01

    Reaction resonance is a frontier topic in chemical dynamics research, and it is also essential to the understanding of mechanisms of elementary chemical reactions. This short article describes an important development in the frontier of research. Experimental evidence of reaction resonance has been detected in a full quantum state resolved reactive scattering study of the F+H2 reaction. Highly accurate full quantum scattering theoretical modeling shows that the reaction resonance is caused by two Feshbach resonance states. Further studies show that quantum interference is present between the two resonance states for the forward scattering product. This study is a significant step forward in our understanding of chemical reaction resonance in the benchmark F+H2 system. Further experimental studies on the effect of H2 rotational excitation on dynamical resonance have been carried out. Dynamical resonance in the F+H2 (j = 1) reaction has also been observed.

  18. Can Strange Nonchaotic Dynamics be induced through Stochastic Driving?

    CERN Document Server

    Prasad, A K; Prasad, Awadhesh; Ramaswamy, Ramakrishna

    1999-01-01

    Upon addition of noise, chaotic motion in low-dimensional dynamical systems can sometimes be transformed into nonchaotic dynamics: namely, the largest Lyapunov exponent can be made nonpositive. We study this phenomenon in model systems with a view to understanding the circumstances when such behaviour is possible. This technique for inducing ``order'' through stochastic driving works by modifying the invariant measure on the attractor: by appropriately increasing measure on those portions of the attractor where the dynamics is contracting, the overall dynamics can be made nonchaotic, however {\\it not} a strange nonchaotic attractor. Alternately, by decreasing measure on contracting regions, the largest Lyapunov exponent can be enhanced. A number of different chaos control and anticontrol techniques are known to function on this paradigm.

  19. Mixed chemical-induced oxidative stress in occupational exposure ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-03-06

    Mar 6, 2009 ... INTRODUCTION. The risk of chemical toxicity is recognized to be greatest ... Arsenic. Mercury. Cyanide. Chloroform. Alcohol. Ether. Formalin. Phenol. Xylene ..... prevention of cancer and other diseases caused by genome ...

  20. Dynamical and chemical evolution of the thin disc

    Science.gov (United States)

    Just, A.; Rybizki, J.

    2016-09-01

    Our detailed analytic local disc model (JJ-model) quantifies the interrelation between kinematic properties (e.g. velocity dispersions and asymmetric drift), spatial parameters (scale-lengths and vertical density profiles), and properties of stellar sub-populations (age and abundance distributions). Any consistent radial extension of the disc evolution model should predict specific features in the different distribution functions and in their correlations. Large spectroscopic surveys (SEGUE, RAVE, APOGEE, Gaia-ESO) allow significant constraints on the long-term evolution of the thin disc. We discuss the qualitative difference of correlations (like the α-enhancement as function of metallicity) and distribution functions (e.g. in [Mg/H] or [Fe/H]) for the construction of a disc model. In the framework of the JJ-model we build a local chemical enrichment model and show that significant vertical gradients for main sequence and red clump stars are expected in the thin disc. A Jeans analysis of the asymmetric drift provides a link to the radial structure of the disc. The derived metallicity-dependent radial scale-lengths can be combined in the future with the abundance distributions at different Galactocentric distances to construct full disc models. We expect to be able to constrain possible scenarios of inside-out growth of the thin disc and to characterise those populations, which require significant radial migration.

  1. Dynamical and chemical evolution of the thin disc

    CERN Document Server

    Just, Andreas

    2015-01-01

    Our detailed analytic local disc model (JJ-model) quantifies the interrelation between kinematic properties (e.g. velocity dispersions and asymmetric drift), spatial parameters (scale-lengths and vertical density profiles), and properties of stellar sub-populations (age and abundance distributions). Any consistent radial extension of the disc evolution model should predict specific features in the different distribution functions and in their correlations. Large spectroscopic surveys (SEGUE, RAVE, APOGEE, Gaia-ESO) allow significant constraints on the long-term evolution of the thin disc. We discuss the qualitative difference of correlations (like the alpha-enhancement as function of metallicity) and distribution functions (e.g. in [Mg/H] or [Fe/H]) for the construction of a disc model. In the framework of the JJ-model we build a local chemical enrichment model and show that significant vertical gradients for main sequence and red clump stars are expected in the thin disc. A Jeans analysis of the asymmetric d...

  2. Dynamic range in small-world networks of Hodgkin-Huxley neurons with chemical synapses

    Science.gov (United States)

    Batista, C. A. S.; Viana, R. L.; Lopes, S. R.; Batista, A. M.

    2014-09-01

    According to Stevens' law the relationship between stimulus and response is a power-law within an interval called the dynamic range. The dynamic range of sensory organs is found to be larger than that of a single neuron, suggesting that the network structure plays a key role in the behavior of both the scaling exponent and the dynamic range of neuron assemblies. In order to verify computationally the relationships between stimulus and response for spiking neurons, we investigate small-world networks of neurons described by the Hodgkin-Huxley equations connected by chemical synapses. We found that the dynamic range increases with the network size, suggesting that the enhancement of the dynamic range observed in sensory organs, with respect to single neurons, is an emergent property of complex network dynamics.

  3. Microtubule dynamics control HGF-induced lung endothelial barrier enhancement.

    Directory of Open Access Journals (Sweden)

    Xinyong Tian

    Full Text Available Microtubules (MT play a vital role in many cellular functions, but their role in peripheral actin cytoskeletal dynamics which is essential for control of endothelial barrier and monolayer integrity is less understood. We have previously described the enhancement of lung endothelial cell (EC barrier by hepatocyte growth factor (HGF which was associated with Rac1-mediated remodeling of actin cytoskeleton. This study investigated involvement of MT-dependent mechanisms in the HGF-induced enhancement of EC barrier. HGF-induced Rac1 activation was accompanied by phosphorylation of stathmin, a regulator of MT dynamics. HGF also stimulated MT peripheral growth monitored by time lapse imaging and tracking analysis of EB-1-decorated MT growing tips, and increased the pool of acetylated tubulin. These effects were abolished by EC pretreatment with HGF receptor inhibitor, downregulation of Rac1 pathway, or by expression of a stathmin-S63A phosphorylation deficient mutant. Expression of stathmin-S63A abolished the HGF protective effects against thrombin-induced activation of RhoA cascade, permeability increase, and EC barrier dysfunction. These results demonstrate a novel MT-dependent mechanism of HGF-induced EC barrier regulation via Rac1/PAK1/stathmin-dependent control of MT dynamics.

  4. Magnetization dynamics induced by Rashba effect in a Permalloy nanodisk

    Science.gov (United States)

    Li, Huanan; Hua, Zhong; Li, Dongfei

    2017-02-01

    Magnetic vortex dynamics mediated by spin-polarized ac current of different amplitudes and frequencies are investigated by micromagnetic simulations in a system lacking structure inversion symmetry. Micromagnetic calculations reveal that the critical current density required to induce vortex core reversal may be decreased to below 1010 A m-2 due to strong transverse magnetic field by Rashba effect. We also find the spin torque of ac current plays a trivial role in magnetic vortex dynamics in a broken inversion symmetry system when the current density is on the order of 1010 A m-2 and the current with frequency close to the vortex eigenfrequency is the most efficient for reversal.

  5. A Grid-Based Cyber Infrastructure for High Performance Chemical Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Khadka Prashant

    2008-10-01

    Full Text Available Chemical dynamics simulation is an effective means to study atomic level motions of molecules, collections of molecules, liquids, surfaces, interfaces of materials, and chemical reactions. To make chemical dynamics simulations globally accessible to a broad range of users, recently a cyber infrastructure was developed that provides an online portal to VENUS, a popular chemical dynamics simulation program package, to allow people to submit simulation jobs that will be executed on the web server machine. In this paper, we report new developments of the cyber infrastructure for the improvement of its quality of service by dispatching the submitted simulations jobs from the web server machine onto a cluster of workstations for execution, and by adding an animation tool, which is optimized for animating the simulation results. The separation of the server machine from the simulation-running machine improves the service quality by increasing the capacity to serve more requests simultaneously with even reduced web response time, and allows the execution of large scale, time-consuming simulation jobs on the powerful workstation cluster. With the addition of an animation tool, the cyber infrastructure automatically converts, upon the selection of the user, some simulation results into an animation file that can be viewed on usual web browsers without requiring installation of any special software on the user computer. Since animation is essential for understanding the results of chemical dynamics simulations, this animation capacity provides a better way for understanding simulation details of the chemical dynamics. By combining computing resources at locations under different administrative controls, this cyber infrastructure constitutes a grid environment providing physically and administratively distributed functionalities through a single easy-to-use online portal

  6. Enhanced chemical reactivity of graphene induced by mechanical strain.

    Science.gov (United States)

    Bissett, Mark A; Konabe, Satoru; Okada, Susumu; Tsuji, Masaharu; Ago, Hiroki

    2013-11-26

    Control over chemical reactivity is essential in the field of nanotechnology. Graphene is a two-dimensional atomic sheet of sp(2) hybridized carbon with exceptional properties that can be altered by chemical functionalization. Here, we transferred single-layer graphene onto a flexible substrate and investigated the functionalization using different aryl diazonium molecules while applying mechanical strain. We found that mechanical strain can alter the structure of graphene, and dramatically increase the reaction rate, by a factor of up to 10, as well as increase the final degree of functionalization. Furthermore, we demonstrate that mechanical strain enables functionalization of graphene for both p- and n-type dopants, where unstrained graphene showed negligible reactivity. Theoretical calculations were also performed to support the experimental findings. Our findings offer a simple approach to control the chemical reactivity of graphene through the application of mechanical strain, allowing for a tuning of the properties of graphene.

  7. Dynamics of Coalescence-Induced Jumping Water Droplets

    CERN Document Server

    Miljkovic, Nenad; Enright, Ryan; Wang, Evelyn N

    2013-01-01

    This fluid dynamics video shows the different interaction mechanisms of coalescence-induced droplet jumping during condensation on a nanostructured superhydrophobic surface. High speed imaging was used to show jumping behavior on superhydrophobic copper oxide and carbon nanotube surfaces. Videos demonstrating multi-jumping droplets, jumping droplet return to the surface, and droplet-droplet electrostatic repulsions were analyzed. Experiments using external electric fields in conjunction with high speed imaging in a custom built experimental chamber were used to show that all coalescence-induced jumping droplets on superhydrophobic surfaces become positively charged upon leaving the surface, which is detailed in the video.

  8. Simulating Quantum Chemical Dynamics with Improved Superconducting Qubits

    Science.gov (United States)

    Megrant, Anthony E.

    quantum dynamics resulting from a collision between Na and He atoms by encoding the problem into a time-dependent multi-qubit interaction. We compute a scattering cross section by measuring the probability of exciting the Na atom over a wide range of collision parameters. The scattering cross-section shows that there is a velocity where the excitation probability is maximized, in agreement with scattering experiments.

  9. Brownian dynamics simulations of an idealized chemical reaction network under spatial confinement and crowding conditions

    CERN Document Server

    Bellesia, Giovanni

    2015-01-01

    We investigate, via Brownian dynamics simulations, the reaction dynamics of a simple, non-linear chemical network (the Willamowski-Rossler network) under spatial confinement and crowding conditions. Our results show that the presence of inert crowders has a non-nontrivial effect on the dynamics of the network and, consequently, that effective modeling efforts aiming at a general understanding of the behavior of biochemical networks in vivo should be stochastic in nature and based on an explicit representation of both spatial confinement and macromolecular crowding.

  10. Chlorine Dioxide Induced Multiple Chemical Sensitivity: MMPI Validity Problems.

    Science.gov (United States)

    Tentoni, Stuart C.

    This paper discusses Minnesota Multiphasic Personality Inventory (MMPI) data obtained from individuals exposed to chlorine dioxide in the workplace who developed Multiple Chemical Sensitivity Syndrome. The paper explores current research on chlorine dioxide exposed persons who were misdiagnosed on the basis of MMPI interpretations. Difficulties…

  11. Chlorine Dioxide Induced Multiple Chemical Sensitivity: MMPI Validity Problems.

    Science.gov (United States)

    Tentoni, Stuart C.

    This paper discusses Minnesota Multiphasic Personality Inventory (MMPI) data obtained from individuals exposed to chlorine dioxide in the workplace who developed Multiple Chemical Sensitivity Syndrome. The paper explores current research on chlorine dioxide exposed persons who were misdiagnosed on the basis of MMPI interpretations. Difficulties…

  12. Dynamic optimization of chemical cleaning in dead-end ultra filtration

    NARCIS (Netherlands)

    Zondervan, Edwin; Roffel, Brian

    2008-01-01

    In this paper a control strategy is formulated that minimizes the costs for a single chemical cleaning of a dead-end ultra filtration membrane. From the process model, the performance index and the constraints it can be derived that dynamic optimization will lead to a 'maximum effort control problem

  13. Pacemaker interactions induce reentrant wave dynamics in engineered cardiac culture

    Science.gov (United States)

    Borek, Bartłomiej; Shajahan, T. K.; Gabriels, James; Hodge, Alex; Glass, Leon; Shrier, Alvin

    2012-09-01

    Pacemaker interactions can lead to complex wave dynamics seen in certain types of cardiac arrhythmias. We use experimental and mathematical models of pacemakers in heterogeneous excitable media to investigate how pacemaker interactions can be a mechanism for wave break and reentrant wave dynamics. Embryonic chick ventricular cells are cultured invitro so as to create a dominant central pacemaker site that entrains other pacemakers in the medium. Exposure of those cultures to a potassium channel blocker, E-4031, leads to emergence of peripheral pacemakers that compete with each other and with the central pacemaker. Waves emitted by faster pacemakers break up over the slower pacemaker to form reentrant waves. Similar dynamics are observed in a modified FitzHugh-Nagumo model of heterogeneous excitable media with two distinct sites of pacemaking. These findings elucidate a mechanism of pacemaker-induced reentry in excitable media.

  14. The dynamic transfer function for a cavitating inducer

    Science.gov (United States)

    Brennen, C.; Acosta, A. J.

    1975-01-01

    Knowledge of the dynamic performance of pumps is essential for the prediction of transient behavior and instabilities in hydraulic systems; the necessary information is in the form of a transfer function which relates the instantaneous or fluctuating pressure and mass flow rate at inlet to the same quantities in the discharge from the pump. The presence of cavitation within the pump can have a major effect on this transfer function since dynamical changes in the volume of cavitation contribute to the difference in the instantaneous inlet and discharge mass flow rates. The present paper utilizes results from free streamline cascade theory to evaluate the elements in the transfer function for a cavitating inducer and shows that the numerical results are consistent with the characteristics observed in some dynamic tests on rocket engine turbopumps.

  15. Parvovirus induced alterations in nuclear architecture and dynamics.

    Directory of Open Access Journals (Sweden)

    Teemu O Ihalainen

    Full Text Available The nucleus of interphase eukaryotic cell is a highly compartmentalized structure containing the three-dimensional network of chromatin and numerous proteinaceous subcompartments. DNA viruses induce profound changes in the intranuclear structures of their host cells. We are applying a combination of confocal imaging including photobleaching microscopy and computational methods to analyze the modifications of nuclear architecture and dynamics in parvovirus infected cells. Upon canine parvovirus infection, expansion of the viral replication compartment is accompanied by chromatin marginalization to the vicinity of the nuclear membrane. Dextran microinjection and fluorescence recovery after photobleaching (FRAP studies revealed the homogeneity of this compartment. Markedly, in spite of increase in viral DNA content of the nucleus, a significant increase in the protein mobility was observed in infected compared to non-infected cells. Moreover, analysis of the dynamics of photoactivable capsid protein demonstrated rapid intranuclear dynamics of viral capsids. Finally, quantitative FRAP and cellular modelling were used to determine the duration of viral genome replication. Altogether, our findings indicate that parvoviruses modify the nuclear structure and dynamics extensively. Intranuclear crowding of viral components leads to enlargement of the interchromosomal domain and to chromatin marginalization via depletion attraction. In conclusion, parvoviruses provide a useful model system for understanding the mechanisms of virus-induced intranuclear modifications.

  16. Orbital-specific mapping of chemical dynamics with ultrafast x-rays

    Science.gov (United States)

    Wernet, Philippe

    Charge and spin density changes at the metal sites of transition-metal complexes and in metalloproteins determine reactivity and selectivity. To understand their function and to optimize complexes for photocatalytic applications the changes of charge and spin densities need to be mapped and ultimately controlled. I will discuss how time-resolved soft x-ray spectroscopy enables a fundamental understanding of local atomic and intermolecular interactions and their dynamics on atomic length and time scales of Ångströms and femtoseconds. The approach consists in using time-resolved, atom- and orbital-specific x-ray spectroscopy and quantum chemical theory to map the frontier-orbital interactions and their evolution in real time of ultrafast chemical transformations. We recently used femtosecond resonant inelastic x-ray scattering (RIXS, the x-ray analog of resonant Raman scattering) at the x-ray free-electron laser LINAC Coherent Light Source (LCLS, Stanford, USA) to probe the reaction dynamics of a transition-metal complex in solution on the femtosecond time scale. Spin crossover and ligation are found to define the excited-state dynamics. It is demonstrated how correlating orbital symmetry and orbital interactions with spin multiplicity allows for determining the reactivity of short-lived reaction intermediates. I will discuss how this complements approaches that probe structural dynamics and how it can be extended to map the local chemical interactions and their dynamical evolution in metalloproteins.

  17. Interdependence of conformational and chemical reaction dynamics during ion assembly in polar solvents.

    Science.gov (United States)

    Ji, Minbiao; Hartsock, Robert W; Sun, Zheng; Gaffney, Kelly J

    2011-10-01

    We have utilized time-resolved vibrational spectroscopy to study the interdependence of the conformational and chemical reaction dynamics of ion assembly in solution. We investigated the chemical interconversion dynamics of the LiNCS ion pair and the (LiNCS)(2) ion-pair dimer, as well as the spectral diffusion dynamics of these ionic assemblies. For the strongly coordinating Lewis base solvents benzonitrile, dimethyl carbonate, and ethyl acetate, we observe Li(+) coordination by both solvent molecules and NCS(-) anions, while the weak Lewis base solvent nitromethane shows no evidence for solvent coordination of Li(+) ions. The strong interaction between the ion-pair dimer structure and the Lewis base solvents leads to ion-pair dimer solvation dynamics that proceed more slowly than the ion-pair dimer dissociation. We have attributed the slow spectral diffusion dynamics to electrostatic reorganization of the solvent molecules coordinated to the Li(+) cations present in the ion-pair dimer structure and concluded that the dissociation of ion-pair dimers depends more critically on longer length scale electrostatic reorganization. This unusual inversion of the conformational and chemical reaction rates does not occur for ion-pair dimer dissociation in nitromethane or for ion pair association in any of the solvents.

  18. Crossfit analysis: a novel method to characterize the dynamics of induced plant responses.

    Science.gov (United States)

    Jansen, Jeroen J; van Dam, Nicole M; Hoefsloot, Huub C J; Smilde, Age K

    2009-12-16

    Many plant species show induced responses that protect them against exogenous attacks. These responses involve the production of many different bioactive compounds. Plant species belonging to the Brassicaceae family produce defensive glucosinolates, which may greatly influence their favorable nutritional properties for humans. Each responding compound may have its own dynamic profile and metabolic relationships with other compounds. The chemical background of the induced response is therefore highly complex and may therefore not reveal all the properties of the response in any single model. This study therefore aims to describe the dynamics of the glucosinolate response, measured at three time points after induction in a feral Brassica, by a three-faceted approach, based on Principal Component Analysis. First the large-scale aspects of the response are described in a 'global model' and then each time-point in the experiment is individually described in 'local models' that focus on phenomena that occur at specific moments in time. Although each local model describes the variation among the plants at one time-point as well as possible, the response dynamics are lost. Therefore a novel method called the 'Crossfit' is described that links the local models of different time-points to each other. Each element of the described analysis approach reveals different aspects of the response. The crossfit shows that smaller dynamic changes may occur in the response that are overlooked by global models, as illustrated by the analysis of a metabolic profiling dataset of the same samples.

  19. Crossfit analysis: a novel method to characterize the dynamics of induced plant responses

    Directory of Open Access Journals (Sweden)

    Smilde Age K

    2009-12-01

    Full Text Available Abstract Background Many plant species show induced responses that protect them against exogenous attacks. These responses involve the production of many different bioactive compounds. Plant species belonging to the Brassicaceae family produce defensive glucosinolates, which may greatly influence their favorable nutritional properties for humans. Each responding compound may have its own dynamic profile and metabolic relationships with other compounds. The chemical background of the induced response is therefore highly complex and may therefore not reveal all the properties of the response in any single model. Results This study therefore aims to describe the dynamics of the glucosinolate response, measured at three time points after induction in a feral Brassica, by a three-faceted approach, based on Principal Component Analysis. First the large-scale aspects of the response are described in a 'global model' and then each time-point in the experiment is individually described in 'local models' that focus on phenomena that occur at specific moments in time. Although each local model describes the variation among the plants at one time-point as well as possible, the response dynamics are lost. Therefore a novel method called the 'Crossfit' is described that links the local models of different time-points to each other. Conclusions Each element of the described analysis approach reveals different aspects of the response. The crossfit shows that smaller dynamic changes may occur in the response that are overlooked by global models, as illustrated by the analysis of a metabolic profiling dataset of the same samples.

  20. Feeder cells support the culture of induced pluripotent stem cells even after chemical fixation.

    Directory of Open Access Journals (Sweden)

    Xiao-Shan Yue

    Full Text Available Chemically fixed mouse embryonic fibroblasts (MEFs, instead of live feeder cells, were applied to the maintenance of mouse induced pluripotent stem (miPS cells. Formaldehyde and glutaraldehyde were used for chemical fixation. The chemically fixed MEF feeders maintained the pluripotency of miPS cells, as well as their undifferentiated state. Furthermore, the chemically fixed MEF feeders were reused several times without affecting their functions. These results indicate that chemical fixation can be applied to modify biological feeders chemically, without losing their original functions. Chemically fixed MEF feeders will be applicable to other stem cell cultures as a reusable extracellular matrix candidate that can be preserved on a long-term basis.

  1. Hazard classification of chemicals inducing haemolytic anaemia: An EU regulatory perspective

    DEFF Research Database (Denmark)

    Muller, A.; Jacobsen, Helene; Healy, E.

    2006-01-01

    Haemolytic anaemia is often induced following prolonged exposure to chemical substances. Currently, under EU Council Directive 67/548/EEC, substances which induce such effects are classified as dangerous and assigned the risk phrase R48 'Danger of serious damage to health by prolonged exposure...

  2. Hazard classification of chemicals inducing haemolytic anaemia: An EU regulatory perspective.

    NARCIS (Netherlands)

    Muller, Andre; Jacobsen, Helene; Healy, Edel; McMickan, Sinead; Istace, Fréderique; Blaude, Marie-Noëlle; Howden, Peter; Fleig, Helmut; Schulte, Agnes

    2006-01-01

    Haemolytic anaemia is often induced following prolonged exposure to chemical substances. Currently, under EU Council Directive 67/548/EEC, substances which induce such effects are classified as dangerous and assigned the risk phrase R48 'Danger of serious damage to health by prolonged exposure.' Whi

  3. Hazard classification of chemicals inducing haemolytic anaemia: An EU regulatory perspective.

    NARCIS (Netherlands)

    Muller, Andre; Jacobsen, Helene; Healy, Edel; McMickan, Sinead; Istace, Fréderique; Blaude, Marie-Noëlle; Howden, Peter; Fleig, Helmut; Schulte, Agnes

    2006-01-01

    Haemolytic anaemia is often induced following prolonged exposure to chemical substances. Currently, under EU Council Directive 67/548/EEC, substances which induce such effects are classified as dangerous and assigned the risk phrase R48 'Danger of serious damage to health by prolonged exposure.' Whi

  4. Fluctuations-induced coexistence in public goods dynamics

    Science.gov (United States)

    Behar, H.; Brenner, N.; Ariel, G.; Louzoun, Y.

    2016-10-01

    Cooperative interactions between individuals in a population and their stability properties are central to population dynamics and evolution. We introduce a generic class of nonlinear dynamical systems describing such interactions between producers and non-producers of a rapidly equilibrating common resource extracted from a finite environment. In the deterministic mean field approximation, fast-growing non-producers drive the entire population to extinction. However, the presence of arbitrarily small perturbations destabilizes this fixed point into a stochastic attractor where both phenotypes can survive. Phase space arguments and moment closure are used to characterize the attractor and show that its properties are not determined by the noise amplitude or boundary conditions, but rather it is stabilized by the stochastic nonlinear dynamics. Spatial Monte Carlo simulations with demographic fluctuations and diffusion illustrate a similar effect, supporting the validity of the two-dimensional stochastic differential equation as an approximation. The functional distribution of the noise emerges as the main factor determining the dynamical outcome. Noise resulting from diffusion between different regions, or additive noise, induce coexistence while multiplicative or local demographic noise do not alter the outcome of deterministic dynamics. The results are discussed in a general context of the effect of noise on phase space structure.

  5. Nonlinear dynamical analysis of carbachol induced hippocampal oscillations in mice

    Institute of Scientific and Technical Information of China (English)

    Metin AKAY; Kui WANG; Yasemin M AKAY; Andrei DRAGOMIR; Jie WU

    2009-01-01

    Aim: Hippocampal neuronal network and synaptic impairment underlie learning and memory deficit in Alzheimer's disease (AD) patients and animal models. In this paper, we analyzed the dynamics and complexity of hippocampal neuronal network synchronization induced by acute exposure to carbachol, a nicotinic and muscarinic receptor co-agonist, using the nonlinear dynamical model based on the Lempel-Ziv estimator. We compared the dynamics of hippocampal oscillations between wild-type (WT) and triple-transgenic (3xTg) mice, as an AD animal model. We also compared these dynamic alterations between different age groups (5 and 10 months). We hypothesize that there is an impairment of complexity of CCh-induced hippocampal oscillations in 3xTg AD mice compared to WT mice, and that this impairment is age-dependent. Methods: To test this hypothesis, we used electrophysiological recordings (field potential) in hippocampal slices. Results: Acute exposure to 100 nmol/L CCh induced field potential oscillations in hippocampal CA1 region, which exhibited three distinct patterns: (1) continuous neural firing, (2) repeated burst neural firing and (3) the mixed (continuous and burst) pattern in both WT and 3xTg AD mice. Based on Lempel-Ziv estimator, pattern (2) was significantly lower than patterns (1) and (3) in 3xTg AD mice compared to WT mice (P<0.001), and also in 10-month old WT mice compared to those in 5-month old WT mice (P<0.01).Conclusion: These results suggest that the burst pattern (theta oscillation) of hippocampal network is selectively impaired in 3xTg AD mouse model, which may reflect a learning and memory deficit in the AD patients.

  6. Chemical Reaction Rates from Ring Polymer Molecular Dynamics: Theory and Practical Applications

    CERN Document Server

    Suleimanov, Yury V; Guo, Hua

    2016-01-01

    This Feature Article presents an overview of the current status of Ring Polymer Molecular Dynamics (RPMD) rate theory. We first analyze theory and its connection to quantum transition state theory. We then focus on its practical application to prototypical chemical reactions in the gas phase, which demonstrate how accurate and reliable RPMD is for calculating thermal chemical reaction rates in multifarious cases. This review serves as an important checkpoint in RPMD rate theory development, which shows that RPMD is shifting from being just one of recent novel ideas to a well-established and validated alternative to conventional techniques for calculating thermal chemical rates. We also hope it will motivate further applications of RPMD to various chemical reactions.

  7. Chemical Reaction Rate Coefficients from Ring Polymer Molecular Dynamics: Theory and Practical Applications.

    Science.gov (United States)

    Suleimanov, Yury V; Aoiz, F Javier; Guo, Hua

    2016-11-03

    This Feature Article presents an overview of the current status of ring polymer molecular dynamics (RPMD) rate theory. We first analyze the RPMD approach and its connection to quantum transition-state theory. We then focus on its practical applications to prototypical chemical reactions in the gas phase, which demonstrate how accurate and reliable RPMD is for calculating thermal chemical reaction rate coefficients in multifarious cases. This review serves as an important checkpoint in RPMD rate theory development, which shows that RPMD is shifting from being just one of recent novel ideas to a well-established and validated alternative to conventional techniques for calculating thermal chemical rate coefficients. We also hope it will motivate further applications of RPMD to various chemical reactions.

  8. Klotho Ameliorates Chemically Induced Endoplasmic Reticulum (ER Stress Signaling

    Directory of Open Access Journals (Sweden)

    Srijita Banerjee

    2013-05-01

    Full Text Available Background: Both endoplasmic reticulum (ER stress, a fundamental cell response associated with stress-initiated unfolded protein response (UPR, and loss of Klotho, an anti-aging hormone linked to NF-κB-induced inflammation, occur in chronic metabolic diseases such as obesity and type 2 diabetes. We investigated if the loss of Klotho is causally linked to increased ER stress. Methods: We treated human renal epithelial HK-2, alveolar epithelial A549, HEK293, and SH-SH-SY5Y neuroblastoma cells with ER stress-inducing agents, thapsigargin and/or tunicamycin. Effects of overexpression or siRNA-mediated knockdown of Klotho on UPR signaling was investigated by immunoblotting and Real-time PCR. Results: Elevated Klotho levels in HK-2 cells decreased expression of ER stress markers phospho-IRE1, XBP-1s, BiP, CHOP, pJNK, and phospho-p38, all of which were elevated in response to tunicamycin and/or thapsigargin. Similar results were observed using A549 cells for XBP-1s, BiP, and CHOP in response to thapsigargin. Conversely, knockdown of Klotho in HEK 293 cells using siRNA caused further thapsigargin-induced increases in pIRE-1, XBP-1s, and BiP. Klotho overexpression in A549 cells blocked thapsigargin-induced caspase and PARP cleavage and improved cell viability. Conclusion: Our data indicate that Klotho has an important role in regulating ER stress and that loss of Klotho is causally linked to ER stress-induced apoptosis.

  9. Nonequilibrium Chemical Effects in Single-Molecule SERS Revealed by Ab Initio Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, Sean A.; Apra, Edoardo; Govind, Niranjan; Hess, Wayne P.; El-Khoury, Patrick Z.

    2017-02-03

    Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single molecule SERS spectra and selection rules is a challenging task, and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4’-dimercaptostilbene, DMS) interacting with a metallic cluster (Ag20). This affects our simulated single molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag20-DMS system are used to illustrate both concepts in light of recent experimental results.

  10. Universal imaging: Dissociative ionization of polyatomic molecules, chemical dynamics beamline 9.0.2

    Energy Technology Data Exchange (ETDEWEB)

    Ahmed, M.; Chen, D.; Suits, A.G. [Ernest Orlando Lawrence Berkeley National Lab., CA (United States)

    1997-04-01

    A third endstation was recently added to the Chemical Dynamics beamline, designed to exploit the high flux broadband undulator light for a range of studies of reactive scattering, photochemistry and photoionization processes using time-of-flight mass spectroscopy coupled with position-sensitive detection. Two molecular beam sources are fixed at right angles, with the undulator light, or laser beams, intersecting the molecular beams at 45{degrees}. To date, beamline experiments have included a study of dissociative photoionization of a variety of molecules including N{sub 2}O and SF{sub 6}. In this mode, a single molecular beam source is used, with the tunable undulator light inducing, in SF{sub 6} for example, the process SF{sub 6} {r_arrow} SF{sub 6}{sup +} + e{sup {minus}} {r_arrow} SF{sub 5}{sup +} + F + e{sup {minus}}. The SF{sub 5}{sup +} ions are accelerated up the flight tube, mass selected and detected as a function of position on a phosphor screen viewed by a CCD camera. The position directly reveals the recoil speed (or translational energy release) and angular distribution for the dissociative ionization process. Furthermore, this measurement is obtained for all recoil speeds and angles simultaneously. Such detailed angular information has not previously been obtained for dissociative ionization processes; typically ion time-of-flight profiles are deconvoluted to yield rough insight into the angular distributions. The recorded image is actually a 2-dimensional projection of the nascent 3-dimensional velocity distribution, but established tomographic techniques enable the authors to reconstruct the 3-D distribution.

  11. Dynamical behavior of laser-induced nanoparticles during remote processing

    Science.gov (United States)

    Scholz, Tobias; Dickmann, Klaus; Ostendorf, Andreas

    2014-02-01

    Laser remote processing is used in a wide field of industrial applications. Among other things, it is characterized by flexible beam guidance in combination with high processing velocities. But in most cases process gas support in the interaction zone is omitted. Consequently, interaction mechanism between the vapor plume and the incident laser radiation can dynamically affect the process stability. Referring to remote welding with high brilliant laser sources having a wavelength around 1 μm, the interaction between the incident laser radiation and formed particles plays an important role. The presented work shows results of the investigation of the laser-induced particle formation during the laser welding of stainless steel with a 2 kW fiber laser under remote conditions. It is therefore concentrated on the dynamical behavior of the laser-induced particle formation and the dependence of the particle formation on the laser beam power. TEM images of formed particles were analyzed. In addition, the radiation of a LED was directed through the vapor plume. On the one hand, the dynamic of the attenuation was considered. On the other hand, the Rayleigh approximation was used in order to evaluate the detected signals.

  12. Silicon Nitride Bioceramics Induce Chemically Driven Lysis in Porphyromonas gingivalis.

    Science.gov (United States)

    Pezzotti, Giuseppe; Bock, Ryan M; McEntire, Bryan J; Jones, Erin; Boffelli, Marco; Zhu, Wenliang; Baggio, Greta; Boschetto, Francesco; Puppulin, Leonardo; Adachi, Tetsuya; Yamamoto, Toshiro; Kanamura, Narisato; Marunaka, Yoshinori; Bal, B Sonny

    2016-03-29

    Organisms of Gram-negative phylum bacteroidetes, Porphyromonas gingivalis, underwent lysis on polished surfaces of silicon nitride (Si3N4) bioceramics. The antibacterial activity of Si3N4 was mainly the result of chemically driven principles. The lytic activity, although not osmotic in nature, was related to the peculiar pH-dependent surface chemistry of Si3N4. A buffering effect via the formation of ammonium ions (NH4(+)) (and their modifications) was experimentally observed by pH microscopy. Lysis was confirmed by conventional fluorescence spectroscopy, and the bacteria's metabolism was traced with the aid of in situ Raman microprobe spectroscopy. This latter technique revealed the formation of peroxynitrite within the bacterium itself. Degradation of the bacteria's nucleic acid, drastic reduction in phenilalanine, and reduction of lipid concentration were observed due to short-term exposure (6 days) to Si3N4. Altering the surface chemistry of Si3N4 by either chemical etching or thermal oxidation influenced peroxynitrite formation and affected bacteria metabolism in different ways. Exploiting the peculiar surface chemistry of Si3N4 bioceramics could be helpful in counteracting Porphyromonas gingivalis in an alkaline pH environment.

  13. Caspase-2 deficiency accelerates chemically induced liver cancer in mice.

    Science.gov (United States)

    Shalini, S; Nikolic, A; Wilson, C H; Puccini, J; Sladojevic, N; Finnie, J; Dorstyn, L; Kumar, S

    2016-10-01

    Aberrant cell death/survival has a critical role in the development of hepatocellular carcinoma (HCC). Caspase-2, a cell death protease, limits oxidative stress and chromosomal instability. To study its role in reactive oxygen species (ROS) and DNA damage-induced liver cancer, we assessed diethylnitrosamine (DEN)-mediated tumour development in caspase-2-deficient (Casp2(-/-)) mice. Following DEN injection in young animals, tumour development was monitored for 10 months. We found that DEN-treated Casp2(-/-) mice have dramatically elevated tumour burden and accelerated tumour progression with increased incidence of HCC, accompanied by higher oxidative damage and inflammation. Furthermore, following acute DEN injection, liver injury, DNA damage, inflammatory cytokine release and hepatocyte proliferation were enhanced in mice lacking caspase-2. Our study demonstrates for the first time that caspase-2 limits the progression of tumourigenesis induced by an ROS producing and DNA damaging reagent. Our findings suggest that after initial DEN-induced DNA damage, caspase-2 may remove aberrant cells to limit liver damage and disease progression. We propose that Casp2(-/-) mice, which are more susceptible to genomic instability, are limited in their ability to respond to DNA damage and thus carry more damaged cells resulting in accelerated tumourigenesis.

  14. Interleukin 19 reduces inflammation in chemically induced experimental colitis.

    Science.gov (United States)

    Matsuo, Yukiko; Azuma, Yasu-Taka; Kuwamura, Mitsuru; Kuramoto, Nobuyuki; Nishiyama, Kazuhiro; Yoshida, Natsuho; Ikeda, Yoshihito; Fujimoto, Yasuyuki; Nakajima, Hidemitsu; Takeuchi, Tadayoshi

    2015-12-01

    Inflammatory bowel disease results from chronic dysregulation of the mucosal immune system and aberrant activation of both the innate and adaptive immune responses. Interleukin (IL)-19, a member of the IL-10 family, functions as an anti-inflammatory cytokine. Here, we investigated the contribution of IL-19 to intestinal inflammation in a model of T cell-mediated colitis in mice. Inflammatory responses in IL-19-deficient mice were assessed using the 2,4,6-trinitrobenzene sulfonic acid (TNBS) model of acute colitis. IL-19 deficiency aggravated TNBS-induced colitis and compromised intestinal recovery in mice. Additionally, the exacerbation of TNBS-induced colonic inflammation following genetic ablation of IL-19 was accompanied by increased production of interferon-gamma, IL-12 (p40), IL-17, IL-22, and IL-33, and decreased production of IL-4. Moreover, the exacerbation of colitis following IL-19 knockout was also accompanied by increased production of CXCL1, G-CSF and CCL5. Using this model of induced colitis, our results revealed the immunopathological relevance of IL-19 as an anti-inflammatory cytokine in intestinal inflammation in mice.

  15. Intraluminal bubble dynamics induced by lithotripsy shock wave

    Science.gov (United States)

    Song, Jie; Bai, Jiaming; Zhou, Yufeng

    2016-12-01

    Extracorporeal shock wave lithotripsy (ESWL) has been the first option in the treatment of calculi in the upper urinary tract since its introduction. ESWL-induced renal injury is also found after treatment and is assumed to associate with intraluminal bubble dynamics. To further understand the interaction of bubble expansion and collapse with the vessel wall, the finite element method (FEM) was used to simulate intraluminal bubble dynamics and calculate the distribution of stress in the vessel wall and surrounding soft tissue during cavitation. The effects of peak pressure, vessel size, and stiffness of soft tissue were investigated. Significant dilation on the vessel wall occurs after contacting with rapid and large bubble expansion, and then vessel deformation propagates in the axial direction. During bubble collapse, large shear stress is found to be applied to the vessel wall at a clinical lithotripter setting (i.e. 40 MPa peak pressure), which may be the mechanism of ESWL-induced vessel rupture. The decrease of vessel size and viscosity of soft tissue would enhance vessel deformation and, consequently, increase the generated shear stress and normal stresses. Meanwhile, a significantly asymmetric bubble boundary is also found due to faster axial bubble expansion and shrinkage than in radial direction, and deformation of the vessel wall may result in the formation of microjets in the axial direction. Therefore, this numerical work would illustrate the mechanism of ESWL-induced tissue injury in order to develop appropriate counteractive strategies for reduced adverse effects.

  16. Magnetization dynamics and spin pumping induced by standing elastic waves

    Science.gov (United States)

    Azovtsev, A. V.; Pertsev, N. A.

    2016-11-01

    The magnetization dynamics induced by standing elastic waves excited in a thin ferromagnetic film is described with the aid of micromagnetic simulations taking into account the magnetoelastic coupling between spins and lattice strains. Our calculations are based on the numerical solution of the Landau-Lifshitz-Gilbert equation comprising the damping term and the effective magnetic field with all relevant contributions. The simulations have been performed for 2-nm-thick F e81G a19 film dynamically strained by longitudinal and transverse standing waves with various frequencies, which span a wide range around the resonance frequency νres of coherent magnetization precession in unstrained F e81G a19 film. It is found that standing elastic waves give rise to complex local magnetization dynamics and spatially inhomogeneous dynamic patterns in the form of standing spin waves with the same wavelength. Remarkably, the amplitude of magnetization precession does not go to zero at nodes of these spin waves, which cannot be precisely described by simple analytical formulae. In the steady-state regime, magnetization oscillates with the frequency of the elastic wave, except in the case of longitudinal waves with frequencies well below νres, where the magnetization precesses with variable frequency strongly exceeding the wave frequency. The results obtained for the magnetization dynamics driven by elastic waves are used to calculate the spin current pumped from the dynamically strained ferromagnet into adjacent paramagnetic metal. Numerical calculations demonstrate that the transverse charge current in the paramagnetic layer, which is created by the spin current via inverse spin Hall effect, is high enough to be measured experimentally.

  17. Chemical Composition and Dynamics of the Upper Troposphere and the Lower Stratosphere: Overview of the Project

    Science.gov (United States)

    Sofieva, V. F.; Liu, C.; Huang, F.; Kyrola, E.; Liu, Y.; Ialongo, I.; Hakkarainen, J.; Zhang, Y.

    2016-08-01

    The DRAGON-3 cooperation study on the upper troposphere and the lower stratosphere (UTLS) is based on new satellite data and modern atmospheric models. The objectives of the project are: (i) assessment of satellite data on chemical composition in UTLS, (ii) dynamical and chemical structures of the UTLS and its variability, (iii) multi-scale variability of stratospheric ozone, (iv) climatology of the stratospheric aerosol layer and its variability, and (v) updated ozone climatology and its relation to tropopause/multiple tropopauses.In this paper, we present the main results of the project.

  18. Involvement of MAPK proteins in bystander effects induced by chemicals and ionizing radiation

    Energy Technology Data Exchange (ETDEWEB)

    Asur, Rajalakshmi [Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Suite 1370, Detroit, MI 48202-3917 (United States); Balasubramaniam, Mamtha [Research Institute - Biostatistics, William Beaumont Hospital, 3911 W. Thirteen Mile Road, Royal Oak, MI 48073 (United States); Marples, Brian [Department of Radiation Oncology, William Beaumont Hospital, 3811 W. Thirteen Mile Road, Royal Oak, MI 48073 (United States); Thomas, Robert A. [Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Suite 1370, Detroit, MI 48202-3917 (United States); Tucker, James D., E-mail: jtucker@biology.biosci.wayne.edu [Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Suite 1370, Detroit, MI 48202-3917 (United States)

    2010-04-01

    Many studies have examined bystander effects induced by ionizing radiation, however few have evaluated the ability of chemicals to induce similar effects. We previously reported the ability of two chemicals, mitomycin C (MMC) and phleomycin (PHL) to induce bystander effects in normal human lymphoblastoid cell lines. The focus of the current study was to determine the involvement of the MAPK proteins in bystander effects induced by physical and chemical DNA damaging agents and to evaluate the effects of MAPK inhibition on bystander-induced caspase 3/7 activation. The phosphorylation levels of the MAPK proteins ERK1/2, JNK, and p38, were measured from 1 to 24 h following direct or bystander exposure to MMC, PHL or radiation. We observed transient phosphorylation, at early time points, of all 3 proteins in bystander cells. We also evaluated the effect of MAPK inhibition on bystander-induced caspase 3/7 activity to determine the role of MAPK proteins in bystander-induced apoptosis. We observed bystander-induced activation of caspase 3/7 in bystander cells. Inhibition of MAPK proteins resulted in a decrease in caspase 3/7 activity at the early time points, and the caspase activity increased (in the case of ERK inhibition) or returned to basal levels (in the case of JNK or p38 inhibition) between 12 and 24 h. PHL is considered to be a radiomimetic agent, however in the present study PHL behaved more like a chemical and not like radiation in terms of MAPK phosphorylation. These results point to the involvement of MAPK proteins in the bystander effect induced by radiation and chemicals and provide additional evidence that this response is not limited to radiation but is a generalized stress response in cells.

  19. Thermal, chemical and pH induced unfolding of turmeric root lectin: modes of denaturation.

    Directory of Open Access Journals (Sweden)

    Himadri Biswas

    Full Text Available Curcuma longa rhizome lectin, of non-seed origin having antifungal, antibacterial and α-glucosidase inhibitory activities, forms a homodimer with high thermal stability as well as acid tolerance. Size exclusion chromatography and dynamic light scattering show it to be a dimer at pH 7, but it converts to a monomer near pH 2. Circular dichroism spectra and fluorescence emission maxima are virtually indistinguishable from pH 7 to 2, indicating secondary and tertiary structures remain the same in dimer and monomer within experimental error. The tryptophan environment as probed by acrylamide quenching data yielded very similar data at pH 2 and pH 7, implying very similar folding for monomer and dimer. Differential scanning calorimetry shows a transition at 350.3 K for dimer and at 327.0 K for monomer. Thermal unfolding and chemical unfolding induced by guanidinium chloride for dimer are both reversible and can be described by two-state models. The temperatures and the denaturant concentrations at which one-half of the protein molecules are unfolded, are protein concentration-dependent for dimer but protein concentration-independent for monomer. The free energy of unfolding at 298 K was found to be 5.23 Kcal mol-1 and 14.90 Kcal mol-1 for the monomer and dimer respectively. The value of change in excess heat capacity upon protein denaturation (ΔCp is 3.42 Kcal mol-1 K-1 for dimer. The small ΔCp for unfolding of CLA reflects a buried hydrophobic core in the folded dimeric protein. These unfolding experiments, temperature dependent circular dichroism and dynamic light scattering for the dimer at pH 7 indicate its higher stability than for the monomer at pH 2. This difference in stability of dimeric and monomeric forms highlights the contribution of inter-subunit interactions in the former.

  20. CD-REST: a system for extracting chemical-induced disease relation in literature

    Science.gov (United States)

    Xu, Jun; Wu, Yonghui; Zhang, Yaoyun; Wang, Jingqi; Lee, Hee-Jin; Xu, Hua

    2016-01-01

    Mining chemical-induced disease relations embedded in the vast biomedical literature could facilitate a wide range of computational biomedical applications, such as pharmacovigilance. The BioCreative V organized a Chemical Disease Relation (CDR) Track regarding chemical-induced disease relation extraction from biomedical literature in 2015. We participated in all subtasks of this challenge. In this article, we present our participation system Chemical Disease Relation Extraction SysTem (CD-REST), an end-to-end system for extracting chemical-induced disease relations in biomedical literature. CD-REST consists of two main components: (1) a chemical and disease named entity recognition and normalization module, which employs the Conditional Random Fields algorithm for entity recognition and a Vector Space Model-based approach for normalization; and (2) a relation extraction module that classifies both sentence-level and document-level candidate drug–disease pairs by support vector machines. Our system achieved the best performance on the chemical-induced disease relation extraction subtask in the BioCreative V CDR Track, demonstrating the effectiveness of our proposed machine learning-based approaches for automatic extraction of chemical-induced disease relations in biomedical literature. The CD-REST system provides web services using HTTP POST request. The web services can be accessed from http://clinicalnlptool.com/cdr. The online CD-REST demonstration system is available at http://clinicalnlptool.com/cdr/cdr.html. Database URL: http://clinicalnlptool.com/cdr; http://clinicalnlptool.com/cdr/cdr.html PMID:27016700

  1. State-to-state dynamics of elementary chemical reactions using Rydberg H-atom translational spectroscopy

    Science.gov (United States)

    Yang, Xueming

    In this review, a few examples of state-to-state dynamics studies of both unimolecular and bimolecular reactions using the H-atom Rydberg tagging TOF technique were presented. From the H2O photodissociation at 157 nm, a direction dissociation example is provided, while photodissociation of H2O at 121.6 has provided an excellent dynamical case of complicated, yet direct dissociation process through conical intersections. The studies of the O(1D) + H2 → OH + H reaction has also been reviewed here. A prototype example of state-to-state dynamics of pure insertion chemical reaction is provided. Effect of the reagent rotational excitation and the isotope effect on the dynamics of this reaction have also been investigated. The detailed mechanism for abstraction channel in this reaction has also been closely studied. The experimental investigations of the simplest chemical reaction, the H3 system, have also been described here. Through extensive collaborations between theory and experiment, the mechanism for forward scattering product at high collision energies for the H + HD reaction was clarified, which is attributed to a slow down mechanism on the top of a quantized barrier transition state. Oscillations in the product quantum state resolved different cross sections have also been observed in the H + D2 reaction, and were attributed to the interference of adiabatic transition state pathways from detailed theoretical analysis. The results reviewed here clearly show the significant advances we have made in the studies of the state-to-state molecular reaction dynamics.

  2. THE INDUCED REPRESENTATION OF C*-GROUPOID DYNAMIC SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    FANGXIAOCHUN

    1996-01-01

    Let G be a second countable locally compact groupoid with Haar system {λuH}, H be aclosed subgroupoid containing G0 with Haar system {λuH}. T.Masuda introduced the C*-Groupoid dynamic system (G, A, α) and its reduced crossed product Crea(G, A) in [2]: where A is C*-algebra α is the komomorphism G → Aut(A). In this paper the author introduces the C*-groupoid dynamic systems (H,A, α/H) and (H\\G2,A,-α) induced by (G,A,α) and proves that C*red(H, A) and C*red(H\\G2, A) are strongly Morita equivalent Moreover the inducedrepresentation from C*red(H, A) to C*red(G,A) is got.

  3. Nematicides induced changes in the chemical constituents of potato tubers.

    Science.gov (United States)

    Marwaha, R S

    1988-01-01

    Changes in the chemical constitutents of potato tubers grown under different concentrations of 3 synthetic organic nematicides (carbofuran, aldicarb and phorate) and a natural plant product (sawdust) were investigated. There were no significant differences in the specific gravity, dry matter and starch content of tubers from different treatments. A significant increase in the content of non-reducing and total sugars was observed in all the treatments. Nematicidal treatments had significant effects on reducing sugars, true protein, free amino acids, orthodihydroxy phenols, beta-carotene and ascorbic acid. Application of nematicides reduced the content of total phenolic compounds which is a desirable change from a processing viewpoint. Potatoes grown under different nematicidal treatments can be processed into chips and French fries as they contain permissible levels of reducing sugars required for these forms of processing.

  4. Altered Acer Rubrum Fecundity Induced By Chemical Climate Change

    Science.gov (United States)

    Deforest, J. L.; Peters, A.

    2014-12-01

    Red maple (Acer rubrum L.) is becoming the most dominating tree in North American eastern deciduous forests. Concurrently, human activities have altered the chemical climate of terrestrial ecosystems via acidic deposition, which increases the available of nitrogen (N), while decreasing phosphorus (P) availability. Once a minor forest component prior to European settlement, the abundance of red maple may be a symptom of the modern age. The current paradigm explaining red maple's rise to prominence concerns fire suppression that excludes competitors. However, this still does not explain why red maple is unique compared to other functionally similar trees. The objective of this study was to investigate the interactive influence of acid rain mitigation on the fecundity of red maple. Objectives were achieved by measuring flowering, seed production, germination, and growth from red maple on plots that have been experimentally manipulated to increase soil pH, P, or both in three unglaciated eastern deciduous hardwood forests. At least 50% of the red maple population is seed bearing in our control soils, however the median percent of seed-bearing trees declined to zero when mitigating soils from acidic deposition. This can be explained by the curious fact that red maple is polygamodioecious, or has labile sex-expression, in which an individual tree can change its sex-expression in response to the environment. Furthermore, seed-bearing trees in the mitigated plots grew less, produced less seeds, and germinated at lower rates than their counterparts in control soils. Our results provide evidence that chemical climate change could be the primary contributing factor accelerating the dominance of red maple in eastern North American forests. Our observations can provide a boarder conceptual framework for understanding how nutrient limitations can be applied beyond plant productivity towards explaining distribution changes in vegetation.

  5. Gene expression in rat skin induced by irritating chemicals.

    Science.gov (United States)

    Rogers, James V; Garrett, Carol M; McDougal, James N

    2003-01-01

    Occupational skin disease is the second most significant cause of occupational disease, after accidents. Irritation from occupational chemicals such as solvents, hydrocarbons, and surfactants are one cause of this disease. Gene expression studies provide useful information about normal processes in the skin and responses of the skin to exogenous chemicals. We exposed rats, cutaneously, to sodium lauryl sulfate (SLS, 1% and 10% aqueous solution), m-xylene (pure liquid), and d-limonene (pure liquid) for 1 h and measured transcriptional responses at the end of the exposure and 3 h later for comparison with untreated skin samples. Total skin RNA was isolated and analyzed using the Affymetrix RatTox U34 array. Using the Affymetrix software, we found that 234 of approximately 850 genes were detected as present in at least 80% of the normal skin samples. The largest number of these genes was related to metabolism, oxidative/cellular stress, and signal transduction. Limonene caused the largest change in mRNA levels with a total of 34 increased transcripts and 4 decreased transcripts. Xylene treatment resulted in 6 increased transcripts and 14 decreased transcripts, while 10% SLS caused 5 transcripts to increase and 17 to decrease. Only two transcripts were observed to change in skin following a 1% SLS exposure. Sodium lauryl sulfate transcript changes increased with dose and were maximum at 4 h. Limonene transcript changes were more numerous at 1 h than at 4 h. The observed differences may reflect different mechanisms of irritation. Copyright 2003 Wiley Periodicals, Inc. J Biochem Mol Toxicol 17:123-137, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.10079

  6. Chemical spots and their dynamical evolution on HgMn stars

    CERN Document Server

    Korhonen, Heidi; Briquet, Maryline; Gonzalez, Federico; Savanov, Igor

    2010-01-01

    Our recent studies of late B-type stars with HgMn peculiarity revealed for the first time the presence of fast dynamical evolution of chemical spots on their surfaces. These observations suggest a hitherto unknown physical process operating in the stars with radiative outer envelopes. Furthermore, we have also discovered existence of magnetic fields on these stars that have up to now been thought to be non-magnetic. Here we will discuss the dynamical spot evolution on HD 11753 and our new results on magnetic fields on AR Aur.

  7. Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT

    Science.gov (United States)

    Kirmizialtin, Serdal; Hennelly, Scott P.; Schug, Alexander; Onuchic, Jose N.; Sanbonmatsu, Karissa Y.

    2016-01-01

    Integration and calibration of molecular dynamics simulations with experimental data remains a challenging endeavor. We have developed a novel method to integrate chemical probing experiments with molecular simulations of RNA molecules by using a native structure-based model. Selective 2’-hydroxyl acylation by primer extension (SHAPE) characterizes the mobility of each residue in the RNA. Our method, SHAPE-FIT, automatically optimizes the potential parameters of the forcefield according to measured reactivities from SHAPE. The optimized parameter set allows simulations of dynamics highly consistent with SHAPE probing experiments. Such atomistic simulations, thoroughly grounded in experiment, can open a new window on RNA structure-function relations. PMID:25726467

  8. Scale effects in the dynamic transfer functions for cavitating inducers

    Science.gov (United States)

    Brennen, C. E.; Meissner, C.; Lo, E. Y.; Hoffman, G. S.

    1980-01-01

    Dynamic transfer functions for two cavitating inducers of the same geometry but different size are presented, compared and discussed. The transfer functions for each inducer indicate similar trends as the cavitation number is decreased; only minor changes are noted with changes in the flow coefficient, the uniformity of the inlet flow or the temperature of the water (21-74 C). The non-dimensional results for the two sizes are compared with themselves and with theoretical calculations based on the bubbly flow model. All three sets of results compare well and lend further credence to the theoretical model. The best values of the two parameters in the model are evaluated and recommended for use in applications.

  9. Fluoropolymer Microstructure and Dynamics: Influence of Molecular Orientation Induced by Uniaxial Drawing

    Science.gov (United States)

    Miranda, Daniel; Yin, Chaoqing; Runt, James

    Fluorinated semi-crystalline polymer films are attractive for dielectric film applications due to their chemical inertness, heat resistance, and high thermal stability. In the present investigation we explore the influence of orientation induced by uniaxial drawing on the crystalline microstructure and relaxation processes of poly(ethylene-tetrafluoroethylene) (ETFE), in order to ascertain how morphological control can benefit polymer dielectric design. When drawn below or near the Tg, the crystallinity of the drawn films is unchanged, and oriented amorphous structures and crystalline microfibrils form at high draw ratios. This orientation slows segmental relaxation, reflected by an increase in the dynamic Tg, and also delays the transition to the high temperature crystalline form of ETFE. When drawing above the Tg, the films undergo strain-induced crystallization at high draw ratios. For these films an increase in the dynamic Tg is also observed, in addition to a second segmental relaxation process, appearing as a shoulder on the primary process. We propose that this represents a contribution from a rigid amorphous fraction, having slowed chain dynamics. Supported by Office of Naval Research.

  10. Chemical process dynamic optimization based on the differential evolution algorithm with an adaptive scheduling mutation strategy

    Science.gov (United States)

    Zhu, Jun; Yan, Xuefeng; Zhao, Weixiang

    2013-10-01

    To solve chemical process dynamic optimization problems, a differential evolution algorithm integrated with adaptive scheduling mutation strategy (ASDE) is proposed. According to the evolution feedback information, ASDE, with adaptive control parameters, adopts the round-robin scheduling algorithm to adaptively schedule different mutation strategies. By employing an adaptive mutation strategy and control parameters, the real-time optimal control parameters and mutation strategy are obtained to improve the optimization performance. The performance of ASDE is evaluated using a suite of 14 benchmark functions. The results demonstrate that ASDE performs better than four conventional differential evolution (DE) algorithm variants with different mutation strategies, and that the whole performance of ASDE is equivalent to a self-adaptive DE algorithm variant and better than five conventional DE algorithm variants. Furthermore, ASDE was applied to solve a typical dynamic optimization problem of a chemical process. The obtained results indicate that ASDE is a feasible and competitive optimizer for this kind of problem.

  11. A review of dynamical resonances in A  +  BC chemical reactions

    Science.gov (United States)

    Ren, Zefeng; Sun, Zhigang; Zhang, Donghui; Yang, Xueming

    2017-02-01

    The concept of the transition state has played an important role in the field of chemical kinetics and reaction dynamics. Reactive resonances in the transition-state region can dramatically enhance the reaction probability; thus investigation of the reactive resonances has attracted great attention from chemical physicists for many decades. In this review, we mainly focus on the recent progress made in probing the elusive resonance phenomenon in the simple A  +  BC reaction and understanding its nature, especially in the benchmark F/Cl  +  H2 and their isotopic variants. The signatures of reactive resonances in the integral cross section, differential cross section (DCS), forward- and backward-scattered DCS, and anion photodetachment spectroscopy are comprehensively presented in individual prototype reactions. The dynamical origins of reactive resonances are also discussed in this review, based on information on the wave function in the transition-state region obtained by time-dependent quantum wave-packet calculations.

  12. In situ analysis of chemical components induced by steaming between fresh ginseng, steamed ginseng, and red ginseng.

    Science.gov (United States)

    In, Gyo; Ahn, Nam-Geun; Bae, Bong-Seok; Lee, Myoung-Woo; Park, Hee-Won; Jang, Kyoung Hwa; Cho, Byung-Goo; Han, Chang Kyun; Park, Chae Kyu; Kwak, Yi-Seong

    2017-07-01

    The chemical constituents of Panax ginseng are changed by processing methods such as steaming or sun drying. In the present study, the chemical change of Panax ginseng induced by steaming was monitored in situ. Samples were separated from the same ginseng root by incision during the steaming process, for in situ monitoring. Sampling was sequentially performed in three stages; FG (fresh ginseng) → SG (steamed ginseng) → RG (red ginseng) and 60 samples were prepared and freeze dried. The samples were then analyzed to determine 43 constituents among three stages of P. ginseng. The results showed that six malonyl-ginsenoside (Rg1, Rb1, Rb3, Rc, Rd, Rb2) and 15 amino acids were decreased in concentration during the steaming process. In contrast, ginsenoside-Rh1, 20(S)-Rg2, 20(S, R)-Rg3 and Maillard reaction product such as AF (arginine-fructose), AFG (arginine-fructose-glucose), and maltol were newly generated or their concentrations were increased. This study elucidates the dynamic changes in the chemical components of P. ginseng when the steaming process was induced. These results are thought to be helpful for quality control and standardization of herbal drugs using P. ginseng and they also provide a scientific basis for pharmacological research of processed ginseng (Red ginseng).

  13. Transverse relaxation in the rotating frame induced by chemical exchange

    Science.gov (United States)

    Michaeli, Shalom; Sorce, Dennis J.; Idiyatullin, Djaudat; Ugurbil, Kamil; Garwood, Michael

    2004-08-01

    In the presence of radiofrequency irradiation, relaxation of magnetization aligned with the effective magnetic field is characterized by the time constant T1 ρ. On the other hand, the time constant T2 ρ characterizes the relaxation of magnetization that is perpendicular to the effective field. Here, it is shown that T2 ρ can be measured directly with Carr-Purcell sequences composed of a train of adiabatic full-passage (AFP) pulses. During adiabatic rotation, T2 ρ characterizes the relaxation of the magnetization, which under adiabatic conditions remains approximately perpendicular to the time-dependent effective field. Theory is derived to describe the influence of chemical exchange on T2 ρ relaxation in the fast-exchange regime, with time constant defined as T2 ρ,ex . The derived theory predicts the rate constant R 2ρ, ex (=1/T 2ρ, ex) to be dependent on the choice of amplitude- and frequency-modulation functions used in the AFP pulses. Measurements of R2 ρ,ex of the water/ethanol exchanging system confirm the predicted dependence on modulation functions. The described theoretical framework and adiabatic methods represent new tools to probe exchanging systems.

  14. Mthfd1 is a modifier of chemically induced intestinal carcinogenesis.

    Science.gov (United States)

    MacFarlane, Amanda J; Perry, Cheryll A; McEntee, Michael F; Lin, David M; Stover, Patrick J

    2011-03-01

    The causal metabolic pathways underlying associations between folate and risk for colorectal cancer (CRC) have yet to be established. Folate-mediated one-carbon metabolism is required for the de novo synthesis of purines, thymidylate and methionine. Methionine is converted to S-adenosylmethionine (AdoMet), the major one-carbon donor for cellular methylation reactions. Impairments in folate metabolism can modify DNA synthesis, genomic stability and gene expression, characteristics associated with tumorigenesis. The Mthfd1 gene product, C1-tetrahydrofolate synthase, is a trifunctional enzyme that generates one-carbon substituted tetrahydrofolate cofactors for one-carbon metabolism. In this study, we use Mthfd1(gt/+) mice, which demonstrate a 50% reduction in C1-tetrahydrofolate synthase, to determine its influence on tumor development in two mouse models of intestinal cancer, crosses between Mthfd1(gt/+) and Apc(min)(/+) mice and azoxymethane (AOM)-induced colon cancer in Mthfd1(gt/+) mice. Mthfd1 hemizygosity did not affect colon tumor incidence, number or load in Apc(min/+) mice. However, Mthfd1 deficiency increased tumor incidence 2.5-fold, tumor number 3.5-fold and tumor load 2-fold in AOM-treated mice. DNA uracil content in the colon was lower in Mthfd1(gt/+) mice, indicating that thymidylate biosynthesis capacity does not play a significant role in AOM-induced colon tumorigenesis. Mthfd1 deficiency-modified cellular methylation potential, as indicated by the AdoMet: S-adenosylhomocysteine ratio and gene expression profiles, suggesting that changes in the transcriptome and/or decreased de novo purine biosynthesis and associated mutability cause cellular transformation in the AOM CRC model. This study emphasizes the impact and complexity of gene-nutrient interactions with respect to the relationships among folate metabolism and colon cancer initiation and progression.

  15. Effect of dynamic operation on chemical degradation of a polymer electrolyte membrane fuel cell

    Science.gov (United States)

    Jung, Minjae; Williams, Keith A.

    2011-03-01

    Dynamic operation is known as one of the factors for accelerating chemical degradation of the polymer electrolyte membrane in a polymer electrolyte membrane fuel cell (PEMFC). However, little effort has been made dealing with the quantification of the degradation process. In this investigation, cyclic current operation is carried out on a fuel cell system, and the frequency effect of cyclic operation on chemical degradation is investigated. The dynamic behavior of a fuel cell system is analyzed first with the modified Randles model, where the charge double layer is modeled by three components; a charge transfer resistance (Rct), and two RC cells for the Warburg impedance. After calculating each parameter value through exponential curve fitting, the dynamic behaviors of the three components are simulated using MATLAB Simulink®. Fluoride release as a function of the frequency of cyclic operation is evaluated by measuring the concentration of fluoride ion in effluent from a fuel cell exhaust. The frequency effect on chemical degradation is explained by comparing the simulated results and the fluoride release results. Two possible reasons for the accelerated degradation at cyclic operation are also suggested.

  16. Fast Atomic-Scale Chemical Imaging of Crystalline Materials and Dynamic Phase Transformations.

    Science.gov (United States)

    Lu, Ping; Yuan, Ren Liang; Ihlefeld, Jon F; Spoerke, Erik David; Pan, Wei; Zuo, Jian Min

    2016-04-13

    Atomic-scale phenomena fundamentally influence materials form and function that makes the ability to locally probe and study these processes critical to advancing our understanding and development of materials. Atomic-scale chemical imaging by scanning transmission electron microscopy (STEM) using energy-dispersive X-ray spectroscopy (EDS) is a powerful approach to investigate solid crystal structures. Inefficient X-ray emission and collection, however, require long acquisition times (typically hundreds of seconds), making the technique incompatible with electron-beam sensitive materials and study of dynamic material phenomena. Here we describe an atomic-scale STEM-EDS chemical imaging technique that decreases the acquisition time to as little as one second, a reduction of more than 100 times. We demonstrate this new approach using LaAlO3 single crystal and study dynamic phase transformation in beam-sensitive Li[Li0.2Ni0.2Mn0.6]O2 (LNMO) lithium ion battery cathode material. By capturing a series of time-lapsed chemical maps, we show for the first time clear atomic-scale evidence of preferred Ni-mobility in LNMO transformation, revealing new kinetic mechanisms. These examples highlight the potential of this approach toward temporal, atomic-scale mapping of crystal structure and chemistry for investigating dynamic material phenomena.

  17. Dynamics, Miscibility, and Morphology in Polymer-Molecule Blends: The Impact of Chemical Functionality

    KAUST Repository

    Do, Khanh

    2015-10-22

    In the quest to improve the performance of organic bulk-heterojunction solar cells, many recent efforts have focused on developing molecular and polymer alternatives to commonly used fullerene acceptors. Here, molecular dynamics simulations are used to investigate polymer-molecule blends comprised of the polymer donor poly(3-hexylthiophene) (P3HT) with a series of acceptors based on trialkylsilylethynyl-substituted pentacene. A matrix of nine pentacene derivatives, consisting of systematic chemical variation both in the nature of the alkyl groups and electron-withdrawing moieties appended to the acene, is used to draw connections between the chemical structure of the acene acceptor and the nanoscale properties of the polymer-molecule blend. These connections include polymer and molecular diffusivity, donor-acceptor packing and interfacial (contact) area, and miscibility. The results point to the very significant role that seemingly modest changes in chemical structure play during the formation of polymer-molecule blend morphologies.

  18. Increased capsaicin-induced secondary hyperalgesia in patients with multiple chemical sensitivity

    DEFF Research Database (Denmark)

    Holst, Helle; Arendt-Nielsen, Lars; Mosbech, Holger

    2011-01-01

    in experimental pain models to provoke peripheral and central sensitization. In patients with symptoms elicited by odorous chemicals capsaicin-induced secondary hyperalgesia and temporal summation were assessed as markers for abnormal central nociceptive processing together with neurogenic inflammation (flare).......the underlying cause of pathophysiological mechanisms triggering multiple chemical sensitivity (MCS) remains disputed.Recently, alterations in the central nervous system, for example,central sensitization, similar to various chronic pain disorders, have been suggested. Capsaicin is used...

  19. Increased capsaicin-induced secondary hyperalgesia in patients with multiple chemical sensitivity

    DEFF Research Database (Denmark)

    Holst, Helle; Arendt-Nielsen, Lars; Mosbech, Holger;

    2011-01-01

    in experimental pain models to provoke peripheral and central sensitization. In patients with symptoms elicited by odorous chemicals capsaicin-induced secondary hyperalgesia and temporal summation were assessed as markers for abnormal central nociceptive processing together with neurogenic inflammation (flare).......the underlying cause of pathophysiological mechanisms triggering multiple chemical sensitivity (MCS) remains disputed.Recently, alterations in the central nervous system, for example,central sensitization, similar to various chronic pain disorders, have been suggested. Capsaicin is used...

  20. Characterization of Chemically-Induced Bacterial Ghosts (BGs Using Sodium Hydroxide-Induced Vibrio parahaemolyticus Ghosts (VPGs

    Directory of Open Access Journals (Sweden)

    Hyun Jung Park

    2016-11-01

    Full Text Available Acellular bacterial ghosts (BGs are empty non-living bacterial cell envelopes, commonly generated by controlled expression of the cloned lysis gene E of bacteriophage PhiX174. In this study, Vibrio parahaemolyticus ghosts (VPGs were generated by chemically-induced lysis and the method is based on minimum inhibitory concentration (MIC of sodium hydroxide (NaOH, acetic acid, boric acid, citric acid, maleic acid, hydrochloric acid, and sulfuric acid. The MIC values of the respective chemicals were 3.125, 6.25, <50.0, 25.0, 6.25, 1.56, and 0.781 mg/mL. Except for boric acid, the lysis efficiency reached more than 99.99% at 5 min after treatment of all chemicals. Among those chemicals, NaOH-induced VPGs appeared completely DNA-free, which was confirmed by quantitative real-time PCR. Besides, lipopolysaccharides (LPS extracted from the NaOH-induced VPGs showed no distinctive band on SDS-PAGE gel after silver staining. On the other hand, LPS extracted from wild-type bacterial cells, as well as the organic acids-induced VPGs showed triple major bands and LPS extracted from the inorganic acids-induced VPGs showed double bands. It suggests that some surface structures in LPS of the NaOH-induced VPGs may be lost, weakened, or modified by the MIC of NaOH. Nevertheless, Limulus amoebocyte lysate assay revealed that there is no significant difference in endotoxic activity between the NaOH-induced VPGs and wild-type bacterial cells. Macrophages exposed to the NaOH-induced VPGs at 0.5 × 106 CFU/mL showed cell viability of 97.9%, however, the MIC of NaOH did not reduce the cytotoxic effect of wild-type bacterial cells. Like Escherichia coli LPS, the NaOH-induced VPGs are an excellent activator of pro-inflammatory cytokines (IL-1β and iNOS, anti-inflammatory cytokine (IL-10, and dual activities (IL-6 in the stimulated macrophage cells. On the other hand, the induction of TNF-α mRNA was remarkable in the macrophages exposed with wild-type cells. Scanning

  1. Transcription dynamics of inducible genes modulated by negative regulations.

    Science.gov (United States)

    Li, Yanyan; Tang, Moxun; Yu, Jianshe

    2015-06-01

    Gene transcription is a stochastic process in single cells, in which genes transit randomly between active and inactive states. Transcription of many inducible genes is also tightly regulated: It is often stimulated by extracellular signals, activated through signal transduction pathways and later repressed by negative regulations. In this work, we study the nonlinear dynamics of the mean transcription level of inducible genes modulated by the interplay of the intrinsic transcriptional randomness and the repression by negative regulations. In our model, we integrate negative regulations into gene activation process, and make the conventional assumption on the production and degradation of transcripts. We show that, whether or not the basal transcription is temporarily terminated when cells are stimulated, the mean transcription level grows in the typical up and down pattern commonly observed in immune response genes. With the help of numerical simulations, we clarify the delicate impact of the system parameters on the transcription dynamics, and demonstrate how our model generates the distinct temporal gene-induction patterns in mouse fibroblasts discerned in recent experiments.

  2. Quercetin Reverses Rat Liver Preneoplastic Lesions Induced by Chemical Carcinogenesis

    Directory of Open Access Journals (Sweden)

    Gabriela Carrasco-Torres

    2017-01-01

    Full Text Available Quercetin is a flavonoid widely studied as a chemopreventive agent in different types of cancer. Previously, we reported that quercetin has a chemopreventive effect on the liver-induced preneoplastic lesions in rats. Here, we evaluated if quercetin was able not only to prevent but also to reverse rat liver preneoplastic lesions. We used the modified resistant hepatocyte model (MRHM to evaluate this possibility. Treatment with quercetin was used 15 days after the induction of preneoplastic lesions. We found that quercetin reverses the number of preneoplastic lesions and their areas. Our results showed that quercetin downregulates the expression of EGFR and modulates this signaling pathway in spite of the activated status of EGFR as detected by the upregulation of this receptor, with respect to that observed in control rats. Besides, quercetin affects the phosphorylation status of Src-1, STAT5, and Sp-1. The better status of the liver after the treatment with quercetin could also be confirmed by the recovery in the expression of IGF-1. In conclusion, we suggest that quercetin reversed preneoplastic lesions by EGFR modulation and the activation state of Src, STAT5, and Sp1, so as the basal IGF-1.

  3. Cell Therapy for Chemically Induced Ovarian Failure in Mice

    Directory of Open Access Journals (Sweden)

    Paula Terraciano

    2014-01-01

    Full Text Available Cell therapy has been linked to an unexplained return of ovarian function and fertility in some cancer survivors. Studies modeling this in mice have shown that cells transplantation generates donor-derived oocytes in chemotherapy-treated recipients. This study was conducted to further clarify the impact of cell transplantation from different sources on female reproductive function after chemotherapy using a preclinical mouse model. Methods. Female mice were administered 7.5 mg/kg cisplatin followed by cell transplantation (one week later using GFP+ female cell donors. For cell tracking, adipose derived stem cell GFP+ (ADSC, female germline stem cell GFP+/MVH+ (FGSC, or ovary cell suspension GFP+ mice were transplanted into cisplatin-treated wild-type recipients. After 7 or 14 days animals were killed and histological analysis, IHQ for GFP cells, and ELISA for estradiol were performed. Results. Histological examinations showed that ADSC, ovary cell suspension, and FGSC transplant increase the number of follicles with apparent normal structure in the cells recipient group euthanized on day 7. Cell tracking showed GFP+ samples 7 days after transplant. Conclusion. These data suggest that intraovarian injection of ADSCs and FGSC into mice with chemotherapy-induced ovarian failure diminished the damage caused by cisplatin.

  4. Chemical and biological activity in open flows: A dynamical system approach

    Energy Technology Data Exchange (ETDEWEB)

    Tel, Tamas [Institute for Theoretical Physics, Eoetvoes University, P.O. Box 32, H-1518, Budapest (Hungary); Moura, Alessandro de [Instituto de Fisica, Universidade de Sao Paulo, Caixa Postal 66318, 05315-970, Sao Paulo, SP (Brazil); Grebogi, Celso [Instituto de Fisica, Universidade de Sao Paulo, Caixa Postal 66318, 05315-970, Sao Paulo, SP (Brazil) and Max-Plank-Institute for the Physics of Complex Systems, Noethnitzer Str. 38, D-01187 Dresden (Germany)]. E-mail: grebogi@if.usp.br; Karolyi, Gyoergy [Center for Applied Mathematics and Computational Physics, and Department of Structural Mechanics, Budapest University of Technology and Economics, Mueegyetem rkp. 3, H-1521, Budapest (Hungary)

    2005-07-01

    Chemical and biological processes often take place in fluid flows. Many of them, like environmental or microfluidical ones, generate filamentary patterns which have a fractal structure, due to the presence of chaos in the underlying advection dynamics. In such cases, hydrodynamical stirring strongly couples to the reactivity of the advected species: the outcome of the reaction is then typically different from that of the same reaction taking place in a well-mixed environment. Here we review recent progress in this field, which became possible due to the application of methods taken from dynamical system theory. We place special emphasis on the derivation of effective rate equations which contain singular terms expressing the fact that the reaction takes place on a moving fractal catalyst, on the unstable foliation of the reaction free advection dynamics.

  5. Surface chemical reactions induced by molecules electronically-excited in the gas

    DEFF Research Database (Denmark)

    Petrunin, Victor V.

    2011-01-01

    be readily produced. Products of chemical adsorption and/or chemical reactions induced within adsorbates are aggregated on the surface and observed by light scattering. We will demonstrate how pressure and spectral dependencies of the chemical outcomes, polarization of the light and interference of two laser...... and alignment are taking place, guiding all the molecules towards the intersections with the ground state PES, where transitions to the ground state PES will occur with minimum energy dissipation. The accumulated kinetic energy may be used to overcome the chemical reaction barrier. While recombination chemical...... reactions in a gas phase require participation of a third body, this strong limitation on the reaction rates is removed upon interaction with a surface. To observe the predicted phenomenon, we suggested a new experimental approach, Evanescent Wave Photocatalysis1, based on application of total internal...

  6. Force-induced chemical reactions on the metal centre in a single metalloprotein molecule.

    Science.gov (United States)

    Zheng, Peng; Arantes, Guilherme M; Field, Martin J; Li, Hongbin

    2015-06-25

    Metalloproteins play indispensable roles in biology owing to the versatile chemical reactivity of metal centres. However, studying their reactivity in many metalloproteins is challenging, as protein three-dimensional structure encloses labile metal centres, thus limiting their access to reactants and impeding direct measurements. Here we demonstrate the use of single-molecule atomic force microscopy to induce partial unfolding to expose metal centres in metalloproteins to aqueous solution, thus allowing for studying their chemical reactivity in aqueous solution for the first time. As a proof-of-principle, we demonstrate two chemical reactions for the FeS4 centre in rubredoxin: electrophilic protonation and nucleophilic ligand substitution. Our results show that protonation and ligand substitution result in mechanical destabilization of the FeS4 centre. Quantum chemical calculations corroborated experimental results and revealed detailed reaction mechanisms. We anticipate that this novel approach will provide insights into chemical reactivity of metal centres in metalloproteins under biologically more relevant conditions.

  7. Force-induced chemical reactions on the metal centre in a single metalloprotein molecule

    Science.gov (United States)

    Zheng, Peng; Arantes, Guilherme M.; Field, Martin J.; Li, Hongbin

    2015-06-01

    Metalloproteins play indispensable roles in biology owing to the versatile chemical reactivity of metal centres. However, studying their reactivity in many metalloproteins is challenging, as protein three-dimensional structure encloses labile metal centres, thus limiting their access to reactants and impeding direct measurements. Here we demonstrate the use of single-molecule atomic force microscopy to induce partial unfolding to expose metal centres in metalloproteins to aqueous solution, thus allowing for studying their chemical reactivity in aqueous solution for the first time. As a proof-of-principle, we demonstrate two chemical reactions for the FeS4 centre in rubredoxin: electrophilic protonation and nucleophilic ligand substitution. Our results show that protonation and ligand substitution result in mechanical destabilization of the FeS4 centre. Quantum chemical calculations corroborated experimental results and revealed detailed reaction mechanisms. We anticipate that this novel approach will provide insights into chemical reactivity of metal centres in metalloproteins under biologically more relevant conditions.

  8. Tight-binding quantum chemical molecular dynamics simulations for the elucidation of chemical reaction dynamics in SiC etching with SF6/O2 plasma.

    Science.gov (United States)

    Ito, Hiroshi; Kuwahara, Takuya; Kawaguchi, Kentaro; Higuchi, Yuji; Ozawa, Nobuki; Kubo, Momoji

    2016-03-21

    We used our etching simulator [H. Ito et al., J. Phys. Chem. C, 2014, 118, 21580-21588] based on tight-binding quantum chemical molecular dynamics (TB-QCMD) to elucidate SiC etching mechanisms. First, the SiC surface is irradiated with SF5 radicals, which are the dominant etchant species in experiments, with the irradiation energy of 300 eV. After SF5 radicals bombard the SiC surface, Si-C bonds dissociate, generating Si-F, C-F, Si-S, and C-S bonds. Then, etching products, such as SiS, CS, SiFx, and CFx (x = 1-4) molecules, are generated and evaporated. In particular, SiFx is the main generated species, and Si atoms are more likely to vaporize than C atoms. The remaining C atoms on SiC generate C-C bonds that may decrease the etching rate. Interestingly, far fewer Si-Si bonds than C-C bonds are generated. We also simulated SiC etching with SF3 radicals. Although the chemical reaction dynamics are similar to etching with SF5 radicals, the etching rate is lower. Next, to clarify the effect of O atom addition on the etching mechanism, we also simulated SiC etching with SF5 and O radicals/atoms. After bombardment with SF5 radicals, Si-C bonds dissociate in a similar way to the etching without O atoms. In addition, O atoms generate many C-O bonds and COy (y = 1-2) molecules, inhibiting the generation of C-C bonds. This indicates that O atom addition improves the removal of C atoms from SiC. However, for a high O concentration, many C-C and Si-Si bonds are generated. When the O atoms dissociate the Si-C bonds and generate dangling bonds, the O atoms terminate only one or two dangling bonds. Moreover, at high O concentrations there are fewer S and F atoms to terminate the dangling bonds than at low O concentration. Therefore, few dangling bonds of dissociated Si and C atoms are terminated, and they form many Si-Si and C-C bonds. Furthermore, we propose that the optimal O concentration is 50-60% because both Si and C atoms generate many etching products producing fewer C

  9. Computational modeling of glow discharge-induced fluid dynamics

    Science.gov (United States)

    Jayaraman, Balaji

    Glow discharge at atmospheric pressure using a dielectric barrier discharge can induce fluid flow and operate as an actuator for flow control. The largely isothermal surface plasma generation realized above can modify the near-wall flow structure by means of Lorentzian collisions between the ionized fluid and the neutral fluid. Such an actuator has advantages of no moving parts, performance at atmospheric conditions and devising complex control strategies through the applied voltage. However, the mechanism of the momentum coupling between the plasma and the fluid flow is not yet adequately understood. In the present work, a modeling framework is presented to simulate athermal, non-equilibrium plasma discharges in conjunction with low Mach number fluid dynamics at atmospheric pressure. The plasma and fluid species are treated as a two-fluid system exhibiting a few decades of length and time scales. The effect of the plasma dynamics on the fluid dynamics is devised via a body force treatment in the Navier-Stokes equations. Two different approaches of different degrees of fidelity are presented for modeling the plasma dynamics. The first approach, a phenomenological model, is based on a linearized force distribution approximating the discharge structure, and utilizing experimental guidance to deduce the empirical constants. A high fidelity approach is to model the plasma dynamics in a self-consistent manner using a first principle-based hydrodynamic plasma model. The atmospheric pressure regime of interest here enables us to employ local equilibrium assumptions, signifying efficient collisional energy exchange as against thermal heating from inelastic collision processes. The time scale ratios between convection, diffusion, and reaction/ionization mechanisms are O(107), making the system computationally stiff. To handle the stiffness, a sequential finite-volume operator-splitting algorithm capable of conserving space charge is developed; the approach can handle time

  10. Mechanisms of the hepatoprotective effects of tamoxifen against drug-induced and chemical-induced acute liver injuries

    Energy Technology Data Exchange (ETDEWEB)

    Yoshikawa, Yukitaka; Miyashita, Taishi; Higuchi, Satonori [Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920‐1192 (Japan); Tsuneyama, Koichi [Department of Diagnostic Pathology, Graduate School of Medicine and Pharmaceutical Science for Research, University of Toyama, Sugitani, Toyama 930‐0194 (Japan); Endo, Shinya [Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920‐1192 (Japan); Tsukui, Tohru [Research Center for Genomic Medicine, Saitama Medical University, Yamane, Hidaka 350‐1241 (Japan); Toyoda, Yasuyuki; Fukami, Tatsuki; Nakajima, Miki [Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920‐1192 (Japan); Yokoi, Tsuyoshi, E-mail: tyokoi@p.kanazawa-u.ac.jp [Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920‐1192 (Japan)

    2012-10-01

    Although estrogen receptor (ER)α agonists, such as estradiol and ethinylestradiol (EE2), cause cholestasis in mice, they also reduce the degree of liver injury caused by hepatotoxicants as well as ischemia–reperfusion. The functional mechanisms of ERα have yet to be elucidated in drug-induced or chemical-induced liver injury. The present study investigated the effects of an ERα agonist, selective ER modulators (SERMs) and an ER antagonist on drug-induced and chemical-induced liver injuries caused by acetaminophen, bromobenzene, diclofenac, and thioacetamide (TA). We observed hepatoprotective effects of EE2, tamoxifen (TAM) and raloxifene pretreatment in female mice that were exposed to a variety of hepatotoxic compounds. In contrast, the ER antagonist did not show any hepatoprotective effects. DNA microarray analyses suggested that monocyte to macrophage differentiation-associated 2 (Mmd2) protein, which has an unknown function, is commonly increased by TAM and RAL pretreatment, but not by pretreatment with the ER antagonist. In ERα-knockout mice, the hepatoprotective effects of TAM and the increased expression of Mmd2 mRNA were not observed in TA-induced liver injury. To investigate the function of Mmd2, the expression level of Mmd2 mRNA was significantly knocked down to approximately 30% in mice by injection of siRNA for Mmd2 (siMmd2). Mmd2 knockdown resulted in a reduction of the protective effects of TAM on TA-induced liver injury in mice. This is the first report of the involvement of ERα in drug-induced or chemical-induced liver injury. Upregulation of Mmd2 protein in the liver was suggested as the mechanism of the hepatoprotective effects of EE2 and SERMs. -- Highlights: ► Liver injury induced by drugs or chemicals was investigated in mice. ► Liver injury was suppressed by pretreatment with tamoxifen in female mice. ► Mmd2, whose function was unknown, could be a candidate gene for liver protection. ► Tamoxifen up-regulated Mmd2 mRNA expression

  11. Laser-induced fluorescence: quantitative analysis of atherosclerotic plaque chemical content in human aorta

    Science.gov (United States)

    Dai, Erbin; Wishart, David; Khoury, Samir; Kay, Cyril M.; Jugdutt, Bodh I.; Tulip, John; Lucas, Alexandra

    1996-05-01

    We have been studying laser-induced fluorescence as a technique for identification of selected changes in the chemical composition of atherosclerotic plaque. Formulae for quantification of chemical changes have been developed based upon analysis of fluorescence emission spectra using multiple regression analysis and the principal of least squares. The intima of human aortic necropsy specimens was injected with chemical compounds present in atherosclerotic plaque. Spectra recorded after injection of selected chemical components found in plaque (collagen I, III, IV, elastin and cholesterol) at varying concentrations (0.01 - 1.0 mg) were compared with saline injection. A single fiber system was used for both fluorescence excitation (XeCl excimer laser, 308 nm, 1.5 - 2.0 mJ/ pulse, 5 Hz) and fluorescence emission detection. Average spectra for each chemical have been developed and the wavelengths of peak emission intensity identified. Curve fitting analysis as well as multiple regression analysis were used to develop formulae for assessment of chemical content. Distinctive identifying average curves were established for each chemical. Excellent correlations were identified for collagen I, III, and IV, elastin, and cholesterol (R2 equals 0.92 6- 0.997). Conclusions: (1) Fluorescence spectra of human aortas were significantly altered by collagen I, collagen III, elastin and cholesterol. (2) Fluorescence spectroscopic analysis may allow quantitative assessment of atherosclerotic plaque chemical content in situ.

  12. Systematic trends in photonic reagent induced reactions in a homologous chemical family.

    Science.gov (United States)

    Tibbetts, Katharine Moore; Xing, Xi; Rabitz, Herschel

    2013-08-29

    The growing use of ultrafast laser pulses to induce chemical reactions prompts consideration of these pulses as "photonic reagents" in analogy to chemical reagents. This work explores the prospect that photonic reagents may affect systematic trends in dissociative ionization reactions of a homologous family of halomethanes, much as systematic outcomes are often observed for reactions between homologous families of chemical reagents and chemical substrates. The experiments in this work with photonic reagents of varying pulse energy and linear spectral chirp reveal systematic correlations between observable ion yields and the following set of natural variables describing the substrate molecules: the ionization energy of the parent molecule, the appearance energy of each fragment ion, and the relative strength of carbon-halogen bonds in molecules containing two different halogens. The results suggest that reactions induced by photonic reagents exhibit systematic behavior analogous to that observed in reactions driven by chemical reagents, which provides a basis to consider empirical "rules" for predicting the outcomes of photonic reagent induced reactions.

  13. Toward Chemically Resolved Computer Simulations of Dynamics and Remodeling of Biological Membranes.

    Science.gov (United States)

    Soares, Thereza A; Vanni, Stefano; Milano, Giuseppe; Cascella, Michele

    2017-08-03

    Cellular membranes are fundamental constituents of living organisms. Apart from defining the boundaries of the cells, they are involved in a wide range of biological functions, associated with both their structural and the dynamical properties. Biomembranes can undergo large-scale transformations when subject to specific environmental changes, including gel-liquid phase transitions, change of aggregation structure, formation of microtubules, or rupture into vesicles. All of these processes are dependent on a delicate interplay between intermolecular forces, molecular crowding, and entropy, and their understanding requires approaches that are able to capture and rationalize the details of all of the involved interactions. Molecular dynamics-based computational models at atom-level resolution are, in principle, the best way to perform such investigations. Unfortunately, the relevant spatial and time dimensionalities involved in membrane remodeling phenomena would require computational costs that are today unaffordable on a routinely basis. Such hurdles can be removed by coarse-graining the representations of the individual molecular components of the systems. This procedure anyway reduces the possibility of describing the chemical variations in the lipid mixtures composing biological membranes. New hybrid particle field multiscale approaches offer today a promising alternative to the more traditional particle-based simulations methods. By combining chemically distinguishable molecular representations with mesoscale-based computationally affordable potentials, they appear as one of the most promising ways to keep an accurate description of the chemical complexity of biological membranes and, at the same time, cover the required scales to describe remodeling events.

  14. Al-induced root cell wall chemical components differences of wheat ...

    African Journals Online (AJOL)

    Jane

    2011-07-13

    Jul 13, 2011 ... Environment, Ministry of Agriculture, Department of Plant Nutrition, ... in cell wall chemical components of root tip cell between wheat lines with different Al tolerances induce ..... the highly significant interaction between cultivar × con- .... formation is a sensitive marker for genotypic aluminium sensitivity in.

  15. A Review on Chemical Effects in Aqueous Solution induced by Plasma with Glow Discharge

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Chemical effects in different aqueous solutions induced by plasma with glow dis charge electrolysis (GDE) and contact glow discharge electrolysis (CGDE) are described in this paper. The experimental and discharge characteristics are also reviewed. These are followed by a discussion of their mechanisms of both anodic and cathodic CGDE..

  16. Supramolecular chemical shift reagents inducing conformational transitions: NMR analysis of carbohydrate homooligomer mixtures

    DEFF Research Database (Denmark)

    Beeren, Sophie; Meier, Sebastian

    2015-01-01

    We introduce the concept of supramolecular chemical shift reagents as a tool to improve signal resolution for the NMR analysis of homooligomers. Non-covalent interactions with the shift reagent can constrain otherwise flexible analytes inducing a conformational transition that results in signal s...

  17. Small Open Chemical Systems Theory: Its Implications to Darwinian Evolution Dynamics, Complex Self-Organization and Beyond

    National Research Council Canada - National Science Library

    QIAN Hong

    2014-01-01

    The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra...

  18. Imprint Control of BaTiO3 Thin Films via Chemically Induced Surface Polarization Pinning.

    Science.gov (United States)

    Lee, Hyungwoo; Kim, Tae Heon; Patzner, Jacob J; Lu, Haidong; Lee, Jung-Woo; Zhou, Hua; Chang, Wansoo; Mahanthappa, Mahesh K; Tsymbal, Evgeny Y; Gruverman, Alexei; Eom, Chang-Beom

    2016-04-13

    Surface-adsorbed polar molecules can significantly alter the ferroelectric properties of oxide thin films. Thus, fundamental understanding and controlling the effect of surface adsorbates are crucial for the implementation of ferroelectric thin film devices, such as ferroelectric tunnel junctions. Herein, we report an imprint control of BaTiO3 (BTO) thin films by chemically induced surface polarization pinning in the top few atomic layers of the water-exposed BTO films. Our studies based on synchrotron X-ray scattering and coherent Bragg rod analysis demonstrate that the chemically induced surface polarization is not switchable but reduces the polarization imprint and improves the bistability of ferroelectric phase in BTO tunnel junctions. We conclude that the chemical treatment of ferroelectric thin films with polar molecules may serve as a simple yet powerful strategy to enhance functional properties of ferroelectric tunnel junctions for their practical applications.

  19. Automatic differentiation tools in the dynamic simulation of chemical engineering processes

    Directory of Open Access Journals (Sweden)

    Castro M.C.

    2000-01-01

    Full Text Available Automatic Differentiation is a relatively recent technique developed for the differentiation of functions applicable directly to the source code to compute the function written in standard programming languages. That technique permits the automatization of the differentiation step, crucial for dynamic simulation and optimization of processes. The values for the derivatives obtained with AD are exact (to roundoff. The theoretical exactness of the AD comes from the fact that it uses the same rules of differentiation as in differential calculus, but these rules are applied to an algorithmic specification of the function rather than to a formula. The main purpose of this contribution is to discuss the impact of Automatic Differentiation in the field of dynamic simulation of chemical engineering processes. The influence of the differentiation technique on the behavior of the integration code, the performance of the generated code and the incorporation of AD tools in consistent initialization tools are discussed from the viewpoint of dynamic simulation of typical models in chemical engineering.

  20. Self-organized mechano-chemical dynamics in amoeboid locomotion of Physarum fragments

    Science.gov (United States)

    Zhang, Shun; Guy, Robert D.; Lasheras, Juan C.; del Álamo, Juan C.

    2017-05-01

    The aim of this work is to quantify the spatio-temporal dynamics of flow-driven amoeboid locomotion in small (∼100 μm) fragments of the true slime mold Physarum polycephalum. In this model organism, cellular contraction drives intracellular flows, and these flows transport the chemical signals that regulate contraction in the first place. As a consequence of these non-linear interactions, a diversity of migratory behaviors can be observed in migrating Physarum fragments. To study these dynamics, we measure the spatio-temporal distributions of the velocities of the endoplasm and ectoplasm of each migrating fragment, the traction stresses it generates on the substratum, and the concentration of free intracellular calcium. Using these unprecedented experimental data, we classify migrating Physarum fragments according to their dynamics, finding that they often exhibit spontaneously coordinated waves of flow, contractility and chemical signaling. We show that Physarum fragments exhibiting symmetric spatio-temporal patterns of endoplasmic flow migrate significantly slower than fragments with asymmetric patterns. In addition, our joint measurements of ectoplasm velocity and traction stress at the substratum suggest that forward motion of the ectoplasm is enabled by a succession of stick-slip transitions, which we conjecture are also organized in the form of waves. Combining our experiments with a simplified convection-diffusion model, we show that the convective transport of calcium ions may be key for establishing and maintaining the spatio-temporal patterns of calcium concentration that regulate the generation of contractile forces.

  1. Nutrient Induced Type 2 and Chemical Induced Type 1 Experimental Diabetes Differently Modulate Gastric GLP-1 Receptor Expression

    Directory of Open Access Journals (Sweden)

    Olga Bloch

    2015-01-01

    Full Text Available T2DM patients demonstrate reduced GLP-1 receptor (GLP-1R expression in their gastric glands. Whether induced T2DM and T1DM differently affect the gastric GLP-1R expression is not known. This study assessed extrapancreatic GLP-1R system in glandular stomach of rodents with different types of experimental diabetes. T2DM and T1DM were induced in Psammomys obesus (PO by high-energy (HE diet and by streptozotocin (STZ in Sprague Dawly (SD rats, respectively. GLP-1R expression was determined in glandular stomach by RT PCR and immunohistomorphological analysis. The mRNA expression and cellular association of the GLP-1R in principal glands were similar in control PO and SD rats. However, nutrient and chemical induced diabetes resulted in opposite alterations of glandular GLP-1R expression. Diabetic PO demonstrated increased GLP-1R mRNA expression, intensity of cellular GLP-1R immunostaining, and frequency of GLP-1R positive cells in the neck area of principal glands compared with controls. In contrast, SD diabetic rats demonstrated decreased GLP-1 mRNA, cellular GLP-1R immunoreactivity, and frequency of GLP-1R immunoreactive cells in the neck area compared with controls. In conclusion, nutrient and chemical induced experimental diabetes result in distinct opposite alterations of GLP-1R expression in glandular stomach. These results suggest that induced T1DM and T2DM may differently modulate GLP-1R system in enteropancreatic axis.

  2. Dynamics of synchrotron VUV-induced intracluster reactions

    Energy Technology Data Exchange (ETDEWEB)

    Grover, J.R. [Brookhaven National Laboratory, Upton, NY (United States)

    1993-12-01

    Photoionization mass spectrometry (PIMS) using the tunable vacuum ultraviolet radiation available at the National Synchrotron Light Source is being exploited to study photoionization-induced reactions in small van der Waals mixed complexes. The information gained includes the observation and classification of reaction paths, the measurement of onsets, and the determination of relative yields of competing reactions. Additional information is obtained by comparison of the properties of different reacting systems. Special attention is given to finding unexpected features, and most of the reactions investigated to date display such features. However, understanding these reactions demands dynamical information, in addition to what is provided by PIMS. Therefore the program has been expanded to include the measurement of kinetic energy release distributions.

  3. Molecular Dynamics Simulations of a Pressure-induced Glass Transition

    CERN Document Server

    Shumway, S L; Jonsson, H; Shumway, Shelly L.; Clarke, Andrew S.

    1994-01-01

    We simulate the compression of a two-component Lennard-Jones liquid at a variety of constant temperatures using a molecular dynamics algorithm in an isobaric-isothermal ensemble. The viscosity of the liquid increases with pressure, undergoing a broadened transition into a structurally arrested, amorphous state. This transition, like the more familiar one induced by cooling, is correlated with a significant increase in icosahedral ordering. In fact, the structure of the final state, as measured by an analysis of the bonding, is essentially the same in the glassy, frozen state whether produced by squeezing or by cooling under pressure. We have computed an effective hard-sphere packing fraction at the transition, defining the transition pressure or temperature by a cutoff in the diffusion constant, analogous to the traditional laboratory definition of the glass transition by an arbitrary, low cutoff in viscosity. The packing fraction at this transition point is not constant, but is consistently higher for runs c...

  4. Dynamically tunable plasmon induced transparency in graphene metamaterials

    Science.gov (United States)

    Fu, Guang-Lai; Zhai, Xiang; Li, Hong-Ju; Xia, Sheng-Xuan; Wang, Ling-Ling

    2017-01-01

    Plasmon induced transparency (PIT) with graphene metamaterials is investigated with the finite-difference time-domain method. Interestingly, the modulation of the PIT transparency window can be achieved by changing not only the gap distance between the two resonators but also the polarization angle of the excitation light. The three-level plasmonic system is employed to clearly explain the formation mechanism of the PIT effect. The analytical results show good consistency with the numerical calculations. Moreover, the PIT resonant wavelength and group delays of incident waves can be dynamically tuned by varying the Fermi energy of the graphene. Our designed graphene nanostructure is promising for the development of compact elements such as tunable sensors, switches and slow-light devices.

  5. Noise-induced bifurcations in magnetization dynamics of uniaxial nanomagnets

    Energy Technology Data Exchange (ETDEWEB)

    Serpico, C., E-mail: serpico@unina.it; Perna, S.; Quercia, A. [Dipartimento di Ingegneria Elettrica e delle Tecnologie dell' Informazione, Università di Napoli “Federico II,” I-80125 Napoli (Italy); Bertotti, G. [Istituto Nazionale di Ricerca Metrologica, I-10135 Torino (Italy); D' Aquino, M. [Dipartimento di Ingegneria, Università di Napoli “Parthenope,” I-80143 Napoli (Italy); Mayergoyz, I. D. [ECE Department and UMIACS, University of Maryland, College Park, Maryland 20742 (United States)

    2015-05-07

    Stochastic magnetization dynamics in uniformly magnetized nanomagnets is considered. The system is assumed to have rotational symmetry as the anisotropy axis, the applied field, and the spin polarization are all aligned along an axis of symmetry. By appropriate integration of the Fokker-Planck equation associated to the problem, the stochastic differential equation governing the evolution of the angle between the magnetization orientation and the symmetry axis is derived. The drift terms present in this equation contain a noise-induced drift term, which, in combination with drift terms of deterministic origin, can be written as the derivative of an effective potential. Superparamagnetic-like transitions are studied in connections with the bifurcations of the effective potential as temperature and excitation conditions are varied.

  6. Dynamic response of shear thickening fluid under laser induced shock

    Science.gov (United States)

    Wu, Xianqian; Zhong, Fachun; Yin, Qiuyun; Huang, Chenguang

    2015-02-01

    The dynamic response of the 57 vol./vol. % dense spherical silica particle-polyethylene glycol suspension at high pressure was investigated through short pulsed laser induced shock experiments. The measured back free surface velocities by a photonic Doppler velocimetry showed that the shock and the particle velocities decreased while the shock wave transmitted in the shear thickening fluid (STF), from which an equation of state for the STF was obtained. In addition, the peak stress decreased and the absorbed energy increased rapidly with increasing the thickness for a thin layer of the STF, which should be attributed to the impact-jammed behavior through compression of particle matrix, the deformation or crack of the hard-sphere particles, and the volume compression of the particles and the polyethylene glycol.

  7. Anomaly-induced dynamical refringence in strong-field QED

    CERN Document Server

    Mueller, Niklas; Berges, Jürgen

    2016-01-01

    We investigate the impact of the Adler-Bell-Jackiw anomaly on the nonequilibrium evolution of strong-field quantum electrodynamics (QED) using real-time lattice gauge theory techniques. For field strengths exceeding the Schwinger limit for pair production, we encounter a highly absorptive medium with anomaly-induced dynamical refractive properties. In contrast to earlier expectations based on equilibrium properties, where net anomalous effects vanish because of the trivial vacuum structure, we find that out-of-equilibrium conditions can have dramatic consequences for the presence of quantum currents with distinctive macroscopic signatures. We observe an intriguing tracking behavior, where the system spends longest times near collinear field configurations with maximum anomalous current. Apart from the potential relevance of our findings for future laser experiments, similar phenomena related to the chiral magnetic effect are expected to play an important role for strong QED fields during initial stages of hea...

  8. Towards Cluster-Assembled Materials of True Monodispersity in Size and Chemical Environment: Synthesis, Dynamics and Activity

    Science.gov (United States)

    2016-10-27

    pathway Status: not yet published Diverse technologies, from catalyst coking to graphene synthesis , entail hydrocarbon dehydrogena- tion and...AFRL-AFOSR-UK-TR-2016-0037 Towards cluster-assembled materials of true monodispersity in size and chemical environment: Synthesis , Dynamics and...Towards cluster-assembled materials of true monodispersity in size and chemical environment: synthesis , dynamics and activity 5a.  CONTRACT NUMBER 5b

  9. Dynamics of laser induced micro bubble clusters on tissue phantoms

    Science.gov (United States)

    Fritz, Andreas; Zegelin, Andrea; Ptaszynski, Lars; Birngruber, Reginald; Brinkmann, Ralf

    2011-03-01

    Selective retina treatment (SRT) is a laser based method to treat retinal diseases associated with disorders of the retinal pigment epithelium (RPE) while preserving photoreceptors and choroid. Applying microsecond laser pulses to the 100- 200 strongly absorbing melanin granules inside the RPE cells induces transient micro bubbles which disrupt the cells. Aim of this work is to understand bubble dynamics in clusters with respect to the influence of the adjacent retina. Bubble dynamics were investigated in vitro on porcine RPE. An about 200 μm thick layer of agarose gel was applied to the RPE layer in order to simulate the mechanical properties of retina. Different laser pulse durations from 1 ns (532 nm, Nd:YAG) to 1.7 μs (527 nm, Nd:YLF) were used. The bubbles were investigated interferometrically (fiber interferometer @ 830 nm) and with fast flash photography (25 ns flash duration). Bubble lifetimes were measured. The results show that with retina phantoms the bubble formation threshold was reached at 2.5 times higher irradiation than without retina phantom for 1.7 μs laser pulses. The microbubbles generated with 1 ns laser pulses were almost not influenced by the agarose layer. Irradiation twofold over bubble formation threshold resulted in 3.5 times longer bubble lifetimes for μs and 2 times longer for ns pulse durations, respectively.

  10. Disturbance induced dynamics of a tritrophic novel ecosystem.

    Science.gov (United States)

    Lakatos, K T; László, Z; Tóthmérész, B

    2017-07-26

    Novel ecosystems formed by invasive plants provide a good opportunity to get insight into early dynamics and pattern formation of these ecosystems. The invasive black locust as host plant, Bruchophagus robiniae as host-specific seed predator and its parasitoids were the components of the studied tritrophic system. To investigate disturbance-driven dynamics of this system we created seed-vacated host plant patches in a field experiment. We removed all pods from selected patches of black locust resulting in an induced local extinction of seed predators and their parasitoids. We hypothesized that disturbance enhances top-down control by parasitoids; this enhanced top-down control decreases seed predation, facilitating the host plant's spread. We found that disturbance modified only parasitism after controlling with year effect: in vacated patches median parasitism was higher than in control patches. Seed predation exceeded its initial level in vacated patches in the third year after the disturbance, but in the fourth year it dropped again presumably due to the strong top-down control. Our findings also suggested that the seed predator was also affected by the bottom-up control of its host plant's density. We found that in the studied new ecosystem the top-down control was strengthened by the disturbance. Since the host plant of the tritrophic system is an invasive species, partial habitat disturbance of such species may increase the severity of parasitoid top-down control, which may reduce seed predation by the herbivores.

  11. Thermo-induced vesicular dynamics of membranes containing cholesterol derivatives.

    Science.gov (United States)

    Yoda, Tsuyoshi; Vestergaard, Mun'delanji C; Hamada, Tsutomu; Le, Phuc Thi Minh; Takagi, Masahiro

    2012-08-01

    Membrane structural organization is an intrinsic property of a cell membrane. Any changes in lipid composition, and/or any stimuli that affect molecular packing induce structural re-organization. It membrane dynamics provide a means by which changes in structure organization can be determined, upon a change in the membrane internal or external environment. Here, we report on the effect of thermo-stress on membranes containing cholesterol liquid crystal (LC) compounds cholesterol benzoate (BENZO) and oxidized cholesterols. We have (1) revealed that lipid vesicles containing this artificial cholesterol derivative (BENZO) is thermo-responsive, and that this thermo-sensitivity is significantly similar to naturally oxy-cholesterols (2) elucidated the mechanism behind the membrane perturbation. Using Langmuir monolayer experiments, we have demonstrated that membrane perturbation was due to an increase in the molecular surface area, (3) discussed the similarities between cholesterol benzoate in the cholesterol LC state and in lipid bilayer membranes. Last, (4) drawing from previously reported findings, our new data on membrane dynamics, and the discussion above, we propose that artificial cholesterol derivatives such as BENZO, open new possibilities for controlled and tailored design using model membrane systems. Examples could include the development of membrane technology and provide a trigger for progress in thermo-tropical liquid crystal engineering.

  12. Extensional Flow-Induced Dynamic Phase Transitions in Isotactic Polypropylene.

    Science.gov (United States)

    Ju, Jianzhu; Wang, Zhen; Su, Fengmei; Ji, Youxin; Yang, Haoran; Chang, Jiarui; Ali, Sarmad; Li, Xiangyang; Li, Liangbin

    2016-09-01

    With a combination of fast extension rheometer and in situ synchrotron radiation ultra-fast small- and wide-angle X-ray scattering, flow-induced crystallization (FIC) of isotactic polypropylene (iPP) is studied at temperatures below and above the melting point of α crystals (Tmα). A flow phase diagram of iPP is constructed in strain rate-temperature space, composing of melt, non-crystalline shish, α and α&β coexistence regions, based on which the kinetic and dynamic competitions among these four phases are discussed. Above Tmα , imposing strong flow reverses thermodynamic stabilities of the disordered melt and the ordered phases, leading to the occurrence of FIC of β and α crystals as a dynamic phase transition. Either increasing temperature or stain rate favors the competiveness of the metastable β over the stable α crystals, which is attributed to kinetic rate rather than thermodynamic stability. The violent competitions among four phases near the boundary of crystal-melt may frustrate crystallization and result in the non-crystalline shish winning out.

  13. How to distinguish conformational selection and induced fit based on chemical relaxation rates

    CERN Document Server

    Paul, Fabian

    2016-01-01

    Protein binding often involves conformational changes. Important questions are whether a conformational change occurs prior to a binding event ('conformational selection') or after a binding event ('induced fit'), and how conformational transition rates can be obtained from experiments. In this article, we present general results for the chemical relaxation rates of conformational-selection and induced-fit binding processes that hold for all concentrations of proteins and ligands and, thus, go beyond the standard pseudo-first-order approximation of large ligand concentration. These results allow to distinguish conformational-selection from induced-fit processes - also in cases in which such a distinction is not possible under pseudo-first-order conditions - and to extract conformational transition rates of proteins from chemical relaxation data.

  14. Altered magnesium transport in slices of kidney cortex from chemically-induced diabetic rats

    Energy Technology Data Exchange (ETDEWEB)

    Hoskins, B.

    1981-10-01

    The uptake of magnesium-28 was measured in slices of kidney cortex from rats with alloxan-diabetes and from rats with streptozotocin-diabetes of increasing durations. In both forms of chemically-induced diabetes, magnesium-28 uptake by kidney cortex slices was significantly increased over uptake measured in kidney cortex slices from control rats. Immediate institution of daily insulin therapy to the diabetic rats prevented the diabetes-induced elevated uptake of magnesium without controlling blood glucose levels. Late institution of daily insulin therapy was ineffective in restoring the magnesium uptake to control values. These alterations in magnesium uptake occurred prior to any evidence of nephropathy (via the classic indices of proteinuria and increased BUN levels). The implications of these findings, together with our earlier demonstrations of altered calcium transport by kidney cortex slices from chemically-induced diabetic rats, are discussed in terms of disordered divalent cation transport being at least part of the basic pathogenesis underlying diabetic nephropathy.

  15. Chemically induced transition phenomena in polyurethanes as seen from generalized mode Grueneisen parameters

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, U; Philipp, M; Bactavatchalou, R; Sanctuary, R; Baller, J; Zielinski, B; Krueger, J K [Laboratoire de Physique des Materiaux, Universite du Luxembourg, 162A, Avenue de la Faiencerie, L-1115 (Luxembourg); Possart, W; Alnot, P [Laboratoire Europeen de Recherche, Universitaire Saarland-Lorraine (Luxembourg)], E-mail: ulrich.mueller@uni.lu

    2008-05-21

    Many phenomenological properties of reactive polymers like polyurethanes increase or decrease continuously in the course of the curing process before saturating at the end of the chemical reaction. This holds true for instance for the mass density, the refractive index, the chemical turnover and the hypersonic properties. The reason for this monotone behaviour is that the chemical reaction behaves like a continuous succession of irreversible phase transitions. These transitions are superposed by the sol-gel transition and possibly by the chemically induced glass transition, with the drawback that the latter two highlighted transitions are often hidden by the underlying curing process. In this work we propose generalized mode Grueneisen parameters as an alternative probe for elucidating the polymerization process itself and the closely related transition phenomena. As a model system we use polyurethane composed of a diisocyanate and varying ratios of difunctional and trifunctional alcohols.

  16. Ultrafast chemical reactions in shocked nitromethane probed with dynamic ellipsometry and transient absorption spectroscopy.

    Science.gov (United States)

    Brown, Kathryn E; McGrane, Shawn D; Bolme, Cynthia A; Moore, David S

    2014-04-10

    Initiation of the shock driven chemical reactions and detonation of nitromethane (NM) can be sensitized by the addition of a weak base; however, the chemical mechanism by which sensitization occurs remains unclear. We investigated the shock driven chemical reaction in NM and in NM sensitized with diethylenetriamine (DETA), using a sustained 300 ps shock driven by a chirped Ti:sapphire laser. We measured the solutions' visible transient absorption spectra and measured interface particle and shock velocities of the nitromethane solutions using ultrafast dynamic ellipsometry. We found there to be a volume-increasing reaction that takes place around interface particle velocity up = 2.4 km/s and up = 2.2 km/s for neat NM and NM with 5% DETA, respectively. The rate at which transient absorption increases is similar in all mixtures, but with decreasing induction times for solutions with increasing DETA concentrations. This result supports the hypothesis that the chemical reaction mechanisms for shocked NM and NM with DETA are the same. Data from shocked NM are compared to literature experimental and theoretical data.

  17. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

    Science.gov (United States)

    Mathews, David H.; Disney, Matthew D.; Childs, Jessica L.; Schroeder, Susan J.; Zuker, Michael; Turner, Douglas H.

    2004-01-01

    A dynamic programming algorithm for prediction of RNA secondary structure has been revised to accommodate folding constraints determined by chemical modification and to include free energy increments for coaxial stacking of helices when they are either adjacent or separated by a single mismatch. Furthermore, free energy parameters are revised to account for recent experimental results for terminal mismatches and hairpin, bulge, internal, and multibranch loops. To demonstrate the applicability of this method, in vivo modification was performed on 5S rRNA in both Escherichia coli and Candida albicans with 1-cyclohexyl-3-(2-morpholinoethyl) carbodiimide metho-p-toluene sulfonate, dimethyl sulfate, and kethoxal. The percentage of known base pairs in the predicted structure increased from 26.3% to 86.8% for the E. coli sequence by using modification constraints. For C. albicans, the accuracy remained 87.5% both with and without modification data. On average, for these sequences and a set of 14 sequences with known secondary structure and chemical modification data taken from the literature, accuracy improves from 67% to 76%. This enhancement primarily reflects improvement for three sequences that are predicted with <40% accuracy on the basis of energetics alone. For these sequences, inclusion of chemical modification constraints improves the average accuracy from 28% to 78%. For the 11 sequences with <6% pseudoknotted base pairs, structures predicted with constraints from chemical modification contain on average 84% of known canonical base pairs. PMID:15123812

  18. Study on interface behavior of 3D composites reinforced with chemically connected CNTs using molecular dynamics

    Science.gov (United States)

    Yang, Lin; He, Xiaodong; Tong, Liyong

    2009-07-01

    In this study, we used several molecular dynamic models to simulate the pull-out process of a carbon nanotube (CNT) that is assumed to be chemically connected to a carbon fiber, and to calculate the CNTs' geometry variation, displacement, energy and stress during this process. In the simulation, the CNTs' elongation and necking phenomena have been noted prior to the movement of the CNT's end embedded in resin. The simulation yields a CNT's plastic constitutive model in the pull-out process. The fracture resistance capability of a chemically connected CNT is then discussed. In the simulation of shearing, the prediction of the CNTs' capability of shear resistance has been conducted. Finally, by comparing the experiment result with the simulation, we predict the amido link break before the CNT pull-out in the shearing test.

  19. Nonlinear Stochastic Dynamics of Complex Systems, I: A Chemical Reaction Kinetic Perspective with Mesoscopic Nonequilibrium Thermodynamics

    CERN Document Server

    Qian, Hong

    2016-01-01

    We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity, but population wise with statistical rate laws in their syntheses, degradations, spatial diffusion, individual state transitions, and interactions. Such a formal kinetic system in a small volume $V$, like a single cell, can be rigorously treated in terms of a Markov process describing its nonlinear kinetics as well as nonequilibrium thermodynamics at a mesoscopic scale. We introduce notions such as open, driven chemical systems, entropy production, free energy dissipation, etc. Then in the macroscopic limit, we illustrate how two new "laws", in terms of a generalized free energy of the mesoscopic stochastic dynamics, emerge. Detailed balance and complex balance are two special classes of "simple" nonlinear kinetics. Phase transition is intrinsically related to multi-stability...

  20. Molecular dynamics study of phase separation in fluids with chemical reactions.

    Science.gov (United States)

    Krishnan, Raishma; Puri, Sanjay

    2015-11-01

    We present results from the first d=3 molecular dynamics (MD) study of phase-separating fluid mixtures (AB) with simple chemical reactions (A⇌B). We focus on the case where the rates of forward and backward reactions are equal. The chemical reactions compete with segregation, and the coarsening system settles into a steady-state mesoscale morphology. However, hydrodynamic effects destroy the lamellar morphology which characterizes the diffusive case. This has important consequences for the phase-separating structure, which we study in detail. In particular, the equilibrium length scale (ℓ(eq)) in the steady state suggests a power-law dependence on the reaction rate ε:ℓ(eq)∼ε(-θ) with θ≃1.0.

  1. Steady dynamics of exothermic chemical wave fronts in van der Waals fluids

    Science.gov (United States)

    Dumazer, G.; Antoine, C.; Lemarchand, A.; Nowakowski, B.

    2009-12-01

    We study the steady dynamics of an exothermic Fisher-Kolmogorov-Petrovsky-Piskunov chemical wave front traveling in a one-dimensional van der Waals fluid. The propagating wave is initiated by a nonuniformity in reactant concentration contrary to usual combustion ignition processes. The heat release and activation energy of the reaction play the role of control parameters. We recently proved that the propagation of an exothermic chemical wave front in a perfect gas displays a forbidden interval of stationary wave front speeds [G. Dumazer, M. Leda, B. Nowakowski, and A. Lemarchand, Phys. Rev. E 78, 016309 (2008)]. We examine how this result is modified for nonideal fluids and determine the effect of the van der Waals parameters and fluid density on the bifurcation between diffusion flames and Chapman-Jouguet detonation waves as heat release increases. Analytical predictions are confirmed by the numerical solution of the hydrodynamic equations including reaction kinetics.

  2. On-line Dynamic Model Correction Based Fault Diagnosis in Chemical Processes

    Institute of Scientific and Technical Information of China (English)

    田文德; 孙素莉

    2007-01-01

    A novel fault detection and diagnosis method was proposed,using dynamic simulation to monitor chemical process and identify faults when large tracking deviations occur.It aims at parameter failures,and the parameters are updated via on-line correction.As it can predict the trend of process and determine the existence of malfunctions simultaneously,this method does not need to design problem-specific observer to estimate unmeasured state variables.Application of the proposed method is presented on one water tank and one aromatization reactor,and the results are compared with those from the traditional method.

  3. TRENDS OF CURRENT DYNAMICS OF CHEMICAL PROCESSES IN THE SOILS OF ODESSA REGION

    Directory of Open Access Journals (Sweden)

    Bilanchyn Yaroslav

    2012-06-01

    Full Text Available Results of chemical processes’ dynamic studies of many years (1971-2011 in the soils of Odessa Region have been described. The most significant in the last 15-20 years have been changes of humus content and ecological & agrochemical status of black soils. In spite of some increase in the norm of fertilizers input for the last 5 years the negative balance of plant nutrition elements in soils is preserved. Ways of optimization of humus and ecological & agrochemical status of soils in the region and increase of their fertility have been proposed.

  4. Influence of the work of adhesion on the dynamic wetting of chemically heterogeneous surfaces.

    Science.gov (United States)

    Ray, Santanu; Sedev, Rossen; Priest, Craig; Ralston, John

    2008-11-18

    The velocity dependence of the dynamic contact angle for a glycerol-water mixture wetting two different chemically heterogeneous surfaces (mixed thiols on gold and partially methylated titania, 16 samples in all) was studied. The molecular kinetic theory (MKT) of wetting was used to interpret the dynamic contact angle data. The equilibrium displacement frequency ( K 0) was predominantly determined by the viscous contribution from the bulk liquid, with a minor contribution from the surface. The mean distance between surface sites (lambda) decreased with increasing work of adhesion. The contact line friction coefficient zeta 0 was found to vary exponentially with the work of adhesion, enabling the unit flow volume of the liquid to be obtained.

  5. Analysis of forward and inverse problems in chemical dynamics and spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Rabitz, H.

    1992-01-01

    The forward aspects of the research were concerned with mapping the relation between input potential surface structure, and laboratory dynamical and kinetic observables. The research on inverse analysis complemented the forward analysis studies; objective was to develop algorithms for inversion of quality laboratory data, back to underlying potential surfaces. 24 items of research in molecular dynamics and chemical kinetics are reported. The following collisions/reactions were studied: H + H[sub 2], He - H[sub 2], He - Xe/C(0001), thermal explosions, CO/H[sub 2]/O[sub 2], H[sub 2] + HD, H[sup +] + F([sup 2]P[sub 1/2]), He[sup +] + Ne(2p[sup 6]), Na + I, F + H[sub 2], CO - H[sub 2] - O[sub 2].

  6. Analysis of forward and inverse problems in chemical dynamics and spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Rabitz, H.

    1991-01-01

    This research is concerned with the development and application of advanced analysis tools for studying dynamics, kinetics, and spectroscopic phenomena from a forward and inverse perspective. In particular, the forward problem is concerned with understanding how detailed interatomic potential information maps onto a hierarchy of chemical dynamic and kinetic observables. The inverse aspects of the research are concerned with exactly the reverse of this process, whereby we desire to understand how particular measurements project back to yield information regarding the potential surface. Thus, in the latter domain, our research is concerned with the development of theoretically based tools ultimately aimed at applications to the inversion of quality laboratory data for the extraction of microscopic potential information.

  7. CHEMICALS

    CERN Document Server

    Medical Service

    2002-01-01

    It is reminded that all persons who use chemicals must inform CERN's Chemistry Service (TIS-GS-GC) and the CERN Medical Service (TIS-ME). Information concerning their toxicity or other hazards as well as the necessary individual and collective protection measures will be provided by these two services. Users must be in possession of a material safety data sheet (MSDS) for each chemical used. These can be obtained by one of several means : the manufacturer of the chemical (legally obliged to supply an MSDS for each chemical delivered) ; CERN's Chemistry Service of the General Safety Group of TIS ; for chemicals and gases available in the CERN Stores the MSDS has been made available via EDH either in pdf format or else via a link to the supplier's web site. Training courses in chemical safety are available for registration via HR-TD. CERN Medical Service : TIS-ME :73186 or service.medical@cern.ch Chemistry Service : TIS-GS-GC : 78546

  8. The relationship between chemical-induced kidney weight increases and kidney histopathology in rats.

    Science.gov (United States)

    Craig, Evisabel A; Yan, Zhongyu; Zhao, Q Jay

    2015-07-01

    The kidney is a major site of chemical excretion, which results in its propensity to exhibit chemically-induced toxicological effects at a higher rate than most other organs. Although the kidneys are often weighed in animal toxicity studies, the manner in which these kidney weight measurements are interpreted and the value of this information in predicting renal damage remains controversial. In this study we sought to determine whether a relationship exists between chemically-induced kidney weight changes and renal histopathological alterations. We also examined the relative utility of absolute and relative (kidney-to-body weight ratio) kidney weight in the prediction of renal toxicity. For this, data extracted from oral chemical exposure studies in rats performed by the National Toxicology Program were qualitatively and quantitatively evaluated. Our analysis showed a statistically significant correlation between absolute, but not relative, kidney weight and renal histopathology in chemically-treated rats. This positive correlation between absolute kidney weight and histopathology was observed even with compounds that statistically decreased terminal body weight. Also, changes in absolute kidney weight, which occurred at subchronic exposures, were able to predict the presence or absence of kidney histopathology at both subchronic and chronic exposures. Furthermore, most increases in absolute kidney weight reaching statistical significance (irrespective of the magnitude of change) were found to be relevant for the prediction of histopathological changes. Hence, our findings demonstrate that the evaluation of absolute kidney weight is a useful method for identifying potential renal toxicants.

  9. In vivo regulation of erythropoiesis by chemically inducible dimerization of the erythropoietin receptor intracellular domain.

    Directory of Open Access Journals (Sweden)

    Norio Suzuki

    Full Text Available Erythropoietin (Epo and its receptor (EpoR are required for the regulation of erythropoiesis. Epo binds to the EpoR homodimer on the surface of erythroid progenitors and erythroblasts, and positions the intracellular domains of the homodimer to be in close proximity with each other. This conformational change is sufficient for the initiation of Epo-EpoR signal transduction. Here, we established a system of chemically regulated erythropoiesis in transgenic mice expressing a modified EpoR intracellular domain (amino acids 247-406 in which dimerization is induced using a specific compound (chemical inducer of dimerization, CID. Erythropoiesis is reversibly induced by oral administration of the CID to the transgenic mice. Because transgene expression is limited to hematopoietic cells by the Gata1 gene regulatory region, the effect of the CID is limited to erythropoiesis without adverse effects. Additionally, we show that the 160 amino acid sequence is the minimal essential domain of EpoR for intracellular signaling of chemically inducible erythropoiesis in vivo. We propose that the CID-dependent dimerization system combined with the EpoR intracellular domain and the Gata1 gene regulatory region generates a novel peroral strategy for the treatment of anemia.

  10. Application of computational fluid dynamics to regional dosimetry of inhaled chemicals in the upper respiratory tract of the rat.

    Science.gov (United States)

    Kimbell, J S; Gross, E A; Joyner, D R; Godo, M N; Morgan, K T

    1993-08-01

    For certain inhaled air pollutants, such as reactive, water soluble gases, the distribution of nasal lesions observed in F344 rats may be closely related to regional gas uptake patterns in the nose. These uptake patterns can be influenced by the currents of air flowing through the upper respiratory tract during the breathing cycle. Since data on respiratory tract lesions in F344 rats are extrapolated to humans to make predictions of risk to human health, a better understanding of the factors affecting these responses is needed. To assess potential effects of nasal airflow on lesion location and severity, a methodology was developed for creation of computer simulations of steady-state airflow and gas transport using a three-dimensional finite element grid reconstructed from serial step-sections of the nasal passages of a male F344 rat. Simulations on a supercomputer used the computational fluid dynamics package FIDAP (FDI, Evanston, IL). Distinct streams of bulk flow evident in the simulations matched inspiratory streams reported for the F344 rat. Moreover, simulated regional flow velocities matched measured velocities in concurrent laboratory experiments with a hollow nasal mold. Computer-predicted flows were used in simulations of gas transport to nasal passage walls, with formaldehyde as a test case. Results from the uptake simulations were compared with the reported distribution of formaldehyde-induced nasal lesions observed in the F344 rat, and indicated that airflow-driven uptake patterns probably play an important role in determining the location of certain nasal lesions induced by formaldehyde. This work demonstrated the feasibility of applying computational fluid dynamics to airflow-driven dosimetry of inhaled chemicals in the upper respiratory tract.

  11. Dynamics and Kinetics Study of "In-Water" Chemical Reactions by Enhanced Sampling of Reactive Trajectories.

    Science.gov (United States)

    Zhang, Jun; Yang, Y Isaac; Yang, Lijiang; Gao, Yi Qin

    2015-11-12

    High potential energy barriers and engagement of solvent coordinates set challenges for in silico studies of chemical reactions, and one is quite commonly limited to study reactions along predefined reaction coordinate(s). A systematic protocol, QM/MM MD simulations using enhanced sampling of reactive trajectories (ESoRT), is established to quantitatively study chemical transitions in complex systems. A number of trajectories for Claisen rearrangement in water and toluene were collected and analyzed, respectively. Evidence was found that the bond making and breaking during this reaction are concerted processes in solutions, preferentially through a chairlike configuration. Water plays an important dynamic role that helps stabilize the transition sate, and the dipole-dipole interaction between water and the solute also lowers the transition barrier. The calculated rate coefficient is consistent with the experimental measurement. Compared with water, the reaction pathway in toluene is "narrower" and the reaction rate is slower by almost three orders of magnitude due to the absence of proper interactions to stabilize the transition state. This study suggests that the "in-water" nature of the Claisen rearrangement in aqueous solution influences its thermodynamics, kinetics, as well as dynamics.

  12. Bromophenacyl bromide, a phospholipase A2 inhibitor attenuates chemically induced gastroduodenal ulcers in rats

    Institute of Scientific and Technical Information of China (English)

    Mohammad Tariq; Ibrahim Elfaki; Haseeb Ahmad Khan; Mohammad Arshaduddin; Samia Sobki; Meshal Al Moutaery

    2006-01-01

    AIM: To study the effect of bromophenacyl bromide (BPB), a phospholipase A2 inhibitor on gastric secretion and to protect chemically induced gastric and duodenal ulcers in rats.METHODS: Acid secretion studies were undertaken in pylorus-ligated rats with BPB treatment (0, 5, 15 and 45 mg/kg). Gastric and duodenal lesions in the rats were induced by ethanol and cysteamine respectively. The levels of gastric wall mucus, nonprotein sulfhydryls (NPSH) and myeloperoxidase (MPO) were also measured in the glandular stomach of rats following ethanol induced gastric lesions.RESULTS: BPB produced a dose-dependent inhibition of gastric acid secretion and acidity in rats. Pretreatment with BPB significantly attenuated the formation of ethanol induced gastric lesion. BPB also protected intestinal mucosa against cysteamine-induced duodenal ulcers.The antiulcer activity of BPB was associated with significant inhibition of ethanol-induced depletion of gastric wall mucus, NP-SH and MPO. These findings pointed towards the mediation of sulfhydryls in BPB induced gastrointestinal cytoprotection.CONCLUSION: BPB possesses significant antiulcer and cytoprotective activity against experimentally induced gastroduodenal lesions.

  13. Programming chemical kinetics: engineering dynamic reaction networks with DNA strand displacement

    Science.gov (United States)

    Srinivas, Niranjan

    Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ "chemical wiring" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the abstractions, design principles, verification and fabrication techniques in place for programming with silicon, we have no comparable understanding or expertise for programming chemistry. In this thesis we take a small step towards the goal of learning how to systematically engineer prescribed non-equilibrium dynamical behaviors in chemical systems. We use the formalism of chemical reaction networks (CRNs), combined with mass-action kinetics, as our programming language for specifying dynamical behaviors. Leveraging the tools of nucleic acid nanotechnology (introduced in Chapter 1), we employ synthetic DNA molecules as our molecular architecture and toehold-mediated DNA strand displacement as our reaction primitive. Abstraction, modular design and systematic fabrication can work only with well-understood and quantitatively characterized tools. Therefore, we embark on a detailed study of the "device physics" of DNA strand displacement (Chapter 2). We present a unified view of strand displacement biophysics and kinetics by studying the process at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model that incorporates three-dimensional geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Our findings are consistent with previously measured or inferred rates for

  14. Computational Cellular Dynamics Based on the Chemical Master Equation: A Challenge for Understanding Complexity.

    Science.gov (United States)

    Liang, Jie; Qian, Hong

    2010-01-01

    Modern molecular biology has always been a great source of inspiration for computational science. Half a century ago, the challenge from understanding macromolecular dynamics has led the way for computations to be part of the tool set to study molecular biology. Twenty-five years ago, the demand from genome science has inspired an entire generation of computer scientists with an interest in discrete mathematics to join the field that is now called bioinformatics. In this paper, we shall lay out a new mathematical theory for dynamics of biochemical reaction systems in a small volume (i.e., mesoscopic) in terms of a stochastic, discrete-state continuous-time formulation, called the chemical master equation (CME). Similar to the wavefunction in quantum mechanics, the dynamically changing probability landscape associated with the state space provides a fundamental characterization of the biochemical reaction system. The stochastic trajectories of the dynamics are best known through the simulations using the Gillespie algorithm. In contrast to the Metropolis algorithm, this Monte Carlo sampling technique does not follow a process with detailed balance. We shall show several examples how CMEs are used to model cellular biochemical systems. We shall also illustrate the computational challenges involved: multiscale phenomena, the interplay between stochasticity and nonlinearity, and how macroscopic determinism arises from mesoscopic dynamics. We point out recent advances in computing solutions to the CME, including exact solution of the steady state landscape and stochastic differential equations that offer alternatives to the Gilespie algorithm. We argue that the CME is an ideal system from which one can learn to understand "complex behavior" and complexity theory, and from which important biological insight can be gained.

  15. Prediction of dynamic loads and induced vibrations in stall

    Energy Technology Data Exchange (ETDEWEB)

    Thirstrup Petersen, J.; Aagaard Madsen, H. [Risoe National Lab. (Denmark); Bjoerck, A. [Aeronautical Research Inst. of Sweden (Sweden); Enevoldsen, P. [Bonus Energy A/S (Denmark); Oeye, S. [The Technical Univ. of Denmark (Denmark); Ganander, H. [Teknikgruppen AB (Sweden); Winkelaar, D. [Netherlands Energy Research Foundation (Netherlands)

    1998-05-01

    Results from research in an EC Joule-III project and from national projects are presented. The objectives are improvement of design methods for stall regulated wind turbines with emphasis on stall induced vibrations and dynamic stall. The primary concern is limitation of the edgewise vibrations in the fundamental blade natural mode shape, which have caused trouble on modern wind turbines of approximate size 500 kW nominal power and 40 m rotor diameter. A theoretical study of quasi-steady aerodynamics confirms that the vibrations are driven basically by energy supplied from the aerodynamic forces during stalled operation. This energy exchange is equivalent to negative aerodynamic damping. The theoretical approach identifies the main parameters controlling the phenomenon. These parameters describe the steady and the dynamic airfoil characteristics, the overall aerodynamic layout of the blade, e.g. chord length and twist, the structural properties of the blade, e.g. structural damping and properties controlling the resulting vibration direction. Furthermore, full aeroelastic calculations and comparison with measurements show that the properties of the supporting structure, i.e. the main shaft, the nacelle and the tower, are important, as the global vibration of the rotor on its support may exchange energy with the blade vibration, when the blade natural frequency is close to one of the frequencies of the coupled rotor tilt-yaw mode shapes, usually denoted the global rotor whirl frequencies. It is confirmed that the influence of changing the primary design parameters can be determined by use of qualified aeroelastic calculations. Presented design guidelines therefore build on both the simple quasi-steady models, which can be used for the preliminary choice of the design variables mentioned above, and on full aeroelastic calculations. The aeroelastic calculations refine the design basis and should be used for choosing the final design variables and for final

  16. Motif analysis for small-number effects in chemical reaction dynamics

    Science.gov (United States)

    Saito, Nen; Sughiyama, Yuki; Kaneko, Kunihiko

    2016-09-01

    The number of molecules involved in a cell or subcellular structure is sometimes rather small. In this situation, ordinary macroscopic-level fluctuations can be overwhelmed by non-negligible large fluctuations, which results in drastic changes in chemical-reaction dynamics and statistics compared to those observed under a macroscopic system (i.e., with a large number of molecules). In order to understand how salient changes emerge from fluctuations in molecular number, we here quantitatively define small-number effect by focusing on a "mesoscopic" level, in which the concentration distribution is distinguishable both from micro- and macroscopic ones and propose a criterion for determining whether or not such an effect can emerge in a given chemical reaction network. Using the proposed criterion, we systematically derive a list of motifs of chemical reaction networks that can show small-number effects, which includes motifs showing emergence of the power law and the bimodal distribution observable in a mesoscopic regime with respect to molecule number. The list of motifs provided herein is helpful in the search for candidates of biochemical reactions with a small-number effect for possible biological functions, as well as for designing a reaction system whose behavior can change drastically depending on molecule number, rather than concentration.

  17. Motif analysis for small-number effects in chemical reaction dynamics.

    Science.gov (United States)

    Saito, Nen; Sughiyama, Yuki; Kaneko, Kunihiko

    2016-09-07

    The number of molecules involved in a cell or subcellular structure is sometimes rather small. In this situation, ordinary macroscopic-level fluctuations can be overwhelmed by non-negligible large fluctuations, which results in drastic changes in chemical-reaction dynamics and statistics compared to those observed under a macroscopic system (i.e., with a large number of molecules). In order to understand how salient changes emerge from fluctuations in molecular number, we here quantitatively define small-number effect by focusing on a "mesoscopic" level, in which the concentration distribution is distinguishable both from micro- and macroscopic ones and propose a criterion for determining whether or not such an effect can emerge in a given chemical reaction network. Using the proposed criterion, we systematically derive a list of motifs of chemical reaction networks that can show small-number effects, which includes motifs showing emergence of the power law and the bimodal distribution observable in a mesoscopic regime with respect to molecule number. The list of motifs provided herein is helpful in the search for candidates of biochemical reactions with a small-number effect for possible biological functions, as well as for designing a reaction system whose behavior can change drastically depending on molecule number, rather than concentration.

  18. The Dynamical and Chemical Evolution of Dwarf Spheroidal Galaxies with GEAR

    CERN Document Server

    Revaz, Yves

    2011-01-01

    We present a fully parallel chemo-dynamical Tree/SPH code, GEAR, which allows to perform high resolution simulations with detailed chemical diagnostics. Starting from the public version of Gadget-2, we included the complex treatment of the baryon physics: gas cooling, star formation law, chemical evolution and supernovae feedback. We qualified the performances of GEAR with the case of dSph galaxies. GEAR conserves the total energy budget of the systems to better than 5% over 14Gyr and proved excellent convergence of the results with numerical resolution. We showed that models of dSphs in a static Euclidean space, where the expansion of the universe is neglected are valid. In addition, we tackled some of the existing open questions in the field, like the stellar mass fraction of dSphs and its link with the predicted dark matter halo mass function, the effect of the supernova feedback, the spatial distribution of the stellar populations, and the origin of the diversity in star formation histories and chemical a...

  19. An infrared free-electron laser for the Chemical Dynamics Research Laboratory. Design report

    Energy Technology Data Exchange (ETDEWEB)

    Vaughan, D. [comp.

    1992-04-01

    This document describes a free-electron laser (FEL) proposed as part of the Chemical Dynamics Research Laboratory (CDRL), a user facility that also incorporates several advanced lasers of conventional design and two beamlines for the ALS. The FEL itself addresses the needs of the chemical sciences community for a high-brightness, tunable source covering a broad region of the infrared spectrum -- from 3 to 50 {mu}m. All of these sources, together with a variety of sophisticated experimental stations, will be housed in a new building to be located adjacent to the ALS. The radiation sources can be synchronized to permit powerful two-color, pump-probe experiments that will further our fundamental understanding of chemical dynamics at the molecular level, especially those aspects relevant to practical issues in combustion chemistry. The technical approach adopted in this design makes use of superconducting radiofrequency (SCRF) accelerating structures. The primary motivation for adopting this approach was to meet the user requirement for wavelength stability equal to one part in 10{sup 4}. Previous studies concluded that a wavelength stability of only one part in 10{sup 3} could be achieved with currently available room-temperature technology. In addition, the superconducting design operates in a continuous-wave (cw) mode and hence offers considerably higher average optical output power. It also allows for various pulse-gating configurations that will permit simultaneous multiuser operations. A summary of the comparative performance attainable with room-temperature and superconducting designs is given. The FEL described in this report provides a continuous train of 30-ps micropulses, with 100{mu}J of optical energy per micropulse, at a repetition rate of 6.1 MHz. The device can also deliver pulses at a cw repetition rate of 12.2 MHz, with a peak power of 50 {mu}J per micropulse. 70 ref.

  20. An infrared free-electron laser for the Chemical Dynamics Research Laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Vaughan, D. (comp.)

    1992-04-01

    This document describes a free-electron laser (FEL) proposed as part of the Chemical Dynamics Research Laboratory (CDRL), a user facility that also incorporates several advanced lasers of conventional design and two beamlines for the ALS. The FEL itself addresses the needs of the chemical sciences community for a high-brightness, tunable source covering a broad region of the infrared spectrum -- from 3 to 50 {mu}m. All of these sources, together with a variety of sophisticated experimental stations, will be housed in a new building to be located adjacent to the ALS. The radiation sources can be synchronized to permit powerful two-color, pump-probe experiments that will further our fundamental understanding of chemical dynamics at the molecular level, especially those aspects relevant to practical issues in combustion chemistry. The technical approach adopted in this design makes use of superconducting radiofrequency (SCRF) accelerating structures. The primary motivation for adopting this approach was to meet the user requirement for wavelength stability equal to one part in 10{sup 4}. Previous studies concluded that a wavelength stability of only one part in 10{sup 3} could be achieved with currently available room-temperature technology. In addition, the superconducting design operates in a continuous-wave (cw) mode and hence offers considerably higher average optical output power. It also allows for various pulse-gating configurations that will permit simultaneous multiuser operations. A summary of the comparative performance attainable with room-temperature and superconducting designs is given. The FEL described in this report provides a continuous train of 30-ps micropulses, with 100{mu}J of optical energy per micropulse, at a repetition rate of 6.1 MHz. The device can also deliver pulses at a cw repetition rate of 12.2 MHz, with a peak power of 50 {mu}J per micropulse. 70 ref.

  1. Role of the Slug Transcription Factor in Chemically-Induced Skin Cancer

    Directory of Open Access Journals (Sweden)

    Kristine von Maltzan

    2016-02-01

    Full Text Available The Slug transcription factor plays an important role in ultraviolet radiation (UVR-induced skin carcinogenesis, particularly in the epithelial-mesenchymal transition (EMT occurring during tumor progression. In the present studies, we investigated the role of Slug in two-stage chemical skin carcinogenesis. Slug and the related transcription factor Snail were expressed at high levels in skin tumors induced by 7,12-dimethylbenz[α]anthracene application followed by 12-O-tetradecanoylphorbol-13-acetate (TPA treatment. TPA-induced transient elevation of Slug and Snail proteins in normal mouse epidermis and studies in Slug transgenic mice indicated that Slug modulates TPA-induced epidermal hyperplasia and cutaneous inflammation. Although Snail family factors have been linked to inflammation via interactions with the cyclooxygenase-2 (COX-2 pathway, a pathway that also plays an important role in skin carcinogenesis, transient TPA induction of Slug and Snail appeared unrelated to COX-2 expression. In cultured human keratinocytes, TPA induced Snail mRNA expression while suppressing Slug expression, and this differential regulation was due specifically to activation of the TPA receptor. These studies show that Slug and Snail exhibit similar patterns of expression during both UVR and chemical skin carcinogenesis, that Slug and Snail can be differentially regulated under some conditions and that in vitro findings may not recapitulate in vivo results.

  2. Chemical leucoderma induced by ear-ring stoppers made of polyvinyl chloride

    Directory of Open Access Journals (Sweden)

    Reena Sharma

    2012-01-01

    Full Text Available We report a case of chemical leucoderma (CL in a 15-year-old girl, who developed patterned depigmentation at the back of both ear lobules after contact with plastic ear-ring stoppers made of polyvinyl chloride (PVC after continuous use for 6-7 months. Patch test with Indian standard series and cosmetic series was negative after 48 h, but she refused patch testing for extended duration as the possibility of induced depigmentation at the test site was unacceptable to her. To the best of our knowledge, this is the first report of plastic ear-ring stopper induced CL.

  3. Modulatory activity of Brazilian red propolis on chemically induced dermal carcinogenesis.

    Science.gov (United States)

    Pinheiro, Kariny Souza; Ribeiro, Danielle Rodrigues; Alves, Angela Valéria Farias; Pereira-Filho, Rose Nely; Oliveira, Clauberto Rodrigues de; Lima, Sônia Oliveira; Reis, Francisco Prado; Cardoso, Juliana Cordeiro; Albuquerque-Júnior, Ricardo Luiz Cavalcanti de

    2014-02-01

    To evaluate modulatory effects of a hydroalcoholic extract of Brazilian red propolis (HERP) on dermal carcinogenesis using a murine model. The HERP was used at concentrations of 10, 50 and 100 mg/kg (PROP10, PROP50 and PROP100, respectively) to modulate dermal carcinogenesis induced by the application of 9,10-dimetil-1,2-benzatraceno (DMBA) on the backs of animals. The chemical compounds identified in HERP included propyl gallate, catechin, epicatechin and formononetin. PROP100 treatment resulted in significantly decreased tumor multiplicity throughout the five weeks of tumor promotion (p0.05). The oral administration of hydroalcoholic extract of Brazilian red propolis at a dose of 100 mg/kg had a significant modulatory effect on the formation, differentiation and progression of chemically induced squamous cell carcinoma in a murine experimental model.

  4. Laser-Shot-Induced Chemical Reactions inside Nanotubes: a TDDFT investigation

    Science.gov (United States)

    Zhang, Hong; Miyamoto, Yoshiyuki; Rubio, Angel

    2011-03-01

    We present the application of the time-dependent density functional theory (TDDFT) on ultrafast laser pulse which induces dynamics in molecules encapsulated by a nanotube. A strong laser pulse polarized perpendicular to the tube axis induces a giant bond-stretch of an HCl molecule inside both C and BN nanotubes. Depending on the initial orientation of the HCl molecule, the subsequent laser-induced dynamics is different. We also observed a radial motion of the nanotube and vacancies appear on the tube wall when the HCl is perpendicular to tube axis. Furthermore, the disintegration of HCl molecules took place when their molecular axis tilted to tube axis. These simulations are important to analyze light-induced nanochemistry and manipulation of nanostructures encapsulated in organic and inorganic nanotubes. The computational scheme used in present work was a combination of the molecular dynamics and real-time propagation of electron wave functions under presence of strong optical field [2,3]. The energy conservation rule was checked to monitor the numerical stability.

  5. Metabolomic Assessment of Induced and Activated Chemical Defence in the Invasive Red Alga Gracilaria vermiculophylla

    Science.gov (United States)

    Nylund, Göran M.; Weinberger, Florian; Rempt, Martin; Pohnert, Georg

    2011-01-01

    In comparison with terrestrial plants the mechanistic knowledge of chemical defences is poor for marine macroalgae. This restricts our understanding in the chemically mediated interactions that take place between algae and other organisms. Technical advances such as metabolomics, however, enable new approaches towards the characterisation of the chemically mediated interactions of organisms with their environment. We address defence responses in the red alga Gracilaria vermiculophylla using mass spectrometry based metabolomics in combination with bioassays. Being invasive in the north Atlantic this alga is likely to possess chemical defences according to the prediction that well-defended exotics are most likely to become successful invaders in systems dominated by generalist grazers, such as marine macroalgal communities. We investigated the effect of intense herbivore feeding and simulated herbivory by mechanical wounding of the algae. Both processes led to similar changes in the metabolic profile. Feeding experiments with the generalist isopod grazer Idotea baltica showed that mechanical wounding caused a significant increase in grazer resistance. Structure elucidation of the metabolites of which some were up-regulated more than 100 times in the wounded tissue, revealed known and novel eicosanoids as major components. Among these were prostaglandins, hydroxylated fatty acids and arachidonic acid derived conjugated lactones. Bioassays with pure metabolites showed that these eicosanoids are part of the innate defence system of macroalgae, similarly to animal systems. In accordance with an induced defence mechanism application of extracts from wounded tissue caused a significant increase in grazer resistance and the up-regulation of other pathways than in the activated defence. Thus, this study suggests that G. vermiculophylla chemically deters herbivory by two lines of defence, a rapid wound-activated process followed by a slower inducible defence. By unravelling

  6. Metabolomic assessment of induced and activated chemical defence in the invasive red alga Gracilaria vermiculophylla.

    Directory of Open Access Journals (Sweden)

    Göran M Nylund

    Full Text Available In comparison with terrestrial plants the mechanistic knowledge of chemical defences is poor for marine macroalgae. This restricts our understanding in the chemically mediated interactions that take place between algae and other organisms. Technical advances such as metabolomics, however, enable new approaches towards the characterisation of the chemically mediated interactions of organisms with their environment. We address defence responses in the red alga Gracilaria vermiculophylla using mass spectrometry based metabolomics in combination with bioassays. Being invasive in the north Atlantic this alga is likely to possess chemical defences according to the prediction that well-defended exotics are most likely to become successful invaders in systems dominated by generalist grazers, such as marine macroalgal communities. We investigated the effect of intense herbivore feeding and simulated herbivory by mechanical wounding of the algae. Both processes led to similar changes in the metabolic profile. Feeding experiments with the generalist isopod grazer Idotea baltica showed that mechanical wounding caused a significant increase in grazer resistance. Structure elucidation of the metabolites of which some were up-regulated more than 100 times in the wounded tissue, revealed known and novel eicosanoids as major components. Among these were prostaglandins, hydroxylated fatty acids and arachidonic acid derived conjugated lactones. Bioassays with pure metabolites showed that these eicosanoids are part of the innate defence system of macroalgae, similarly to animal systems. In accordance with an induced defence mechanism application of extracts from wounded tissue caused a significant increase in grazer resistance and the up-regulation of other pathways than in the activated defence. Thus, this study suggests that G. vermiculophylla chemically deters herbivory by two lines of defence, a rapid wound-activated process followed by a slower inducible

  7. Fabrication of chemical templates via selective laser-induced desorption of hexadecanethiol self-assembled monolayers

    Science.gov (United States)

    Schröter, Anja; Mathieu, Mareike; Franzka, Steffen; Feydt, Jürgen; Irsen, Stephan; Hartmann, Nils

    2013-08-01

    A nonlinear photothermal laser patterning technique for rapid fabrication of chemical templates is demonstrated. Hexadecanethiol monolayers on Au-coated Si substrates are processed at λ = 532 nm, a 1/e2 spot diameter of d=2.8 μm and ambient conditions. Local laser irradiation at high laser powers and short irradiation times in the micro-/millisecond range induces desorption of thiol molecules. The laser-depleted areas are backfilled with mercaptohexadecanoic acid in order to build up chemical templates. Atomic force microscopy, scanning electron microscopy and scanning Auger electron spectroscopy are used for characterization of these templates. In agreement with a selective laser process, the results indicate the formation of flat chemical patterns with well-defined boundaries. Complementary condensation experiments demonstrate the functionality of the patterns as hydrophilic/hydrophobic templates. In particular, upon decreasing the temperature below the dew point, selective formation of water droplets on the backfilled areas is observed.

  8. Amoeba-Inspired Heuristic Search Dynamics for Exploring Chemical Reaction Paths.

    Science.gov (United States)

    Aono, Masashi; Wakabayashi, Masamitsu

    2015-09-01

    We propose a nature-inspired model for simulating chemical reactions in a computationally resource-saving manner. The model was developed by extending our previously proposed heuristic search algorithm, called "AmoebaSAT [Aono et al. 2013]," which was inspired by the spatiotemporal dynamics of a single-celled amoeboid organism that exhibits sophisticated computing capabilities in adapting to its environment efficiently [Zhu et al. 2013]. AmoebaSAT is used for solving an NP-complete combinatorial optimization problem [Garey and Johnson 1979], "the satisfiability problem," and finds a constraint-satisfying solution at a speed that is dramatically faster than one of the conventionally known fastest stochastic local search methods [Iwama and Tamaki 2004] for a class of randomly generated problem instances [ http://www.cs.ubc.ca/~hoos/5/benchm.html ]. In cases where the problem has more than one solution, AmoebaSAT exhibits dynamic transition behavior among a variety of the solutions. Inheriting these features of AmoebaSAT, we formulate "AmoebaChem," which explores a variety of metastable molecules in which several constraints determined by input atoms are satisfied and generates dynamic transition processes among the metastable molecules. AmoebaChem and its developed forms will be applied to the study of the origins of life, to discover reaction paths for which expected or unexpected organic compounds may be formed via unknown unstable intermediates and to estimate the likelihood of each of the discovered paths.

  9. Reaction mechanisms of aqueous monoethanolamine with carbon dioxide: a combined quantum chemical and molecular dynamics study.

    Science.gov (United States)

    Hwang, Gyeong S; Stowe, Haley M; Paek, Eunsu; Manogaran, Dhivya

    2015-01-14

    Aqueous monoethanolamine (MEA) has been extensively studied as a solvent for CO2 capture, yet the underlying reaction mechanisms are still not fully understood. Combined ab initio and classical molecular dynamics simulations were performed to revisit and identify key elementary reactions and intermediates in 25-30 wt% aqueous MEA with CO2, by explicitly taking into account the structural and dynamic effects. Using static quantum chemical calculations, we also analyzed in more detail the fundamental interactions involved in the MEA-CO2 reaction. We find that both the CO2 capture by MEA and solvent regeneration follow a zwitterion-mediated two-step mechanism; from the zwitterionic intermediate, the relative probability between deprotonation (carbamate formation) and CO2 removal (MEA regeneration) tends to be determined largely by the interaction between the zwitterion and neighboring H2O molecules. In addition, our calculations clearly demonstrate that proton transfer in the MEA-CO2-H2O solution primarily occurs through H-bonded water bridges, and thus the availability and arrangement of H2O molecules also directly impacts the protonation and/or deprotonation of MEA and its derivatives. This improved understanding should contribute to developing more comprehensive kinetic models for use in modeling and optimizing the CO2 capture process. Moreover, this work highlights the importance of a detailed atomic-level description of the solution structure and dynamics in order to better understand molecular mechanisms underlying the reaction of CO2 with aqueous amines.

  10. Amoeba-Inspired Heuristic Search Dynamics for Exploring Chemical Reaction Paths

    Science.gov (United States)

    Aono, Masashi; Wakabayashi, Masamitsu

    2015-09-01

    We propose a nature-inspired model for simulating chemical reactions in a computationally resource-saving manner. The model was developed by extending our previously proposed heuristic search algorithm, called "AmoebaSAT [Aono et al. 2013]," which was inspired by the spatiotemporal dynamics of a single-celled amoeboid organism that exhibits sophisticated computing capabilities in adapting to its environment efficiently [Zhu et al. 2013]. AmoebaSAT is used for solving an NP-complete combinatorial optimization problem [Garey and Johnson 1979], "the satisfiability problem," and finds a constraint-satisfying solution at a speed that is dramatically faster than one of the conventionally known fastest stochastic local search methods [Iwama and Tamaki 2004] for a class of randomly generated problem instances [http://www.cs.ubc.ca/~hoos/5/benchm.html]. In cases where the problem has more than one solution, AmoebaSAT exhibits dynamic transition behavior among a variety of the solutions. Inheriting these features of AmoebaSAT, we formulate "AmoebaChem," which explores a variety of metastable molecules in which several constraints determined by input atoms are satisfied and generates dynamic transition processes among the metastable molecules. AmoebaChem and its developed forms will be applied to the study of the origins of life, to discover reaction paths for which expected or unexpected organic compounds may be formed via unknown unstable intermediates and to estimate the likelihood of each of the discovered paths.

  11. Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase.

    Science.gov (United States)

    Luk, Louis Y P; Ruiz-Pernía, J Javier; Adesina, Aduragbemi S; Loveridge, E Joel; Tuñón, Iñaki; Moliner, Vincent; Allemann, Rudolf K

    2015-07-27

    Chemical ligation has been used to alter motions in specific regions of dihydrofolate reductase from E. coli and to investigate the effects of localized motional changes on enzyme catalysis. Two isotopic hybrids were prepared; one with the mobile N-terminal segment containing heavy isotopes ((2) H, (13) C, (15) N) and the remainder of the protein with natural isotopic abundance, and the other one with only the C-terminal segment isotopically labeled. Kinetic investigations indicated that isotopic substitution of the N-terminal segment affected only a physical step of catalysis, whereas the enzyme chemistry was affected by protein motions from the C-terminal segment. QM/MM studies support the idea that dynamic effects on catalysis mostly originate from the C-terminal segment. The use of isotope hybrids provides insights into the microscopic mechanism of dynamic coupling, which is difficult to obtain with other studies, and helps define the dynamic networks of intramolecular interactions central to enzyme catalysis.

  12. Plant flavonol isorhamnetin attenuates chemically induced inflammatory bowel disease via a PXR-dependent pathway

    OpenAIRE

    Dou, Wei; Zhang, Jingjing; Li, Hao; Kortagere, Sandhya; Sun, Katherine; Ding, Lili; Ren, Gaiyan; Wang, Zhengtao; Mani, Sridhar

    2014-01-01

    Isorhamnetin is an O-methylated flavonol present in fruit and vegetables. We recently reported the identification of isorhamnetin as an activator of the human pregnane X receptor (PXR), a known target for abrogating inflammation in inflammatory bowel disease (IBD). The current study investigated the role of isorhamnetin as a putative mouse PXR activator in ameliorating chemically induced IBD. Using two different models (Ulcerative colitis-like and Crohn’s disease-like) of experimental IBD in ...

  13. Optically induced dynamic nuclear spin polarisation in diamond

    Science.gov (United States)

    Scheuer, Jochen; Schwartz, Ilai; Chen, Qiong; Schulze-Sünninghausen, David; Carl, Patrick; Höfer, Peter; Retzker, Alexander; Sumiya, Hitoshi; Isoya, Junichi; Luy, Burkhard; Plenio, Martin B.; Naydenov, Boris; Jelezko, Fedor

    2016-01-01

    The sensitivity of magnetic resonance imaging (MRI) depends strongly on nuclear spin polarisation and, motivated by this observation, dynamical nuclear spin polarisation has recently been applied to enhance MRI protocols (Kurhanewicz et al 2011 Neoplasia 13 81). Nuclear spins associated with the 13C carbon isotope (nuclear spin I = 1/2) in diamond possess uniquely long spin lattice relaxation times (Reynhardt and High 2011 Prog. Nucl. Magn. Reson. Spectrosc. 38 37). If they are present in diamond nanocrystals, especially when strongly polarised, they form a promising contrast agent for MRI. Current schemes for achieving nuclear polarisation, however, require cryogenic temperatures. Here we demonstrate an efficient scheme that realises optically induced 13C nuclear spin hyperpolarisation in diamond at room temperature and low ambient magnetic field. Optical pumping of a nitrogen-vacancy centre creates a continuously renewable electron spin polarisation which can be transferred to surrounding 13C nuclear spins. Importantly for future applications we also realise polarisation protocols that are robust against an unknown misalignment between magnetic field and crystal axis.

  14. Synchronization dynamics of chemically coupled cells with activator–inhibitor pathways

    Energy Technology Data Exchange (ETDEWEB)

    Guemkam Ghomsi, P. [Complex Systems and Theoretical Biology Group, Laboratory of Research on Advanced Materials and Nonlinear Science (LaRAMaNS), Department of Physics, Faculty of Science, University of Buea, P.O. Box 63, Buea (Cameroon); Laboratoire de Mécanique, Department of Physics, Faculty of Science, University of Yaoundé I, P.O. Box 812, Yaoundé (Cameroon); Moukam Kakmeni, F.M., E-mail: moukam.kakmeni@ubuea.cm [Complex Systems and Theoretical Biology Group, Laboratory of Research on Advanced Materials and Nonlinear Science (LaRAMaNS), Department of Physics, Faculty of Science, University of Buea, P.O. Box 63, Buea (Cameroon); Kofane, T.C.; Tchawoua, C. [Laboratoire de Mécanique, Department of Physics, Faculty of Science, University of Yaoundé I, P.O. Box 812, Yaoundé (Cameroon)

    2014-08-01

    Systems of interacting cells containing an activator–inhibitor pathway, regulating naturally in their inner parts their end-product concentrations through a sequence of biochemical reactions with feedback-loops: an end-product inhibition of the first substrate, and an autocatalytic activation of the end-product through an allosteric enzyme-mediated reaction are investigated. The individual cells are considered to be identical and are described by nonlinear differential equations recently proposed following the concerted transition model. The chemical and electrical coupling types, realized by exchange of metabolites across concentration of the cells are used in order to analyze the onset of phase and complete synchronization in the biochemical system. It is found that depending on the coupling nature and the range of coupling strength, cells enter into different synchronization regimes going from low-quality to high-quality synchronization. The synchronization manifold's stability is analyzed. The results are supported by numerical simulations using indicators such as the conditional Lyapunov exponents and the rate of change of the Lyapunov function. The results indicate that the system cannot completely synchronize under the single action of the chemical coupling. The combined effect of both chemical and electrical couplings is found to be of capital importance in the onset of complete synchronization and high quality synchronization. - Highlights: • We investigate the dynamics and synchronization of cells with activator–inhibitor pathways. • A complete study of fixed points' stability and bifurcations of the system is done. • It is found that chemically coupled cells only display phase synchronization. • Electrical coupling is important for complete synchronization in the coupled cells. • High quality synchronization is observed in the coupled cells.

  15. Bioanalytical evidence that chemicals in tattoo ink can induce adaptive stress responses.

    Science.gov (United States)

    Neale, Peta A; Stalter, Daniel; Tang, Janet Y M; Escher, Beate I

    2015-10-15

    Tattooing is becoming increasingly popular, particularly amongst young people. However, tattoo inks contain a complex mixture of chemical impurities that may pose a long-term risk for human health. As a first step towards the risk assessment of these complex mixtures we propose to assess the toxicological hazard potential of tattoo ink chemicals with cell-based bioassays. Targeted modes of toxic action and cellular endpoints included cytotoxicity, genotoxicity and adaptive stress response pathways. The studied tattoo inks, which were extracted with hexane as a proxy for the bioavailable fraction, caused effects in all bioassays, with the red and yellow tattoo inks having the greatest response, particularly inducing genotoxicity and oxidative stress response endpoints. Chemical analysis revealed the presence of polycyclic aromatic hydrocarbons in the tested black tattoo ink at concentrations twice the recommended level. The detected polycyclic aromatic hydrocarbons only explained 0.06% of the oxidative stress response of the black tattoo ink, thus the majority of the effect was caused by unidentified components. The study indicates that currently available tattoo inks contain components that induce adaptive stress response pathways, but to evaluate the risk to human health further work is required to understand the toxicokinetics of tattoo ink chemicals in the body.

  16. Thermochemical model for shock-induced chemical reactions in porous thermite: The heat detonation model

    Energy Technology Data Exchange (ETDEWEB)

    Boslough, M.B.

    1989-01-01

    A thermochemical model has been developed that treats a shock-induced solid state chemical reaction as a special type of detonation, called a ''heat detonation'' to distinguish it from an ordinary explosive detonation and describe the final form that the chemical energy takes. According to shock temperature measurements, chemical energy can be released from porous reactive solids on a time scale shorter than shock-transit times in laboratory samples. By comparing the experimental shock temperature for porous thermite to that calculated by the model, the amount of thermite reacted when shocked to about 4 GPa was estimated to be between 60 and 70%. Calculated shock temperatures are extremely strong functions of the extent of reaction, but are relatively insensitive to the initial porosity and amount of volatile impurities. Thus, shock temperature measurements are the most useful for real-time studies of shock-induced exothermic chemical reactions in solids. 11 refs., 5 figs., 1 tab.

  17. Soft X-ray induced chemical modification of polysaccharides in vascular plant cell walls

    Energy Technology Data Exchange (ETDEWEB)

    Cody, George D. [Geophysical Laboratory, Carnegie Institution of Washington, 5251 Broad Branch Rd. NW, Washington, DC 20015 (United States)], E-mail: cody@gl.ciw.edu; Brandes, Jay [Skidaway Institute of Oceangraphy, Savannah, GA (United States); Jacobsen, Chris; Wirick, Susan [Department of Physics, State University of New York, Stony Brook, NY (United States)

    2009-03-15

    Scanning transmission X-ray microscopy and micro carbon X-ray Absorption Near Edge Spectroscopy (C-XANES) can provide quantitative information regarding the distribution of the biopolymers cellulose, hemicellulose, and lignin in vascular plant cell walls. In the case of angiosperms, flowering plants, C-XANES may also be able to distinguish variations in lignin monomer distributions throughout the cell wall. Polysaccharides are susceptible to soft X-ray irradiation induced chemical transformations that may complicate spectral analysis. The stability of a model polysaccharide, cellulose acetate, to variable doses of soft X-rays under conditions optimized for high quality C-XANES spectroscopy was investigated. The primary chemical effect of soft X-ray irradiation on cellulose acetate involves mass loss coincident with de-acetylation. A lesser amount of vinyl ketone formation also occurs. Reduction in irradiation dose via defocusing does enable high quality pristine spectra to be obtained. Radiation induced chemical modification studies of oak cell wall reveals that cellulose and hemicellulose are less labile to chemical modification than cellulose acetate. Strategies for obtaining pristine C-XANES spectra of polysaccharides are presented.

  18. Infrared Chemical Nano-Imaging: Accessing Structure, Coupling, and Dynamics on Molecular Length Scales

    Energy Technology Data Exchange (ETDEWEB)

    Muller, Eric A.; Pollard, Benjamin; Raschke, Markus Bernd

    2015-04-02

    This Perspective highlights recent advances in infrared vibrational chemical nano-imaging. In its implementations of scattering scanning near-field optical microscopy (s-SNOM) and photothermal-induced resonance (PTIR), IR nanospectroscopy provides few-nanometer spatial resolution for the investigation of polymer, biomaterial, and related soft-matter surfaces and nanostructures. Broad-band IR s-SNOM with coherent laser and synchrotron sources allows for chemical recognition with small-ensemble sensitivity and the potential for sensitivity reaching the single-molecule limit. Probing selected vibrational marker resonances, it gives access to nanoscale chemical imaging of composition, domain morphologies, order/disorder, molecular orientation, or crystallographic phases. Local intra- and intermolecular coupling can be measured through frequency shifts of a vibrational marker in heterogeneous environments and associated inhomogeneities in vibrational dephasing. In combination with ultrafast spectroscopy, the vibrational coherent evolution of homogeneous sub-ensembles coupled to their environment can be observed. Outstanding challenges are discussed in terms of extensions to coherent and multidimensional spectroscopies, implementation in liquid and in situ environments, general sample limitations, and engineering s-SNOM scanning probes to better control the nano-localized optical excitation and to increase sensitivity.

  19. The dynamic behavior of a liquid ethanol-water mixture: a perspective from quantum chemical topology.

    Science.gov (United States)

    Mejía, Sol M; Mills, Matthew J L; Shaik, Majeed S; Mondragon, Fanor; Popelier, Paul L A

    2011-05-07

    Quantum Chemical Topology (QCT) is used to reveal the dynamics of atom-atom interactions in a liquid. A molecular dynamics simulation was carried out on an ethanol-water liquid mixture at its azeotropic concentration (X(ethanol)=0.899), using high-rank multipolar electrostatics. A thousand (ethanol)(9)-water heterodecamers, respecting the water-ethanol ratio of the azeotropic mixture, were extracted from the simulation. Ab initio electron densities were computed at the B3LYP/6-31+G(d) level for these molecular clusters. A video shows the dynamical behavior of a pattern of bond critical points and atomic interaction lines, fluctuating over 1 ns. A bond critical point distribution revealed the fluctuating behavior of water and ethanol molecules in terms of O-H···O, C-H···O and H···H interactions. Interestingly, the water molecule formed one to six C-H···O and one to four O-H···O interactions as a proton acceptor. We found that the more localized a dynamical bond critical point distribution, the higher the average electron density at its bond critical points. The formation of multiple C-H···O interactions affected the shape of the oxygen basin of the water molecule, which is shown in three dimensions. The hydrogen atoms of water strongly preferred to form H···H interactions with ethanol's alkyl hydrogen atoms over its hydroxyl hydrogen. This journal is © the Owner Societies 2011

  20. Onset of chaotic dynamics in a ball mill: Attractors merging and crisis induced intermittency

    Science.gov (United States)

    Manai, G.; Delogu, F.; Rustici, M.

    2002-09-01

    In mechanical treatment carried out by ball milling, powder particles are subjected to repeated high-energy mechanical loads which induce heavy plastic deformations together with fracturing and cold-welding events. Owing to the continuous defect accumulation and interface renewal, both structural and chemical transformations occur. The nature and the rate of such transformations have been shown to depend on variables, such as impact velocity and collision frequency that depend, in turn, on the whole dynamics of the system. The characterization of the ball dynamics under different impact conditions is then to be considered a necessary step in order to gain a satisfactory control of the experimental set up. In this paper we investigate the motion of a ball in a milling device. Since the ball motion is governed by impulsive forces acting during each collision, no analytical expression for the complete ball trajectory can be obtained. In addition, mechanical systems exhibiting impacts are strongly nonlinear due to sudden changes of velocities at the instant of impact. Many different types of periodic and chaotic impact motions exist indeed even for simple systems with external periodic excitation forces. We present results of the analysis on the ball trajectory, obtained from a suitable numerical model, under growing degree of impact elasticity. A route to high dimensional chaos is obtained. Crisis and attractors merging are also found.

  1. ThermoData engine (TDE): software implementation of the dynamic data evaluation concept. 4. Chemical reactions.

    Science.gov (United States)

    Diky, Vladimir; Chirico, Robert D; Kazakov, Andrei F; Muzny, Chris D; Frenkel, Michael

    2009-12-01

    ThermoData Engine (TDE) is the first full-scale software implementation of the dynamic data evaluation concept, as reported recently in this journal. This paper describes the first application of this concept to the evaluation of thermodynamic properties for chemical reactions. Reaction properties evaluated are the enthalpies, entropies, Gibbs energies, and thermodynamic equilibrium constants. Details of key considerations in the critical evaluation of enthalpies of formation and of standard entropies for organic compounds are discussed in relation to their application in the calculation of reaction properties. Extensions to the class structure of the program are described that allow close linkage between the derived reaction properties and the underlying pure-component properties. Derivation of pure-component enthalpies of formation and of standard entropies through the use of directly measured reaction properties (enthalpies of reaction and equilibrium constants) is described. Directions for future enhancements are outlined.

  2. Dynamics of wicking in silicon nanopillars fabricated with interference lithography and metal-assisted chemical etching.

    Science.gov (United States)

    Mai, Trong Thi; Lai, Chang Quan; Zheng, H; Balasubramanian, Karthik; Leong, K C; Lee, P S; Lee, Chengkuo; Choi, W K

    2012-08-07

    The capillary rise of liquid on a surface, or "wicking", has potential applications in biological and industrial processes such as drug delivery, oil recovery, and integrated circuit chip cooling. This paper presents a theoretical study on the dynamics of wicking on silicon nanopillars based on a balance between the driving capillary forces and viscous dissipation forces. Our model predicts that the invasion of the liquid front follows a diffusion process and strongly depends on the structural geometry. The model is validated against experimental observations of wicking in silicon nanopillars with different heights synthesized by interference lithography and metal-assisted chemical etching techniques. Excellent agreement between theoretical and experimental results, from both our samples and data published in the literature, was achieved.

  3. In vivo studies on chemically induced aneuploidy in mouse somatic and germinal cells.

    Science.gov (United States)

    Leopardi, P; Zijno, A; Bassani, B; Pacchierotti, F

    1993-05-01

    Within the context of a coordinated program to study aneuploidy induction sponsored by the European Community, nine chemicals were tested in mouse bone marrow and spermatocytes after intraperitoneal injection. In somatic cells, cell progression delay, hyperploidy, polyploidy induction and induction of micronucleated polychromatic erythrocyte (MnPCE) were studied. In germ cells hyperploidy induction was evaluated. The chemicals selected were: colchicine (COL), econazole (EZ), hydroquinone (HQ), thiabendazole (TB), diazepam (DZ), chloral hydrate (CH), cadmium chloride (CD), pyrimethamine (PY) and thimerosal (TM). Using literature data on c-mitotic effects in bone marrow as a reference, the same doses were tested in somatic and germ cells in order to compare the effects induced. Bone marrow cells were sampled 18 or 24 h after treatment. Germ cells were sampled 6, 8 or 18 h after treatment. Effects of COL and HQ in bone marrow have been reported elsewhere. Somatic effects were induced by CH (hyperploidy and cell cycle lengthening), TB (MnPCEs and cell cycle lengthening) and by PY (MnPCEs). EZ, DZ, CD and TM did not induce any kind of somatic effects. An increase in the incidence of hyperploid spermatocytes was induced by COL, at three dose levels, and by one dose of HQ and TB. All the other chemicals did not induce germinal aneuploidy at any dose or time tested. The hyperploidy control frequency ranged between 0.4 and 1.0% in somatic cells and from 0.3 to 0.9% in germ cells. In both somatic and germ cells, the maximum yield of induced hyperploidy did not exceed 3.5%. The time period of target cell sensitivity is probably restricted and this, associated with the heterogeneity and the asynchrony of cellular maturation processes, may account for our data. Under these circumstances, the negative data should be interpreted with some caution, particularly in germ cells, where additional indicators of chemical-cell interaction and cell cycle effects were not provided by

  4. Chemical and dynamical impacts of stratospheric sudden warmings on Arctic ozone variability

    Science.gov (United States)

    Strahan, S. E.; Douglass, A. R.; Steenrod, S. D.

    2016-10-01

    We use the Global Modeling Initiative (GMI) chemistry and transport model with Modern-Era Retrospective Analysis for Research and Applications (MERRA) meteorological fields to quantify heterogeneous chemical ozone loss in Arctic winters 2005-2015. Comparisons to Aura Microwave Limb Sounder N2O and O3 observations show the GMI simulation credibly represents the transport processes and net heterogeneous chemical loss necessary to simulate Arctic ozone. We find that the maximum seasonal ozone depletion varies linearly with the number of cold days and with wave driving (eddy heat flux) calculated from MERRA fields. We use this relationship and MERRA temperatures to estimate seasonal ozone loss from 1993 to 2004 when inorganic chlorine levels were in the same range as during the Aura period. Using these loss estimates and the observed March mean 63-90°N column O3, we quantify the sensitivity of the ozone dynamical resupply to wave driving, separating it from the sensitivity of ozone depletion to wave driving. The results show that about 2/3 of the deviation of the observed March Arctic O3 from an assumed climatological mean is due to variations in O3 resupply and 1/3 is due to depletion. Winters with a stratospheric sudden warming (SSW) before mid-February have about 1/3 the depletion of winters without one and export less depletion to the midlatitudes. However, a larger effect on the spring midlatitude ozone comes from dynamical differences between warm and cold Arctic winters, which can mask or add to the impact of exported depletion.

  5. On the convergence of complex Langevin dynamics: the three-dimensional XY model at finite chemical potential

    CERN Document Server

    Aarts, Gert

    2010-01-01

    The three-dimensional XY model is studied at finite chemical potential using complex Langevin dynamics. The validity of the approach is probed at small chemical potential using imaginary chemical potential and continuity arguments, and at larger chemical potential by comparison with the world line method. While complex Langevin works for larger beta, we find that it fails for smaller beta, in the region of the phase diagram corresponding to the disordered phase. Diagnostic tests are developed to identify symptoms correlated with incorrect convergence. We argue that the erroneous behaviour at smaller beta is not due to the sign problem, but rather resembles dynamics observed in complex Langevin simulations of simple models with complex noise.

  6. Chemical Control for Host-Parasitoid Model within the Parasitism Season and Its Complex Dynamics

    Directory of Open Access Journals (Sweden)

    Tao Wang

    2016-01-01

    Full Text Available In the present paper, we develop a host-parasitoid model with Holling type II functional response function and chemical control, which can be applied at any time of each parasitism season or pest generation, and focus on addressing the importance of the timing of application pesticide during the parasitism season or pest generation in successful pest control. Firstly, the existence and stability of both the host and parasitoid populations extinction equilibrium and parasitoid-free equilibrium have been investigated. Secondly, the effects of key parameters on the threshold conditions have been discussed in more detail, which shows the importance of pesticide application times on the pest control. Thirdly, the complex dynamics including multiple attractors coexistence, chaotic behavior, and initial sensitivity have been studied by using numerical bifurcation analyses. Finally, the uncertainty and sensitivity of all the parameters on the solutions of both the host and parasitoid populations are investigated, which can help us to determine the key parameters in designing the pest control strategy. The present research can help us to further understand the importance of timings of pesticide application in the pest control and to improve the classical chemical control and to make management decisions.

  7. Computational modelling of the complex dynamics of chemically blown polyurethane foam

    Science.gov (United States)

    Ireka, I. E.; Niedziela, D.; Schäfer, K.; Tröltzsch, J.; Steiner, K.; Helbig, F.; Chinyoka, T.; Kroll, L.

    2015-11-01

    This study presents computational analysis of the complex dynamics observed in chemically blown polyurethane foams during reaction injection molding process. The mathematical formulation introduces an experimentally motivated non-divergence free setup for the continuity equations which reflects the self expanding behaviour observed in the physical system. The foam growth phenomena which is normally initiated by adequate pre-mixing of necessary reactant polymers, leading to an exothermic polymerization reaction, bubble nucleation, and gas formation, is captured numerically. We assume the dependence of material viscosity on the degree of cure/polymerization, gas volume fraction, and temperature as well as non-dependence of mixture density on pressure. The set of unsteady nonlinear coupled partial differential equations describing the dynamics of the system are solved numerically for state variables using finite volume techniques such that the front of the flow is tracked with high resolution interface capturing schemes. Graphical representation of the foam volume fraction, evolution of foam heights, and temperature distributions is presented. Results from our simulations are validated with experimental data. These results show good quantitative agreement with observations from experiments.

  8. Water Organization and Dynamics on Mineral Surfaces Interrogated by Graph Theoretical Analyses of Intermolecular Chemical Networks

    Directory of Open Access Journals (Sweden)

    Abdullah Ozkanlar

    2014-03-01

    Full Text Available Intermolecular chemical networks defined by the hydrogen bonds formed at the α-quartz|water interface have been data-mined using graph theoretical methods so as to identify and quantify structural patterns and dynamic behavior. Using molecular-dynamics simulations data, the hydrogen bond (H-bond distributions for the water-water and water-silanol H-bond networks have been determined followed by the calculation of the persistence of the H-bond, the dipole-angle oscillations that water makes with the surface silanol groups over time, and the contiguous H-bonded chains formed at the interface. Changes in these properties have been monitored as a function of surface coverage. Using the H-bond distribution between water and the surface silanol groups, the actual number of waters adsorbed to the surface is found to be 0.6 H2O/10 Å2, irrespective of the total concentration of waters within the system. The unbroken H-bond network of interfacial waters extends farther than in the bulk liquid; however, it is more fluxional at low surface coverages (i.e., the H-bond persistence in a monolayer of water is shorter than in the bulk Concentrations of H2O at previously determined water adsorption sites have also been quantified. This work demonstrates the complementary information that can be obtained through graph theoretical analysis of the intermolecular H-bond networks relative to standard analyses of molecular simulation data.

  9. Transport model of chemical secretion process for tracking exocytotic event dynamics using electroanalysis.

    Science.gov (United States)

    Fan, Tai-Hsi; Fedorov, Andrei G

    2004-08-01

    A unified model is developed to analyze the key features of the chemical secretion process observed in experimental studies of various vesicles with application to electroanalytical measurements of vesicular exocytosis. The intimately coupled dynamics and kinetics are simultaneously resolved based on continuum fluid flow, mass transport, and linear elasticity theories combined with biomembrane mechanics. We report three case studies of exocytosis, including a large electroporated granule of the mast cell, a small and clear synaptic vesicle, and a medium size vesicle in the chromaffin cell. The simulation results for each case are compared with electroanalytical measurements from the literature. The results provide a theoretical ground for defining the rate-controlling step(s) of an exocytotic sequence, allowing interpretation of electroanalysis data. Thus, it provides a tool for theoretical verification of competing hypotheses of what controls/limits messenger release during exocytosis. Simulations show that the pore size, the pore opening velocity, and the swelling dynamics of the granule matrix play the key roles in controlling the messenger release kinetics.

  10. Classical molecular dynamics and ab initio simulations of chemical-mechanical polishing of amorphous silica

    Science.gov (United States)

    Chagarov, Evgueni Anatolievich

    Chemical-mechanical polishing (CMP) is a widely accepted process in the semiconductor industry. Despite intense theoretical and experimental research on CMP, there is a serious lack of fundamental understanding of the physical-chemical processes of polishing. The present work is intended to investigate these fundamental processes on an atomistic level. To model CMP on the atomic scale, a model of the amorphous silica is prepared by applying Design of Experiments (DOE) techniques to systematically investigate molecular dynamics preparation. These simulations yield high-quality models of amorphous silica, which are in excellent agreement with experimental results and are defect-free. Molecular dynamics simulations are performed to investigate the mechanical deformation during CMP of silica for different geometries and relative velocities. The simulations clarify asperity shape evolution during the process of shear and reveal temperature distributions as a function of time. It is found that the ratio of radii of a particle and asperity strongly affects the amount of the material removed whereas the relative velocity has a weaker affect on it. During shear, a significant local temperature increase occurs. This temperature increase lasts for a short time (picoseconds), but it can have a major impact on the amount of material removed. It is found that there could be significant deposition of the material from the particle to the slab, which can fill surface trenches and thereby make the surface smoother. An analytic model is developed for describing the amount of material removed as a function of asperity and particle radii and relative velocity. Density-functional calculations of different surfaces of two silica polymorphs, alpha-quartz and beta-cristobalite, are performed. The surface energies are calculated as a function of oxygen partial pressure for several different surface reconstructions and terminations. The case of hydrogen passivation is investigated to

  11. Dynamic three-dimensional micropatterned cell co-cultures within photocurable and chemically degradable hydrogels.

    Science.gov (United States)

    Sugiura, Shinji; Cha, Jae Min; Yanagawa, Fumiki; Zorlutuna, Pinar; Bae, Hojae; Khademhosseini, Ali

    2016-08-01

    In this paper we report on the development of dynamically controlled three-dimensional (3D) micropatterned cellular co-cultures within photocurable and chemically degradable hydrogels. Specifically, we generated dynamic co-cultures of micropatterned murine embryonic stem (mES) cells with human hepatocellular carcinoma (HepG2) cells within 3D hydrogels. HepG2 cells were used due to their ability to direct the differentiation of mES cells through secreted paracrine factors. To generate dynamic co-cultures, mES cells were first encapsulated within micropatterned photocurable poly(ethylene glycol) (PEG) hydrogels. These micropatterned cell-laden PEG hydrogels were subsequently surrounded by calcium alginate (Ca-Alg) hydrogels containing HepG2 cells. After 4 days, the co-culture step was halted by exposing the system to sodium citrate solution, which removed the alginate gels and the encapsulated HepG2 cells. The encapsulated mES cells were then maintained in the resulting cultures for 16 days and cardiac differentiation was analysed. We observed that the mES cells that were exposed to HepG2 cells in the co-cultures generated cells with higher expression of cardiac genes and proteins, as well as increased spontaneous beating. Due to its ability to control the 3D microenvironment of cells in a spatially and temporally regulated manner, the method presented in this study is useful for a range of cell-culture applications related to tissue engineering and regenerative medicine. Copyright © 2013 John Wiley & Sons, Ltd.

  12. Anticonvulsant activity of B2, an adenosine analog, on chemical convulsant-induced seizures.

    Directory of Open Access Journals (Sweden)

    Min Li

    Full Text Available Epilepsy is a chronic neurological disorder characterized by recurrent seizures. However, approximately one-third of epilepsy patients still suffer from uncontrolled seizures. Effective treatments for epilepsy are yet to be developed. N (6-(3-methoxyl-4-hydroxybenzyl adenine riboside (B2 is a N(6-substitued adenosine analog. Here we describe an investigation of the effects and mechanisms of B2 on chemical convulsant-induced seizures. Seizures were induced in mice by administration of 4-aminopyridine (4-AP, pentylenetetrazol (PTZ, picrotoxin, kainite acid (KA, or strychnine. B2 has a dose-related anticonvulsant effect in these chemical-induced seizure models. The protective effects of B2 include increased latency of seizure onset, decreased seizure occurrence, shorter seizure duration and reduced mortality rate. Radioligand binding and cAMP accumulation assays indicated that B2 might be a functional ligand for both adenosine A1 and A2A receptors. Furthermore, DPCPX, a selective A1 receptor antagonist, but not SCH58261, a selective A2A receptor antagonist, blocked the anticonvulsant effect of B2 on PTZ-induced seizure. c-Fos is a cellular marker for neuronal activity. Immunohistochemical and western blot analyses indicated that B2 significantly reversed PTZ-induced c-Fos expression in the hippocampus. Together, these results indicate that B2 has significant anticonvulsant effects. The anticonvulsant effects of B2 may be attributed to adenosine A1 receptor activation and reduced neuronal excitability in the hippocampus. These observations also support that the use of adenosine receptor agonist may be a promising approach for the treatment of epilepsy.

  13. Histopathological image analysis of chemical-induced hepatocellular hypertrophy in mice.

    Science.gov (United States)

    Asaoka, Yoshiji; Togashi, Yuko; Mutsuga, Mayu; Imura, Naoko; Miyoshi, Tomoya; Miyamoto, Yohei

    2016-04-01

    Chemical-induced hepatocellular hypertrophy is frequently observed in rodents, and is mostly caused by the induction of phase I and phase II drug metabolic enzymes and peroxisomal lipid metabolic enzymes. Liver weight is a sensitive and commonly used marker for detecting hepatocellular hypertrophy, but is also increased by a number of other factors. Histopathological observations subjectively detect changes such as hepatocellular hypertrophy based on the size of a hepatocyte. Therefore, quantitative microscopic observations are required to evaluate histopathological alterations objectively. In the present study, we developed a novel quantitative method for an image analysis of hepatocellular hypertrophy using liver sections stained with hematoxylin and eosin, and demonstrated its usefulness for evaluating hepatocellular hypertrophy induced by phenobarbital (a phase I and phase II enzyme inducer) and clofibrate (a peroxisomal enzyme inducer) in mice. The algorithm of this imaging analysis was designed to recognize an individual hepatocyte through a combination of pixel-based and object-based analyses. Hepatocellular nuclei and the surrounding non-hepatocellular cells were recognized by the pixel-based analysis, while the areas of the recognized hepatocellular nuclei were then expanded until they ran against their expanding neighboring hepatocytes and surrounding non-hepatocellular cells by the object-based analysis. The expanded area of each hepatocellular nucleus was regarded as the size of an individual hepatocyte. The results of this imaging analysis showed that changes in the sizes of hepatocytes corresponded with histopathological observations in phenobarbital and clofibrate-treated mice, and revealed a correlation between hepatocyte size and liver weight. In conclusion, our novel image analysis method is very useful for quantitative evaluations of chemical-induced hepatocellular hypertrophy. Copyright © 2015 Elsevier GmbH. All rights reserved.

  14. From the exposome to mechanistic understanding of chemical-induced adverse effects.

    Science.gov (United States)

    Escher, Beate I; Hackermüller, Jörg; Polte, Tobias; Scholz, Stefan; Aigner, Achim; Altenburger, Rolf; Böhme, Alexander; Bopp, Stephanie K; Brack, Werner; Busch, Wibke; Chadeau-Hyam, Marc; Covaci, Adrian; Eisenträger, Adolf; Galligan, James J; Garcia-Reyero, Natalia; Hartung, Thomas; Hein, Michaela; Herberth, Gunda; Jahnke, Annika; Kleinjans, Jos; Klüver, Nils; Krauss, Martin; Lamoree, Marja; Lehmann, Irina; Luckenbach, Till; Miller, Gary W; Müller, Andrea; Phillips, David H; Reemtsma, Thorsten; Rolle-Kampczyk, Ulrike; Schüürmann, Gerrit; Schwikowski, Benno; Tan, Yu-Mei; Trump, Saskia; Walter-Rohde, Susanne; Wambaugh, John F

    2017-02-01

    The exposome encompasses an individual's exposure to exogenous chemicals, as well as endogenous chemicals that are produced or altered in response to external stressors. While the exposome concept has been established for human health, its principles can be extended to include broader ecological issues. The assessment of exposure is tightly interlinked with hazard assessment. Here, we explore if mechanistic understanding of the causal links between exposure and adverse effects on human health and the environment can be improved by integrating the exposome approach with the adverse outcome pathway (AOP) concept that structures and organizes the sequence of biological events from an initial molecular interaction of a chemical with a biological target to an adverse outcome. Complementing exposome research with the AOP concept may facilitate a mechanistic understanding of stress-induced adverse effects, examine the relative contributions from various components of the exposome, determine the primary risk drivers in complex mixtures, and promote an integrative assessment of chemical risks for both human and environmental health.

  15. First-Principles Simulations of Chemical Reactions in an HCl Molecule Embedded inside a C or BN Nanotube Induced by Ultrafast Laser Pulses

    Science.gov (United States)

    Miyamoto, Yoshiyuki; Zhang, Hong; Rubio, Angel

    2010-12-01

    We show by first-principles simulations that ultrafast laser pulses induce different chemical reactions in a molecule trapped inside a nanotube. A strong laser pulse polarized perpendicular to the tube axis induces a giant bond stretch of an encapsulated HCl molecule in semiconducting carbon nanotube or in a BN nanotube. Depending on the initial orientation of the HCl molecule, the subsequent laser-induced dynamics is different: either complete disintegration or rebonding of the HCl molecule. Radial motion of the nanotube is always observed and a vacancy appears on the tube wall when the HCl is perpendicular to the tube axis. Those results are important to analyze confined nanochemistry and to manipulate molecules and nanostructures encapsulated in organic and inorganic nanotubes.

  16. Chemical ordering in magnetic FePd/Pd (001) epitaxial thin films induced by annealing

    Science.gov (United States)

    Halley, D.; Gilles, B.; Bayle-Guillemaud, P.; Arenal, R.; Marty, A.; Patrat, G.; Samson, Y.

    2004-11-01

    Chemically disordered FePd epitaxial layers are grown at room temperature by molecular beam epitaxy on a Pd(001) buffer layer and then annealed in order to induce the chemically ordered L 10 (AuCu I) structure. Contrary to what is observed in the case of ordering during growth above room temperature, the ordered structure appears here with the three possible variants of the L 10 phase. The ratio of the three different variant volumes is set by the residual epitaxial strain in the layer before annealing. It thus explains that for long annealing times, the long-range order parameter associated with the L 10 variant with c along the (100) growth direction saturates at a value close to 0.65, and never reaches unity. Magnetic consequences of the ordering are studied.

  17. Laser Induced Breakdown Spectroscopy applications to meteorites: Chemical analysis and composition profiles

    Science.gov (United States)

    Dell'Aglio, M.; De Giacomo, A.; Gaudiuso, R.; Pascale, O. De; Senesi, G. S.; Longo, S.

    2010-12-01

    A fast procedure for chemical analysis of different meteorites is presented, based on LIBS (Laser Induced Breakdown Spectroscopy). The technique is applied to several test cases (Dhofar 019, Dhofar 461, Sahara 98222, Toluca, Sikhote Alin and Campo del Cielo) and can be useful for rapid meteorite identification providing geologists with specific chemical information for meteorite classification. Concentration profiles of Fe, Ni and Co are simultaneously detected across the Widmanstätten structure of the iron meteorite Toluca with a view to determining cooling rates. The LIBS analysis of meteorites is also used as a laboratory test for analogous studies on the respective parent bodies (Mars, asteroids) in space exploration missions where one clear advantage of the proposed technique is that no direct contact with the sample is required.

  18. Self-grooming induced by sexual chemical signals in male root voles (Microtus oeconomus Pallas).

    Science.gov (United States)

    Yu, Honghao; Yue, Pengpeng; Sun, Ping; Zhao, Xinquan

    2010-03-01

    Sniffing is one-way animals collect chemical signals, and many males self-groom when they encounter the odor of opposite-sex conspecifics. We tested the hypothesis that sexual chemical signals from females can induce self-grooming behavior in male root voles (Microtus oeconomus Pallas). Specifically, we investigated the sniffing pattern of male root voles in response to odors from the head, trunk, and tail areas of lactating and non-lactating females. The self-grooming behavior of males in response to female individual odorant stimuli was documented, and the relationship between self-grooming and sniffing of odors from the head, trunk, and tails areas were analyzed. Sniffing pattern results showed that males are most interested in odors from the head area, and more interested in odors from the tail as compared to the trunk area. Males displayed different sniffing and self-grooming behaviors when they were exposed to odors from lactating females as compared to non-lactating females. Males also spent more time sniffing and engaged in more sniffing behaviors in response to odors from the lactating females' tail area as compared to the same odors from non-lactating females. Similarly, males spent more time self-grooming and engaged in more self-grooming behaviors in the presence of individual odors from lactating females as compared to individual odors from non-lactating females. Partial correlation analyses revealed that the frequency of self-grooming was significantly correlated with the frequency of tail area sniffs. Results from this experiment suggest that sexual attractiveness of lactating females is stronger than that of non-lactating females. Furthermore, the partial correlation analysis demonstrated that self-grooming in males is induced by odors from the tail area of females. Collectively, these results support the hypothesis that sexual chemical signals from females can induce self-grooming behavior in male root voles. Self-grooming may also reflect the

  19. Noise-induced Input Dependence in a Convective Unstable Dynamical System

    CERN Document Server

    Fujimoto, K; Fujimoto, Koichi; Kaneko, Kunihiko

    1998-01-01

    Unidirectionally coupled dynamical system is studied by focusing on the input (or boundary) dependence. Due to convective instability, noise at an up-flow is spatially amplified to form an oscillation. The response, given by the down-flow dynamics, shows both analogue and digital changes, where the former is represented by oscillation frequency and the latter by different type of dynamics. The underlying universal mechanism for these changes is clarified by the spatial change of the co-moving Lyapunov exponent, with which the condition for the input dependence is formulated. The mechanism has a remarkable dependence on the noise strength, and works only within its medium range. Relevance of our mechanism to intra-cellular signal dynamics is discussed, by making our dynamics correspond to the auto-catalytic biochemical reaction for the chemical concentration, and the input to the external signal, and the noise to the concentration fluctuation of chemicals.

  20. Acceleration-induced nonlocality: kinetic memory versus dynamic memory

    OpenAIRE

    Chicone, C.; Mashhoon, B.

    2001-01-01

    The characteristics of the memory of accelerated motion in Minkowski spacetime are discussed within the framework of the nonlocal theory of accelerated observers. Two types of memory are distinguished: kinetic and dynamic. We show that only kinetic memory is acceptable, since dynamic memory leads to divergences for nonuniform accelerated motion.

  1. Hot spot formation and chemical reaction initiation in shocked HMX crystals with nanovoids: a large-scale reactive molecular dynamics study.

    Science.gov (United States)

    Zhou, Tingting; Lou, Jianfeng; Zhang, Yangeng; Song, Huajie; Huang, Fenglei

    2016-07-14

    We report million-atom reactive molecular dynamic simulations of shock initiation of β-cyclotetramethylene tetranitramine (β-HMX) single crystals containing nanometer-scale spherical voids. Shock induced void collapse and subsequent hot spot formation as well as chemical reaction initiation are observed which depend on the void size and impact strength. For an impact velocity of 1 km s(-1) and a void radius of 4 nm, the void collapse process includes three stages; the dominant mechanism is the convergence of upstream molecules toward the centerline and the downstream surface of the void forming flowing molecules. Hot spot formation also undergoes three stages, and the principal mechanism is kinetic energy transforming to thermal energy due to the collision of flowing molecules on the downstream surface. The high temperature of the hot spot initiates a local chemical reaction, and the breakage of the N-NO2 bond plays the key role in the initial reaction mechanism. The impact strength and void size have noticeable effects on the shock dynamical process, resulting in a variation of the predominant mechanisms leading to void collapse and hot spot formation. Larger voids or stronger shocks result in more intense hot spots and, thus, more violent chemical reactions, promoting more reaction channels and generating more reaction products in a shorter duration. The reaction products are mainly concentrated in the developed hot spot, indicating that the chemical reactivity of the hmx crystal is greatly enhanced by void collapse. The detailed information derived from this study can aid a thorough understanding of the role of void collapse in hot spot formation and the chemical reaction initiation of explosives.

  2. LASER-INDUCED DECOMPOSITION OF METAL CARBONYLS FOR CHEMICAL VAPOR DEPOSITION OF MICROSTRUCTURES

    OpenAIRE

    1989-01-01

    Tungsten and nickel carbonyls were used to produce metal microstructures by laser-induced chemical vapor deposition (CVD) on various substrates. The deposition rate of microstructures produced by thermodecomposition of W(CO)6 on Si substrates heated with a cw Ar+ laser beam was relatively low (10 to 30 nm/s) even at high temperatures (above 900°C). Ni microstructures were deposited on quartz substrates irradiated with a CO2 laser beam. Relatively high laser powers were needed to heat the Ni s...

  3. Improving analytical methods for protein-protein interaction through implementation of chemically inducible dimerization

    DEFF Research Database (Denmark)

    Andersen, Tonni Grube; Nintemann, Sebastian; Marek, Magdalena;

    2016-01-01

    into the widely used split ubiquitin-, bimolecular fluorescence complementation (BiFC)- and Forster resonance energy transfer (FRET)-based methods and investigated different protein-protein interactions in yeast and plants. We demonstrate the functionality of this concept by the analysis of weakly interacting...... proteins from specialized metabolism in the model plant Arabidopsis thaliana. Our results illustrate that chemically induced dimerization can function as a built-in control for split-based systems that is easily implemented and allows for direct evaluation of functionality....

  4. Improving analytical methods for protein-protein interaction through implementation of chemically inducible dimerization

    DEFF Research Database (Denmark)

    Andersen, T. G.; Nintemann, S. J.; Marek, M.;

    2016-01-01

    When investigating interactions between two proteins with complementary reporter tags in yeast two-hybrid or split GFP assays, it remains troublesome to discriminate true-from false-negative results and challenging to compare the level of interaction across experiments. This leads to decreased...... sensitivity and renders analysis of weak or transient interactions difficult to perform. In this work, we describe the development of reporters that can be chemically induced to dimerize independently of the investigated interactions and thus alleviate these issues. We incorporated our reporters...

  5. Analyzing temperature-induced transitions in disordered proteins by NMR spectroscopy and secondary chemical shift analyses

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Poulsen, Flemming Martin; Kragelund, Birthe Brandt

    2012-01-01

    Intrinsically disordered proteins are abundant in nature and perform many important physiological functions. Multidimensional NMR spectroscopy has been crucial for the understanding of the conformational properties of disordered proteins and is increasingly used to probe their conformational...... ensembles. Compared to folded proteins, disordered proteins are more malleable and more easily perturbed by environmental factors. Accordingly, the experimental conditions and especially the temperature modify the structural and functional properties of disordered proteins. This chapter discusses practical...... aspects of NMR studies of temperature-induced structural changes in disordered proteins using chemical shifts....

  6. Effect of etchant concentration on microwave induced chemical etching (MICE) of CR-39 detector

    Energy Technology Data Exchange (ETDEWEB)

    Sahoo, G.S. [Health Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Tripathy, S.P., E-mail: sam.tripathy@gmail.com [Health Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Sharma, S.D. [Radiological Physics and Advisor Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Homi Bhabha National Institute, Mumbai 400094 (India); Bandyopadhyay, T. [Health Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Homi Bhabha National Institute, Mumbai 400094 (India)

    2015-11-11

    The recently introduced microwave induced chemical etching (MICE) has been found to be a fast and effective etching technique for CR-39 detector. In the present work, the MICE technique was used to develop the neutron induced recoil tracks in CR-39 detectors. Special attention was paid in carrying out a systematic investigation to study the effect of etchant concentration and microwave power on the development of tracks and various track parameters. NaOH solution of different concentrations, viz. 3–8 N was tested at 300, 450, 600 and 900 W of microwave power. Temperature profiles for 200 ml solution of each concentration were generated to maintain a fixed operating condition for all concentrations at each microwave power. The bulk etch rate was found to increase with the microwave power as well as with the etchant concentration. Empirical relations were established to relate the variation of bulk etch rate with microwave power and etchant concentration.

  7. Chemical screen identifies FDA-approved drugs and target pathways that induce precocious pancreatic endocrine differentiation.

    Science.gov (United States)

    Rovira, Meritxell; Huang, Wei; Yusuff, Shamila; Shim, Joong Sup; Ferrante, Anthony A; Liu, Jun O; Parsons, Michael J

    2011-11-29

    Pancreatic β-cells are an essential source of insulin and their destruction because of autoimmunity causes type I diabetes. We conducted a chemical screen to identify compounds that would induce the differentiation of insulin-producing β-cells in vivo. To do this screen, we brought together the use of transgenic zebrafish as a model of β-cell differentiation, a unique multiwell plate that allows easy visualization of lateral views of swimming larval fish and a library of clinical drugs. We identified six hits that can induce precocious differentiation of secondary islets in larval zebrafish. Three of these six hits were known drugs with a considerable background of published data on mechanism of action. Using pharmacological approaches, we have identified and characterized two unique pathways in β-cell differentiation in the zebrafish, including down-regulation of GTP production and retinoic acid biosynthesis.

  8. Molecular Simulations of Shear-Induced Dynamics in Nitromethane

    Science.gov (United States)

    2016-09-01

    is one of the simplest nitro-organic molecules containing only one nitro group (NO2) bonded to one methyl group (CH3) through a C-N bond. This makes...it an ideal candidate to study chemical reaction mechanisms associated with conventional explosive initiation and subsequent detonation.3,6,7...However, understanding the ultra-fast reaction mechanisms for initiation is challenging. The study of initiation and chemical reaction mechanisms of

  9. Butafenacil: A positive control for identifying anemia- and variegate porphyria-inducing chemicals

    Directory of Open Access Journals (Sweden)

    Jessica K. Leet

    2015-01-01

    Full Text Available Butafenacil is an herbicide that inhibits protoporphyrinogen oxidase (PPOX, an enzyme that catalyzes oxidation of protoporphyrinogen IX to protoporphyrin IX during chlorophyll and heme biosynthesis. Based on a high-content screen, we previously identified butafenacil as a potent inducer of anemia in zebrafish embryos. Therefore, the objective of this study was to begin investigating the utility of butafenacil as a positive control for identifying anemia- and variegate porphyria-inducing chemicals. Static exposure to butafenacil from 5 to 72 h post-fertilization (hpf in glass beakers resulted in a concentration-dependent decrease in arterial circulation at low micromolar concentrations. At 72 hpf, the magnitude of butafenacil-induced anemia was similar when embryos were exposed in the presence or absence of light, whereas protoporphyrin accumulation and acute toxicity were significantly lower or absent when embryos were exposed under dark conditions. To identify sensitive developmental windows, we treated embryos to butafenacil from 5, 10, 24, or 48 hpf to 72 hpf in the presence of light, and found that anemia and protoporphyrin accumulation were present at 72 hpf following initiation of exposure at 5 and 10 hpf. On the contrary, protoporphyrin accumulation – but not anemia – was present following initiation of exposure at 24 hpf. Lastly, protoporphyrin accumulation at 72 hpf after exposure from 24 to 48 hpf suggests that protoporphyrin was not eliminated over a 24-h recovery period. Collectively, our data suggests that butafenacil may be a reliable positive control for identifying anemia- and variegate porphyria-inducing chemicals.

  10. Chemical modifications of polymer films induced by high energy heavy ions

    Science.gov (United States)

    Zhu, Zhiyong; Sun, Youmei; Liu, Changlong; Liu, Jie; Jin, Yunfan

    2002-06-01

    Polymer films including polyethylene terephthalate (PET), polystyrene (PS) and polycarbonate (PC) were irradiated at room temperature with ions of 35 MeV/u 40Ar, 25 MeV/u 84Kr, 15.1 MeV/u 136Xe and 11.4 MeV/u 238U to fluences ranging from 9×10 9 to 5.5×10 12 ions/cm 2. The radiation-induced chemical changes of the materials were investigated by Fourier-transform infrared (FTIR) and ultraviolet/visible spectroscopies. It is found that the absorbance in the ultraviolet and visible range induced by all irradiations follows a linear relationship with fluence. The radiation-induced absorbance normalized to one particle increases slowly with increasing of electronic energy loss below about 8 keV/nm followed by a sharp increase up to about 15 keV/nm above which saturation is reached. FTIR measurements reveal that the materials suffer serious degradation through bond breaking. The absorbance of the typical infrared bands decays exponentially with increase of ion fluence and the bond-disruption cross-section shows a sigmoid variation with electronic energy loss. In PET loss of crystallinity is attributed to the configuration transformation of the ethylene glycol residue from trans into the gauche. Alkyne end groups are induced in all the materials above certain electronic energy loss threshold, which is found to be about 0.8 keV/nm for PS and 0.4 keV/nm for PC. The production cross-section of alkyne end group increases with increasing of electronic energy loss and shows saturation at high electronic energy loss values. It is concluded that not only the physical processes but also the chemical processes of the energy deposition determine the modification of polymer.

  11. Chemical modifications of polymer films induced by high energy heavy ions

    Energy Technology Data Exchange (ETDEWEB)

    Zhu Zhiyong E-mail: zyzhu@impcas.ac.cn; Sun Youmei; Liu Changlong; Liu Jie; Jin Yunfan

    2002-06-01

    Polymer films including polyethylene terephthalate (PET), polystyrene (PS) and polycarbonate (PC) were irradiated at room temperature with ions of 35 MeV/u {sup 40}Ar, 25 MeV/u {sup 84}Kr, 15.1 MeV/u {sup 136}Xe and 11.4 MeV/u {sup 238}U to fluences ranging from 9x10{sup 9} to 5.5x10{sup 12} ions/cm{sup 2}. The radiation-induced chemical changes of the materials were investigated by Fourier-transform infrared (FTIR) and ultraviolet/visible spectroscopies. It is found that the absorbance in the ultraviolet and visible range induced by all irradiations follows a linear relationship with fluence. The radiation-induced absorbance normalized to one particle increases slowly with increasing of electronic energy loss below about 8 keV/nm followed by a sharp increase up to about 15 keV/nm above which saturation is reached. FTIR measurements reveal that the materials suffer serious degradation through bond breaking. The absorbance of the typical infrared bands decays exponentially with increase of ion fluence and the bond-disruption cross-section shows a sigmoid variation with electronic energy loss. In PET loss of crystallinity is attributed to the configuration transformation of the ethylene glycol residue from trans into the gauche. Alkyne end groups are induced in all the materials above certain electronic energy loss threshold, which is found to be about 0.8 keV/nm for PS and 0.4 keV/nm for PC. The production cross-section of alkyne end group increases with increasing of electronic energy loss and shows saturation at high electronic energy loss values. It is concluded that not only the physical processes but also the chemical processes of the energy deposition determine the modification of polymer.

  12. Contents of chemical elements in stomach during prenatal development: different age-dependent dynamical changes and their significance

    Institute of Scientific and Technical Information of China (English)

    Shao-Fan Hou; Hai-Rong Li; Li-Zhen Wang; De-Zhu Li; Lin-Sheng Yang; Chong-Zheng Li

    2003-01-01

    AIM: To observe dynamic of different chemical elements in stomach tissue during fetal development.METHODS: To determine contents of the 21 chemical elements in each stomach samples from fetus aging four to ten months. The content values were compared to those from adult tissue samples, and the values for each month group were also analyzed for dynamic changes.RESULTS: Three representations were found regarding the relationship between contents of the elements and ages of the fetus, including the positive correlative (K), reversely correlative (Na, Ca, P, Al, Cu, Zn, Fe, Mn, Cr, Sr, Li, Cd, Ba,Se ) and irrelevant groups (Mg, Co, Ni, V, Pb, Ti).CONCLUSION: The chemical elements' contents in stomach tissues were found to change dynamically with the stomach weights. The age-dependent representations for different chemical elements during the prenatal development may be of some significance for assessing development of fetal stomach and some chemical elements. The data may be helpful for the nutritional balance of fetus and mothers during prenatal development and even the perinatal stages.

  13. Contents of chemical elements in stomach during prenatal development: different age-dependent dynamical changes and their significance

    Science.gov (United States)

    Hou, Shao-Fan; Li, Hai-Rong; Wang, Li-Zhen; Li, De-Zhu; Yang, Lin-Sheng; Li, Chong-Zheng

    2003-01-01

    AIM: To observe dynamic of different chemical elements in stomach tissue during fetal development. METHODS: To determine contents of the 21 chemical elements in each stomach samples from fetus aging four to ten months. The content values were compared to those from adult tissue samples, and the values for each month group were also analyzed for dynamic changes. RESULTS: Three representations were found regarding the relationship between contents of the elements and ages of the fetus, including the positive correlative (K), reversely correlative (Na, Ca, P, Al, Cu, Zn, Fe, Mn, Cr, Sr, Li, Cd, Ba, Se) and irrelevant groups (Mg, Co, Ni, V, Pb, Ti). CONCLUSION: The chemical elements’ contents in stomach tissues were found to change dynamically with the stomach weights. The age-dependent representations for different chemical elements during the prenatal development may be of some significance for assessing development of fetal stomach and some chemical elements. The data may be helpful for the nutritional balance of fetus and mothers during prenatal development and even the perinatal stages. PMID:12717857

  14. Reactive molecular dynamics simulation and chemical kinetic modeling of pyrolysis and combustion of n-dodecane

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Quan-De [College of Chemistry, Sichuan University, Chengdu (China); Wang, Jing-Bo; Li, Juan-Qin; Tan, Ning-Xin; Li, Xiang-Yuan [College of Chemical Engineering, Sichuan University, Chengdu (China)

    2011-02-15

    The initiation mechanisms and kinetics of pyrolysis and combustion of n-dodecane are investigated by using the reactive molecular dynamics (ReaxFF MD) simulation and chemical kinetic modeling. From ReaxFF MD simulations, we find the initiation mechanisms of pyrolysis of n-dodecane are mainly through two pathways, (1) the cleavage of C-C bond to form smaller hydrocarbon radicals, and (2) the dehydrogenation reaction to form an H radical and the corresponding n-C{sub 12}H{sub 25} radical. Another pathway is the H-abstraction reactions by small radicals including H, CH{sub 3}, and C{sub 2}H{sub 5}, which are the products after the initiation reaction of n-dodecane pyrolysis. ReaxFF MD simulations lead to reasonable Arrhenius parameters compared with experimental results based on first-order kinetic analysis of n-dodecane pyrolysis. The density/pressure effects on the pyrolysis of n-dodecane are also analyzed. By appropriate mapping of the length and time from macroscopic kinetic modeling to ReaxFF MD, a simple comparison of the conversion of n-dodecane from ReaxFF MD simulations and that from kinetic modeling is performed. In addition, the oxidation of n-dodecane is studied by ReaxFF MD simulations. We find that formaldehyde molecule is an important intermediate in the oxidation of n-dodecane, which has been confirmed by kinetic modeling, and ReaxFF leads to reasonable reaction pathways for the oxidation of n-dodecane. These results indicate that ReaxFF MD simulations can give an atomistic description of the initiation mechanism and product distributions of pyrolysis and combustion for hydrocarbon fuels, and can be further used to provide molecular based robust kinetic reaction mechanism for chemical kinetic modeling of hydrocarbon fuels. (author)

  15. Effect of a high strength chemical industry wastewater on microbial community dynamics and mesophilic methane generation.

    Science.gov (United States)

    Venkatakrishnan, Harish; Tan, Youming; Majid, Maszenan Bin Abdul; Pathak, Santosh; Sendjaja, Antonius Yudi; Li, Dongzhe; Liu, Jerry Jian Lin; Zhou, Yan; Ng, Wun Jern

    2014-04-01

    A high strength chemical industry wastewater was assessed for its impact on anaerobic microbial community dynamics and consequently mesophilic methane generation. Cumulative methane production was 251 mL/g total chemical oxygen demand removed at standard temperature and pressure at the end of 30 days experimental period with a highest recorded methane percentage of 80.6% of total biogas volume. Volatile fatty acids (VFAs) analysis revealed that acetic acid was the major intermediate VFAs produced with propionic acid accumulating over the experimental period. Quantitative analysis of microbial communities in the test and control groups with quantitative real time polymerase chain reaction highlighted that in the test group, Eubacteria (96.3%) was dominant in comparison with methanogens (3.7%). The latter were dominated by Methanomicrobiales and Methanobacteriales while Methanosarcinaceae in test groups increased over the experimental period, reaching a maximum on day 30. Denaturing gradient gel electrophoresis profile was performed, targeting the 16S rRNA gene of Eubacteria and Archaea, with the DNA samples extracted at 3 different time points from the test groups. A phylogenetic tree was constructed for the sequences using the neighborhood joining method. The analysis revealed that the presence of organisms resembling Syntrophomonadaceae could have contributed to increased production of acetic and propionic acid intermediates while decrease of organisms resembling Pelotomaculum sp. could have most likely contributed to accumulation of propionic acid. This study suggested that the degradation of organic components within the high strength industrial wastewater is closely linked with the activity of certain niche microbial communities within eubacteria and methanogens.

  16. Super-resolution chemical imaging with dynamic placement of plasmonic hotspots

    Science.gov (United States)

    Olson, Aeli P.; Ertsgaard, Christopher T.; McKoskey, Rachel M.; Rich, Isabel S.; Lindquist, Nathan C.

    2015-08-01

    We demonstrate dynamic placement of plasmonic "hotspots" for super-resolution chemical imaging via Surface Enhanced Raman Spectroscopy (SERS). A silver nanohole array surface was coated with biological samples and illuminated with a laser. Due to the large plasmonic field enhancements, blinking behavior of the SERS hotspots was observed and processed using a Stochastic Optical Reconstruction Microscopy (STORM) algorithm enabling localization to within 10 nm. However, illumination of the sample with a single static laser beam (i.e., a slightly defocused Gaussian beam) only produced SERS hotspots in fixed locations on the surface, leaving noticeable gaps in any final image. But, by using a spatial light modulator (SLM), the illumination profile of the beam could be altered, shifting any hotspots across the nanohole array surface in sub-wavelength steps. Therefore, by properly structuring an illuminating light field with the SLM, we show the possibility of positioning plasmonic hotspots over a metallic nanohole surface on-the-fly. Using this and our SERS-STORM imaging technique, we show potential for high-resolution chemical imaging without the noticeable gaps that were present with static laser illumination. Interestingly, even illuminating the surface with randomly shifting SLM phase profiles was sufficient to completely fill in a wide field of view for super-resolution SERS imaging of a single strand of 100-nm thick collagen protein fibrils. Images were then compared to those obtained with a scanning electron microscope (SEM). Additionally, we explored alternative methods of phase shifting other than holographic illumination through the SLM to create localization of hotspots necessary for SERS-STORM imaging.

  17. Chemical crosslinking and mass spectrometry studies of the structure and dynamics of membrane proteins and receptors.

    Energy Technology Data Exchange (ETDEWEB)

    Haskins, William E.; Leavell, Michael D.; Lane, Pamela; Jacobsen, Richard B.; Hong, Joohee; Ayson, Marites J.; Wood, Nichole L.; Schoeniger, Joseph S.; Kruppa, Gary Hermann; Sale, Kenneth L.; Young, Malin M.; Novak, Petr

    2005-03-01

    Membrane proteins make up a diverse and important subset of proteins for which structural information is limited. In this study, chemical cross-linking and mass spectrometry were used to explore the structure of the G-protein-coupled photoreceptor bovine rhodopsin in the dark-state conformation. All experiments were performed in rod outer segment membranes using amino acid 'handles' in the native protein sequence and thus minimizing perturbations to the native protein structure. Cysteine and lysine residues were covalently cross-linked using commercially available reagents with a range of linker arm lengths. Following chemical digestion of cross-linked protein, cross-linked peptides were identified by accurate mass measurement using liquid chromatography-fourier transform mass spectrometry and an automated data analysis pipeline. Assignments were confirmed and, if necessary, resolved, by tandem MS. The relative reactivity of lysine residues participating in cross-links was evaluated by labeling with NHS-esters. A distinct pattern of cross-link formation within the C-terminal domain, and between loop I and the C-terminal domain, emerged. Theoretical distances based on cross-linking were compared to inter-atomic distances determined from the energy-minimized X-ray crystal structure and Monte Carlo conformational search procedures. In general, the observed cross-links can be explained by re-positioning participating side-chains without significantly altering backbone structure. One exception, between C3 16 and K325, requires backbone motion to bring the reactive atoms into sufficient proximity for cross-linking. Evidence from other studies suggests that residues around K325 for a region of high backbone mobility. These findings show that cross-linking studies can provide insight into the structural dynamics of membrane proteins in their native environment.

  18. Isotopic and impurity element probes of mesoscale chemical dynamics at mineral fluid interfaces

    Science.gov (United States)

    DePaolo, D. J.

    2012-12-01

    Mesoscale interactions control important Earth processes including the growth of minerals from aqueous solutions and silicate liquids, the diffusion of ions in solids and silicate liquids, and the solid-state deformation and recrystallization that constitutes metamorphism. Most of these processes are typically understood from the classical side in terms of macroscopic physical and thermodynamic properties and classical kinetics, and from the molecular side in terms of single molecule or nearest-neighbor interactions. However, in many cases the controlling processes occur at intermediate scales of both length and time, and involve complex interactions among multiple chemical species. A major limitation has been in characterizing and modeling the dynamic processes that lead to the macroscopic properties and behavior. Advanced microscopy techniques allow phase changes, for example, to be monitored at high resolution, and this capability continues to improve. However, other important information about the phase changes, such as the molecular exchange fluxes between phases and the detailed mechanisms of reaction, are not revealed by microscopy. High-resolution isotopic characterization now allows the molecular exchange fluxes to be quantified, and models suggest that the incorporation of impurity elements is directly tied to these fluxes. One of the main advances is that precise isotopic measurements have recently been extended to include major stoichiometric cations such as Ca, Mg, Fe, and K, as well as key impurity elements such as U, Cd, Mo, and Sr. Isotopic analysis at the nano- to microscale would further clarify the detailed dynamics of mineral chemistry controls but are not yet possible except in a few instances. Impurity element concentrations are more easily measured at these small scales, and they are a key bridge between isotopic measurements and microscopy.Other limitations to advancing our knowledge of the chemical and isotopic effects associated with

  19. Aqueous suspension of anise "Pimpinella anisum" protects rats against chemically induced gastric ulcers

    Institute of Scientific and Technical Information of China (English)

    Ibrahim A Al Mofleh; Abdulqader A Alhaider; Jaber S Mossa; Mohammed O Al-Soohaibani; Syed Rafatullah

    2007-01-01

    AIM:To substantiate the claims of Unani and Arabian traditional medicine practitioners on the gastroprotective potential effect of a popular spice anise,"Pimpinella anisum L." on experimentally-induced gastric ulceration and secretion in rats.METHODS:Acute gastric ulceration in rats was produced by various noxious chemicals including 80% ethanol,0.2 mol/L NaOH,25% NaCl and indomethacin.Anti-secretory studies were undertaken using pylorusligated Shay rat technique.Levels of gastric non-protein sulfhydryls(NP-SH)and wall mucus were estimated and gastric tissue was also examined histologically.Anise aqueous suspension was used in two doses(250 and 500 mg/kg body weight)in all experiments.RESULTS:Anise significantly inhibited gastric mucosal damage induced by necrotizing agents and indomethacin.The anti-ulcer effect was further confirmed histologically.In pylorus-ligated Shay rats,anise suspension significantly reduced the basal gastric acid secretion,acidity and completely inhibited the rumenal ulceration.On the other hand,the suspension significantly replenished ethanol-induced depleted levels of gastric mucosal NP-SH and gastric wall mucus concentration.CONCLUSION:Anise aqueous suspension possesses significant cytoprotective and anti-ulcer activities against experimentally-induced gastric lesions.The anti-ulcer effect of anise is possibly prostaglandin-mediated and/or through its anti-secretory and antioxidative properties.

  20. Dynamics, chemical properties and bioavailability of DOC in an early successional catchment

    Directory of Open Access Journals (Sweden)

    U. Risse-Buhl

    2013-07-01

    Full Text Available The dynamics of dissolved organic carbon (DOC have been intensively studied in mature ecosystems, but little is known about DOC dynamics and the significance of DOC as a substrate for microbial activity in early-successional catchments. We determined the concentration, chemical composition, source, radiocarbon age, and bioavailability of DOC along the hydrological flow path from soil solution to a downstream pond in a recently constructed catchment (Chicken Creek Catchment, Germany. Soil solution, upwelling ground water, stream water, subsurface water in an alluvial fan, and pond water all had high DOC concentrations (averages: 6.0–11.6 mg DOC L–1, despite small carbon stocks in both vegetation and soil of the catchment. Solid-state CPMAS 13C NMR of DOC in upwelling ground water revealed a higher proportion of aromatic compounds (32% and a lower proportion of carbohydrates (33% than in pond water (18% and 45%, respectively. The average 14C age of DOC in upwelling ground water was 2600 to 2900 yr, while organic matter of the Quaternary substrate of the catchment had a 14C age of 3000 to 16 000 yr. Both the 14C age data and 13C NMR spectra suggest that DOC partly derived from organic matter of the Quaternary substrate (about 40 to 90% of the C in the DOC, indicating that both recent and old C of the DOC can support microbial activity during early ecosystem succession. However, in a 70 day incubation experiment, only about 11% of the total DOC was found to be bioavailable. This proportion was irrespective of the water type. Origin of the microbial communities within the catchment (enriched from soil, stream sediment or pond water also had only a marginal effect on overall DOC utilization.

  1. Dynamics, chemical properties and bioavailability of DOC in an early successional catchment

    Directory of Open Access Journals (Sweden)

    U. Risse-Buhl

    2013-01-01

    Full Text Available The dynamics of dissolved organic carbon (DOC have been intensively studied in mature ecosystems, but little is known about DOC dynamics and the significance of DOC as a substrate for microbial activity in early-successional catchments. We determined the concentration, chemical composition, source, radiocarbon age, and bioavailability of DOC along the hydrological flow path from soil solution to a downstream pond in a recently constructed catchment (Chicken Creek Catchment, Germany. Soil solution, upwelling ground water, subsurface water in an alluvial fan, and pond water all had high DOC concentrations (averages of 6.0–11.6 mg DOC L−1, despite small carbon stocks in either vegetation or soil of the early-successional catchment. The mean 14C age of DOC in upwelling ground water was 2600 to 2800 yr. Solid-state CPMAS 13C NMR revealed a higher proportion of aromatic compounds (32% and a lower proportion of carbohydrates (33% in upwelling ground water than in pond water (18% and 45%, respectively. The 14C age and 13C NMR spectra suggest that DOC was partly mobilized from charred organic matter of the Quaternary substrate. In an experimental 70-days incubation experiment, 20% of the total DOC was found to be bioavailable, irrespective of the water type. Origin of microbial communities (enriched from soil, stream sediment or pond water had only marginal effects on overall DOC utilization. Overall, these data suggest that the old DOC can support microbial activity during early ecosystem succession to some extent, although the largest fraction is recalcitrant DOC that is exported from the catchment once it has been mobilized.

  2. Frictional melting dynamics in the upper conduit: A chemical answer to a complex physical question

    Science.gov (United States)

    Henton De Angelis, S.; Lavallee, Y.; Kendrick, J. E.; Hornby, A.; von Aulock, F. W.; Clesham, S.; Hirose, T.; Perugini, D.

    2013-12-01

    During volcanic eruptions the generation of frictional heat along the walls of the shallow conduit leads to melting of the rocks along the slip interface. Frictional melting has previously been described as a process out of thermodynamic equilibrium, but upon slip and mingling of the melt batches, homogeneity can be achieved, and may have an h important rheological control on the dynamics of slip. To test melt homogenization in the frictional melt zones of volcanic conduits we performed constant-rate slip experiments under controlled stress conditions using a high-velocity rotary shear apparatus. Volcanic dome samples from three different volcanoes (Volcán De Colima, Soufrière Hills Volcano and Santiaguito Volcano) were investigated. Each sample was subjected to a stress of 1 MPa and slip rate of 1 m/s. For each sample set 5 experiments were conducted: 1) experiment stopped at the onset of melting; 2) experiment stopped on the formation of a full melt layer; 3) experiment stopped after 5m of slip at steady state conditions; 4) experiment stopped after 10m of slip at steady state conditions; 5) experiment stopped after 15m of slip at steady state conditions. We analyzed the resulting proto-melt zones using micron sized X-ray spectroscopy in the high-brightness synchrotron beamline I18 (at Diamond Light Source UK). Particular focus was given to the concentration variance analysis of Rare Earth Elements as their mobilities can be used to precisely quantify the degree and timescale of homogenisation involved during frictional melting. This study refines our understanding of the chemical process of melting and mixing which carry important consequences for the rheological control on the physical dynamics of slip.

  3. Population dynamics, information transfer, and spatial organization in a chemical reaction network under spatial confinement and crowding conditions

    Science.gov (United States)

    Bellesia, Giovanni; Bales, Benjamin B.

    2016-10-01

    We investigate, via Brownian dynamics simulations, the reaction dynamics of a generic, nonlinear chemical network under spatial confinement and crowding conditions. In detail, the Willamowski-Rossler chemical reaction system has been "extended" and considered as a prototype reaction-diffusion system. Our results are potentially relevant to a number of open problems in biophysics and biochemistry, such as the synthesis of primitive cellular units (protocells) and the definition of their role in the chemical origin of life and the characterization of vesicle-mediated drug delivery processes. More generally, the computational approach presented in this work makes the case for the use of spatial stochastic simulation methods for the study of biochemical networks in vivo where the "well-mixed" approximation is invalid and both thermal and intrinsic fluctuations linked to the possible presence of molecular species in low number copies cannot be averaged out.

  4. Population dynamics, information transfer, and spatial organization in a chemical reaction network under spatial confinement and crowding conditions.

    Science.gov (United States)

    Bellesia, Giovanni; Bales, Benjamin B

    2016-10-01

    We investigate, via Brownian dynamics simulations, the reaction dynamics of a generic, nonlinear chemical network under spatial confinement and crowding conditions. In detail, the Willamowski-Rossler chemical reaction system has been "extended" and considered as a prototype reaction-diffusion system. Our results are potentially relevant to a number of open problems in biophysics and biochemistry, such as the synthesis of primitive cellular units (protocells) and the definition of their role in the chemical origin of life and the characterization of vesicle-mediated drug delivery processes. More generally, the computational approach presented in this work makes the case for the use of spatial stochastic simulation methods for the study of biochemical networks in vivo where the "well-mixed" approximation is invalid and both thermal and intrinsic fluctuations linked to the possible presence of molecular species in low number copies cannot be averaged out.

  5. Lymphohematopoietic Cancers Induced by Chemicals and Other Agents: Overview and Implications for Risk Assessment (External Review Draft)

    Science.gov (United States)

    This draft report provides an overview of the types of mechanisms underlying the lymphohematopoietic cancers induced by chemical agents and radiation in humans, with a primary emphasis on leukemia and leukemia-inducing agents. It focuses on how mechanistic information on human l...

  6. DETECTION OF LOW DOSE RADIATION-AND CHEMICALLY-INDUCED DNA DAMAGE USING TEMPERATURE DIFFERENTIAL FLUORESCENCE ASSAYS

    Science.gov (United States)

    Rapid, sensitive and simple assays for radiation- and chemically-induced DNA damage can be of significant benefit to a number of fields including radiation biology, clinical research, and environmental monitoring. Although temperature-induced DNA strand separation has been use...

  7. Antiinflammatory effects of human milk on chemically induced colitis in rats.

    Science.gov (United States)

    Grazioso, C F; Werner, A L; Alling, D W; Bishop, P R; Buescher, E S

    1997-11-01

    We examined the effects of a human milk diet on rats with chemical colitis induced with a 4% acetic acid enema. Colonic myeloperoxidase activity was used as a surrogate marker for neutrophil infiltration. Control rats fed rat chow had little colonic myeloperoxidase activity; geometric mean, 0.27 U/g of tissue. Rats with colitis fed rat chow had significantly increased colonic myeloperoxidase activity (geometric mean, 6.76 U/g, p Pedialyte (geometric mean, 6.92 and 8.13 U/g, respectively, both p < 0.01 versus no colitis). Animals with colitis fed human milk had significantly lower colonic myeloperoxidase activity (geometric mean, 2.34 U/g) than did animals with colitis fed either chow or infant formula (p < 0.001). Similar effects were seen in rats with colitis fed infant formula supplemented with recombinant human IL-1 receptor antagonist (geometric mean, 1.95 U/g). These data show that orally administered human milk has an antiinflammatory effect on chemically induced colitis in rats, which may be mediated in part by IL-1 receptor antagonist contained in human milk.

  8. Absence of p53 gene expression in selenium molecular prevention of chemically Induced hepatocarcinogenesis in rats

    Directory of Open Access Journals (Sweden)

    Nasar Y Alwahaibi

    2011-01-01

    Full Text Available Background/Aim: p53 pathway is thought by many researchers to be critically involved in selenium′s chemoprevention or in hepatocarcinogenesis. The aim of this study was to investigate the gene expression of p53, p21 and B-cell lymphoma-2 (bcl-2 using preventive and therapeutic approaches of selenium in chemically induced hepatocarcinogenesis in rats. Materials and Methods: Rats were divided randomly into six groups: Negative control, positive control (diethyl nitrosamine +2-acetylaminofluorene, preventive group, preventive control (respective control for preventive group, therapeutic group and therapeutic control (respective control for therapeutic group. p53, p21 and bcl-2 genes on liver tissues were measured using real-time polymerase chain reaction. Results: The expression of p53 was only significant in the therapeutic control. The expression of bcl-2 was insignificant in all the groups. p21 expression was significant in all the groups except the preventive group. Conclusions: The selenium molecular mechanism for liver cancer prevention is not through the p53 pathway. Also, the absence of p53 is not necessary for chemically induced liver cancer in rats.

  9. Implications and applications of current-induced dynamics in molecular junctions.

    Science.gov (United States)

    Jorn, Ryan; Seideman, Tamar

    2010-09-21

    Instances of strongly nonadiabatic electronic-vibrational energy transfer have been studied since the early days of quantum mechanics and remain a topic of fundamental interest. Often such transfers are associated with electronic resonances, temporary states where transient localization of charge on the molecule provides a mechanism for channeling electronic energy into vibrational excitation. Extensively studied in the gas phase, electron resonance scattering also occurs with surface adsorbed molecules, where it manifests itself in broadened cross sections and desorption of adsorbates from metal surfaces. In this Account, we focus on a related topic: the implications of nonadiabatic, resonance-mediated scattering to the exciting field of molecular electronics. In this context, researchers can induce directed nuclear dynamics and control these processes in single molecules in contact with metallic and semiconducting electrodes. We discuss a variety of consequences and applications of current-driven nuclear excitation in molecular devices, ranging from the design of new forms of molecular machines to surface chemistry at the single-molecule level and atom-resolved lithography. We highlight two specific examples of molecular nanomachines. In the first, a Au-C(60)-Au transistor, the current induces the oscillatory motion of the center-of-mass coordinate of the C(60). The second, a zwitterion-based rattle, demonstrates excitation of intramolecular motion as the positively charged moiety is threaded back and forth through the negatively charged carbon ring. Finally, we discuss the current-induced desorption of organic molecules from Si(100) both to suggest the potential for controlled surface nanochemistry and to develop guidelines for the design of stable molecular junctions. Modeling the exchange of energy between tunneling electrons and the vibrational degrees of freedom of a target molecule subject to bias voltage, open boundary conditions in the electronic subspace

  10. Evaluation of Maltose-Induced Chemical Degradation at the Interface of Bilayer Tablets.

    Science.gov (United States)

    Matsuzaki, Naoya; Yamamoto, Yousuke; Murayama, Daisuke; Katakawa, Yoshifumi; Mimura, Hisashi; Kimura, Shin-Ichiro; Iwao, Yasunori; Itai, Shigeru

    2017-01-01

    Fixed dose combination tablets consisting of mirabegron (MB) and solifenacin succinate (SS) were developed and formulated into bilayer tablets in the current study. The results of a chemical stability study showed that the original formulation for the tablets led to a significant increase of unknown degradants in the SS layer. Two compatibility studies were conducted to simulate the interface between the MB and SS layers, and the results revealed that the degradants only formed in the presence of both active pharmaceutical ingredients (APIs), and that the presence of maltose in the SS layer was critical to inducing degradation. High resolution mass spectroscopy coupled with high performance liquid chromatography was used to determine the chemical structures of the degradants, which were identified to MB derivatives bearing one or two sugar units. These findings therefore suggested that the degradation of the API could be attributed to the addition of sugar units from maltose to MB under the acidic conditions caused by SS. With this in mind, we developed a new formulation by replacing maltose with hydroxypropyl cellulose as a polymer-type binder. The results showed that this formulation suppressed the formation of the degradants. The results of this study have shown that chemical degradation can occur at the interface of bilayer tablets and that an alternative strategy is available to formulate more stable MB/SS bilayer tablets.

  11. Fabrication of chemical templates via selective laser-induced desorption of hexadecanethiol self-assembled monolayers

    Energy Technology Data Exchange (ETDEWEB)

    Schröter, Anja; Mathieu, Mareike; Franzka, Steffen [Fakultät für Chemie, Universität Duisburg-Essen, 45117 Essen (Germany); CENIDE – Center for Nanointegration Duisburg-Essen, 47048 Duisburg (Germany); Feydt, Jürgen; Irsen, Stephan [caesar – Center of Advanced European Studies and Research, 53175 Bonn (Germany); Hartmann, Nils, E-mail: nils.hartmann@uni-due.de [Fakultät für Chemie, Universität Duisburg-Essen, 45117 Essen (Germany); CENIDE – Center for Nanointegration Duisburg-Essen, 47048 Duisburg (Germany)

    2013-08-01

    A nonlinear photothermal laser patterning technique for rapid fabrication of chemical templates is demonstrated. Hexadecanethiol monolayers on Au-coated Si substrates are processed at λ = 532 nm, a 1/e{sup 2} spot diameter of d{sub 1/e{sup 2}}=2.8μm and ambient conditions. Local laser irradiation at high laser powers and short irradiation times in the micro-/millisecond range induces desorption of thiol molecules. The laser-depleted areas are backfilled with mercaptohexadecanoic acid in order to build up chemical templates. Atomic force microscopy, scanning electron microscopy and scanning Auger electron spectroscopy are used for characterization of these templates. In agreement with a selective laser process, the results indicate the formation of flat chemical patterns with well-defined boundaries. Complementary condensation experiments demonstrate the functionality of the patterns as hydrophilic/hydrophobic templates. In particular, upon decreasing the temperature below the dew point, selective formation of water droplets on the backfilled areas is observed.

  12. Low Density Supersonic Decelerator (LDSD) Supersonic Flight Dynamics Test (SFDT) Plume Induced Environment Modelling

    Science.gov (United States)

    Mobley, B. L.; Smith, S. D.; Van Norman, J. W.; Muppidi, S.; Clark, I

    2016-01-01

    Provide plume induced heating (radiation & convection) predictions in support of the LDSD thermal design (pre-flight SFDT-1) Predict plume induced aerodynamics in support of flight dynamics, to achieve targeted freestream conditions to test supersonic deceleration technologies (post-flight SFDT-1, pre-flight SFDT-2)

  13. Chemical and Microbial Dynamics during Composting of Herbal Pharmaceutical Industrial Waste

    Directory of Open Access Journals (Sweden)

    Farhan Zameer

    2010-01-01

    Full Text Available A study was performed to analyze the dynamics of chemical, biochemical and microbial parameters during composting of herbal pharmaceutical waste. All the parameters were analyzed at three different intervals of composting (1st, 15th and 60th days. Temperature of the compost pile was initially high (46.2 °C and on 60th day it dropped to 33.3 °C. The pH of the sample was initially acidic (2.39 and with the progress of decomposition gradually changed to neutrality (7.55. Electrical conductivity (EC value was high (3.8 mS during last day of composting compared to other stages. The activity of degradative enzymes namely amylase, invertase and urease were initially high (4.1, 4.79 mg of glucose/g/h and 0.19 mg of ammonia/g/h respectively while it decreased with composting. The beneficial microbial load was initially low and very high at the last stages of decomposition. The bioassay studies using compost extracts revealed that the 60th day old sample was not phytotoxic in nature.

  14. Solving chemical dynamic optimization problems with ranking-based differential evolution algorithms

    Institute of Scientific and Technical Information of China (English)

    Xu Chen; Wenli Du; Feng Qian

    2016-01-01

    Dynamic optimization problems (DOPs) described by differential equations are often encountered in chemical engineering. Deterministic techniques based on mathematic programming become invalid when the models are non-differentiable or explicit mathematical descriptions do not exist. Recently, evolutionary algorithms are gaining popularity for DOPs as they can be used as robust alternatives when the deterministic techniques are in-valid. In this article, a technology named ranking-based mutation operator (RMO) is presented to enhance the previous differential evolution (DE) algorithms to solve DOPs using control vector parameterization. In the RMO, better individuals have higher probabilities to produce offspring, which is helpful for the performance enhancement of DE algorithms. Three DE-RMO algorithms are designed by incorporating the RMO. The three DE-RMO algorithms and their three original DE algorithms are applied to solve four constrained DOPs from the literature. Our simulation results indicate that DE-RMO algorithms exhibit better performance than previous non-ranking DE algorithms and other four evolutionary algorithms.

  15. The imprint of satellite accretion on the chemical and dynamical properties of disc galaxies

    CERN Document Server

    Ruiz-Lara, T; Gibson, B K; Pérez, I; Florido, E; Minchev, I; Sánchez-Blázquez, P

    2015-01-01

    Aims: We study the effects of the cosmological assembly history on the chemical and dynamical properties of the discs of spiral galaxies as a function of radius. Methods: We make use of the simulated Milky-Way mass, fully-cosmological discs, from {\\tt RaDES} (Ramses Disc Environment Study). We analyse their assembly history by examining the proximity of satellites to the galactic disc, instead of their merger trees, to better gauge which satellites impact the disc. We present stellar age and metallicity profiles, Age-Metallicity Relation (AMR), Age-Velocity dispersion Relation (AVR), and Stellar Age Distribution (SAD) in several radial bins for the simulated galaxies. Results: Assembly histories can be divided into three different stages: i) a merger dominated phase, when a large number of mergers with mass ratios of $\\sim$1:1 take place (lasting $\\sim$3.2$\\pm$0.4 Gyr on average); ii) a quieter phase, when $\\sim$1:10 mergers take place (lasting $\\sim$4.4$\\pm$2.0 Gyr) - these two phases are able to kinematical...

  16. Chemical Dynamics Simulations of Intermolecular Energy Transfer: Azulene + N2 Collisions.

    Science.gov (United States)

    Kim, Hyunsik; Paul, Amit K; Pratihar, Subha; Hase, William L

    2016-07-14

    Chemical dynamics simulations were performed to investigate collisional energy transfer from highly vibrationally excited azulene (Az*) in a N2 bath. The intermolecular potential between Az and N2, used for the simulations, was determined from MP2/6-31+G* ab initio calculations. Az* is prepared with an 87.5 kcal/mol excitation energy by using quantum microcanonical sampling, including its 95.7 kcal/mol zero-point energy. The average energy of Az* versus time, obtained from the simulations, shows different rates of Az* deactivation depending on the N2 bath density. Using the N2 bath density and Lennard-Jones collision number, the average energy transfer per collision ⟨ΔEc⟩ was obtained for Az* as it is collisionally relaxed. By comparing ⟨ΔEc⟩ versus the bath density, the single collision limiting density was found for energy transfer. The resulting ⟨ΔEc⟩, for an 87.5 kcal/mol excitation energy, is 0.30 ± 0.01 and 0.32 ± 0.01 kcal/mol for harmonic and anharmonic Az potentials, respectively. For comparison, the experimental value is 0.57 ± 0.11 kcal/mol. During Az* relaxation there is no appreciable energy transfer to Az translation and rotation, and the energy transfer is to the N2 bath.

  17. Molecular dynamics induced by short and intense x-ray pulses from the LCLS

    Science.gov (United States)

    Berrah, Nora

    2016-12-01

    The past six years have led to a wealth of experimental and theoretical data revealing the nature of the interaction between gas-phase molecules and short and intense x-ray pulses, from the Linac coherent light source free electron laser (FEL). We present here a few highlights that describe some of the first photoabsorption measurements of gas-phase molecules. In particular, we report on a three decades long prediction of single-site double core holes (ss-DCH) and two-site double core holes (ts-DCH) in diatomic and triatomic molecules. We also describe recent measurements that validate a simple theory regarding femtosecond intense x-ray induced fragmentation dynamics of C60 as well as photoabsorption measurements of encapsulated fullerenes, Ho3N@C80. The latter investigation opens the way for even more complex molecular studies with FELs. In all of the described highlights, working in close collaboration with theorists enabled the interpretation of, or predicted our measurements, and in some cases our experiments guided the modeling. We conclude this article by describing the potential of new instrumentation for chemical and biological sciences especially in light of new or improved FELs.

  18. Influence of exothermic chemical reactions on laser-induced shock waves.

    Science.gov (United States)

    Gottfried, Jennifer L

    2014-10-21

    Differences in the excitation of non-energetic and energetic residues with a 900 mJ, 6 ns laser pulse (1064 nm) have been investigated. Emission from the laser-induced plasma of energetic materials (e.g. triaminotrinitrobenzene [TATB], cyclotrimethylene trinitramine [RDX], and hexanitrohexaazaisowurtzitane [CL-20]) is significantly reduced compared to non-energetic materials (e.g. sugar, melamine, and l-glutamine). Expansion of the resulting laser-induced shock wave into the air above the sample surface was imaged on a microsecond timescale with a high-speed camera recording multiple frames from each laser shot; the excitation of energetic materials produces larger heat-affected zones in the surrounding atmosphere (facilitating deflagration of particles ejected from the sample surface), results in the formation of additional shock fronts, and generates faster external shock front velocities (>750 m s(-1)) compared to non-energetic materials (550-600 m s(-1)). Non-explosive materials that undergo exothermic chemical reactions in air at high temperatures such as ammonium nitrate and magnesium sulfate produce shock velocities which exceed those of the inert materials but are less than those generated by the exothermic reactions of explosive materials (650-700 m s(-1)). The most powerful explosives produced the highest shock velocities. A comparison to several existing shock models demonstrated that no single model describes the shock propagation for both non-energetic and energetic materials. The influence of the exothermic chemical reactions initiated by the pulsed laser on the velocity of the laser-induced shock waves has thus been demonstrated for the first time.

  19. Characterization of chemically induced liver injuries using gene co-expression modules.

    Directory of Open Access Journals (Sweden)

    Gregory J Tawa

    Full Text Available Liver injuries due to ingestion or exposure to chemicals and industrial toxicants pose a serious health risk that may be hard to assess due to a lack of non-invasive diagnostic tests. Mapping chemical injuries to organ-specific damage and clinical outcomes via biomarkers or biomarker panels will provide the foundation for highly specific and robust diagnostic tests. Here, we have used DrugMatrix, a toxicogenomics database containing organ-specific gene expression data matched to dose-dependent chemical exposures and adverse clinical pathology assessments in Sprague Dawley rats, to identify groups of co-expressed genes (modules specific to injury endpoints in the liver. We identified 78 such gene co-expression modules associated with 25 diverse injury endpoints categorized from clinical pathology, organ weight changes, and histopathology. Using gene expression data associated with an injury condition, we showed that these modules exhibited different patterns of activation characteristic of each injury. We further showed that specific module genes mapped to 1 known biochemical pathways associated with liver injuries and 2 clinically used diagnostic tests for liver fibrosis. As such, the gene modules have characteristics of both generalized and specific toxic response pathways. Using these results, we proposed three gene signature sets characteristic of liver fibrosis, steatosis, and general liver injury based on genes from the co-expression modules. Out of all 92 identified genes, 18 (20% genes have well-documented relationships with liver disease, whereas the rest are novel and have not previously been associated with liver disease. In conclusion, identifying gene co-expression modules associated with chemically induced liver injuries aids in generating testable hypotheses and has the potential to identify putative biomarkers of adverse health effects.

  20. Characterization of Chemically Induced Liver Injuries Using Gene Co-Expression Modules

    Science.gov (United States)

    Tawa, Gregory J.; AbdulHameed, Mohamed Diwan M.; Yu, Xueping; Kumar, Kamal; Ippolito, Danielle L.; Lewis, John A.; Stallings, Jonathan D.; Wallqvist, Anders

    2014-01-01

    Liver injuries due to ingestion or exposure to chemicals and industrial toxicants pose a serious health risk that may be hard to assess due to a lack of non-invasive diagnostic tests. Mapping chemical injuries to organ-specific damage and clinical outcomes via biomarkers or biomarker panels will provide the foundation for highly specific and robust diagnostic tests. Here, we have used DrugMatrix, a toxicogenomics database containing organ-specific gene expression data matched to dose-dependent chemical exposures and adverse clinical pathology assessments in Sprague Dawley rats, to identify groups of co-expressed genes (modules) specific to injury endpoints in the liver. We identified 78 such gene co-expression modules associated with 25 diverse injury endpoints categorized from clinical pathology, organ weight changes, and histopathology. Using gene expression data associated with an injury condition, we showed that these modules exhibited different patterns of activation characteristic of each injury. We further showed that specific module genes mapped to 1) known biochemical pathways associated with liver injuries and 2) clinically used diagnostic tests for liver fibrosis. As such, the gene modules have characteristics of both generalized and specific toxic response pathways. Using these results, we proposed three gene signature sets characteristic of liver fibrosis, steatosis, and general liver injury based on genes from the co-expression modules. Out of all 92 identified genes, 18 (20%) genes have well-documented relationships with liver disease, whereas the rest are novel and have not previously been associated with liver disease. In conclusion, identifying gene co-expression modules associated with chemically induced liver injuries aids in generating testable hypotheses and has the potential to identify putative biomarkers of adverse health effects. PMID:25226513

  1. Intrinsic dynamics induce global symmetry in network controllability.

    Science.gov (United States)

    Zhao, Chen; Wang, Wen-Xu; Liu, Yang-Yu; Slotine, Jean-Jacques

    2015-02-12

    Controlling complex networked systems to desired states is a key research goal in contemporary science. Despite recent advances in studying the impact of network topology on controllability, a comprehensive understanding of the synergistic effect of network topology and individual dynamics on controllability is still lacking. Here we offer a theoretical study with particular interest in the diversity of dynamic units characterized by different types of individual dynamics. Interestingly, we find a global symmetry accounting for the invariance of controllability with respect to exchanging the densities of any two different types of dynamic units, irrespective of the network topology. The highest controllability arises at the global symmetry point, at which different types of dynamic units are of the same density. The lowest controllability occurs when all self-loops are either completely absent or present with identical weights. These findings further improve our understanding of network controllability and have implications for devising the optimal control of complex networked systems in a wide range of fields.

  2. Herbivore-induced chemical and molecular responses of the kelps Laminaria digitata and Lessonia spicata

    Science.gov (United States)

    Ritter, Andrés; Cabioch, Léa; Brillet-Guéguen, Loraine; Corre, Erwan; Cosse, Audrey; Dartevelle, Laurence; Duruflé, Harold; Fasshauer, Carina; Goulitquer, Sophie; Thomas, François; Correa, Juan A.; Potin, Philippe; Faugeron, Sylvain; Leblanc, Catherine

    2017-01-01

    chemical and molecular responses in kelp species, showing similar inducible responses upon specialist herbivores in their respective ecosystems. PMID:28253346

  3. Dynamics of microvortices induced by ion concentration polarization

    CERN Document Server

    de Valenca, Joeri; Lammertink, Rob G H; Tsai, Peichun Amy

    2015-01-01

    We investigate the coupled dynamics of the local hydrodynamics and global electric response of an electrodialysis system, which consists of an electrolyte solution adjacent to a charge selective membrane under electric forcing. Under a DC electric current, counterions transport through the charged membrane while the passage of co-ions is restricted, thereby developing ion concentration polarization (ICP) or gradients. At sufficiently large currents, simultaneous measurements of voltage drop and flow field reveal several distinct dynamic regimes. Initially, the electrodialysis system displays a steady Ohmic voltage difference ($\\Delta V_{ohm}$), followed by a constant voltage jump ($\\Delta V_c$). Immediately after this voltage increase, micro-vortices set in and grow both in size and speed with time. After this growth, the resultant voltage levels off around a fixed value. The average vortex size and speed stabilize as well, while the individual vortices become unsteady and dynamic. These quantitative results ...

  4. Crystallization induced by multiple seeds: dynamical density functional approach.

    Science.gov (United States)

    Neuhaus, T; Schmiedeberg, M; Löwen, H

    2013-12-01

    Using microscopic dynamical density functional theory, we calculate the dynamical formation of polycrystals by following the crystal growth around multiple crystalline seeds imposed to an undercooled fluid. Depending on the undercooling and the size ratio as well as the relative crystal orientation of two neighboring seeds, three possibilities of the final state emerge, namely no crystallization at all, formation of a monocrystal, or two crystallites separated by a curved grain boundary. Our results, which are obtained for two-dimensional hard disk systems using a fundamental-measure density functional, shed new light on the particle-resolved structure and growth of polycrystalline material in general.

  5. Abnormal development of tapetum and microspores induced by chemical hybridization agent SQ-1 in wheat.

    Directory of Open Access Journals (Sweden)

    Shuping Wang

    Full Text Available Chemical hybridization agent (CHA-induced male sterility is an important tool in crop heterosis. To demonstrate that CHA-SQ-1-induced male sterility is associated with abnormal tapetal and microspore development, the cytology of CHA-SQ-1-treated plant anthers at various developmental stages was studied by light microscopy, scanning and transmission electron microscopy, in situ terminal deoxynucleotidyl transferasemediated dUTP nick end-labelling (TUNEL assay and DAPI staining. The results indicated that the SQ-1-treated plants underwent premature tapetal programmed cell death (PCD, which was initiated at the early-uninucleate stage of microspore development and continued until the tapetal cells were completely degraded; the process of microspore development was then blocked. Microspores with low-viability (fluorescein diacetate staining were aborted. The study suggests that premature tapetal PCD is the main cause of pollen abortion. Furthermore, it determines the starting period and a key factor in CHA-SQ-1-induced male sterility at the cell level, and provides cytological evidence to further study the mechanism between PCD and male sterility.

  6. Abnormal development of tapetum and microspores induced by chemical hybridization agent SQ-1 in wheat.

    Science.gov (United States)

    Wang, Shuping; Zhang, Gaisheng; Song, Qilu; Zhang, Yingxin; Li, Zheng; Guo, Jialin; Niu, Na; Ma, Shoucai; Wang, Junwei

    2015-01-01

    Chemical hybridization agent (CHA)-induced male sterility is an important tool in crop heterosis. To demonstrate that CHA-SQ-1-induced male sterility is associated with abnormal tapetal and microspore development, the cytology of CHA-SQ-1-treated plant anthers at various developmental stages was studied by light microscopy, scanning and transmission electron microscopy, in situ terminal deoxynucleotidyl transferasemediated dUTP nick end-labelling (TUNEL) assay and DAPI staining. The results indicated that the SQ-1-treated plants underwent premature tapetal programmed cell death (PCD), which was initiated at the early-uninucleate stage of microspore development and continued until the tapetal cells were completely degraded; the process of microspore development was then blocked. Microspores with low-viability (fluorescein diacetate staining) were aborted. The study suggests that premature tapetal PCD is the main cause of pollen abortion. Furthermore, it determines the starting period and a key factor in CHA-SQ-1-induced male sterility at the cell level, and provides cytological evidence to further study the mechanism between PCD and male sterility.

  7. Hazard classification of chemicals inducing haemolytic anaemia: An EU regulatory perspective.

    Science.gov (United States)

    Muller, Andre; Jacobsen, Helene; Healy, Edel; McMickan, Sinead; Istace, Fréderique; Blaude, Marie-Noëlle; Howden, Peter; Fleig, Helmut; Schulte, Agnes

    2006-08-01

    Haemolytic anaemia is often induced following prolonged exposure to chemical substances. Currently, under EU Council Directive 67/548/EEC, substances which induce such effects are classified as dangerous and assigned the risk phrase R48 'Danger of serious damage to health by prolonged exposure.' Whilst the general classification criteria for this endpoint are outlined in Annex VI of this Directive, they do not provide specific information to assess haemolytic anaemia. This review produced by the EU Working Group on Haemolytic Anaemia provides a toxicological assessment of haemolytic anaemia and proposes criteria that can be used in the assessment for classification of substances which induce such effects. An overview of the primary and secondary effects of haemolytic anaemia which can occur in rodent repeated dose toxicity studies is given. A detailed analysis of the toxicological significance of such effects is then performed and correlated with the general classification criteria used for this endpoint. This review intends to give guidance when carrying out an assessment for classification for this endpoint and to allow for better transparency in the decision-making process on when to classify based on the presence of haemolytic anaemia in repeated dose toxicity studies. The extended classification criteria for haemolytic anaemia outlined in this review were accepted by the EU Commission Working Group on the Classification and Labelling of Dangerous Substances in September 2004.

  8. 3-D Simulations of the Chemical and Dynamical Evolution of the Galactic Bulge

    CERN Document Server

    Nakasato, N; Nakasato, Naohito; Nomoto, Ken'ichi

    2003-01-01

    A three-dimensional hydrodynamical N-body model for the formation of the Galaxy is presented with special attention to the formation of the bulge component. Starting with cosmologically motivated initial conditions, we obtain a qualitatively similar stellar system to the Galaxy. Then we analyze the chemical and kinematic properties of the bulge stars in our model and find qualitative agreement with observational data. The early evolution of our model has revealed that most bulge stars form during the sub-galactic merger (merger component of the bulge stars). Because of the strong star burst induced by the merger, the metallicity distribution function of such stars becomes as wide as observed. We find that another group of the bulge stars forms later in the inner region of the disk (non-merger component of the bulge stars). Because of the difference in the formation epoch, the main source of iron for this group of stars is different from the merger component. Iron in the merger and non-merger components comes ...

  9. Chemical chaperones reduce ionizing radiation-induced endoplasmic reticulum stress and cell death in IEC-6 cells

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Eun Sang; Lee, Hae-June; Lee, Yoon-Jin [Division of Radiation Effects, Korea Institute of Radiological and Medical Sciences, Seoul 139-706 (Korea, Republic of); Jeong, Jae-Hoon [Division of Radiotherapy, Korea Institute of Radiological and Medical Sciences, Seoul 139-706 (Korea, Republic of); Kang, Seongman [Division of Life Sciences, Korea University, Seoul 136-701 (Korea, Republic of); Lim, Young-Bin, E-mail: yblim@kirams.re.kr [Division of Radiation Effects, Korea Institute of Radiological and Medical Sciences, Seoul 139-706 (Korea, Republic of)

    2014-07-25

    Highlights: • UPR activation precedes caspase activation in irradiated IEC-6 cells. • Chemical ER stress inducers radiosensitize IEC-6 cells. • siRNAs that targeted ER stress responses ameliorate IR-induced cell death. • Chemical chaperons prevent cell death in irradiated IEC-6 cells. - Abstract: Radiotherapy, which is one of the most effective approaches to the treatment of various cancers, plays an important role in malignant cell eradication in the pelvic area and abdomen. However, it also generates some degree of intestinal injury. Apoptosis in the intestinal epithelium is the primary pathological factor that initiates radiation-induced intestinal injury, but the mechanism by which ionizing radiation (IR) induces apoptosis in the intestinal epithelium is not clearly understood. Recently, IR has been shown to induce endoplasmic reticulum (ER) stress, thereby activating the unfolded protein response (UPR) signaling pathway in intestinal epithelial cells. However, the consequences of the IR-induced activation of the UPR signaling pathway on radiosensitivity in intestinal epithelial cells remain to be determined. In this study, we investigated the role of ER stress responses in IR-induced intestinal epithelial cell death. We show that chemical ER stress inducers, such as tunicamycin or thapsigargin, enhanced IR-induced caspase 3 activation and DNA fragmentation in intestinal epithelial cells. Knockdown of Xbp1 or Atf6 with small interfering RNA inhibited IR-induced caspase 3 activation. Treatment with chemical chaperones prevented ER stress and subsequent apoptosis in IR-exposed intestinal epithelial cells. Our results suggest a pro-apoptotic role of ER stress in IR-exposed intestinal epithelial cells. Furthermore, inhibiting ER stress may be an effective strategy to prevent IR-induced intestinal injury.

  10. Identification and Quantification of Volatile Chemical Spoilage Indexes Associated with Bacterial Growth Dynamics in Aerobically Stored Chicken.

    Science.gov (United States)

    Mikš-Krajnik, Marta; Yoon, Yong-Jin; Ukuku, Dike O; Yuk, Hyun-Gyun

    2016-08-01

    Volatile organic compounds (VOCs) as chemical spoilage indexes (CSIs) of raw chicken breast stored aerobically at 4, 10, and 21 °C were identified and quantified using solid phase microextraction (SPME) combined with gas chromatography-mass spectrometry (GC-MS). The growth dynamics of total viable count (TVC), psychrotrophs, Pseudomonas spp., lactic acid bacteria (LAB), Brochothrix thermosphacta and H2 S producing bacteria were characterized based on maximum growth rates (μmax ), maximal microbial concentration (Nmax ) and at the moment of microbial shelf life (Svalues ), calculated from Gompertz-fitted growth curves. Pseudomonas spp. was predominant species, while B. thermosphacta was characterized by the highest μmax . The microbiological and sensory shelf lives were estimated based on TVC, Pseudomonas spp., and B. thermosphacta counts and sensory evaluation, respectively. Among 27 VOCs identified by GC-MS in spoiled chicken samples, ethanol (EtOH), 1-butanol-3-methyl (1But-3M), and acetic acid (C2 ) achieved the highest Pearson's correlation coefficients of 0.66, 0.61, and 0.59, respectively, with TVC, regardless of storage temperature. Partial least squares (PLS) regression revealed that the synthesis of 1But-3M and C2 was most likely induced by the metabolic activity of B. thermosphacta and LAB, while EtOH was attributed to Pseudomonas spp. The increase in concentration of selected volatile spoilage markers (EtOH, 1But-3M, and C2 ) in the headspace over spoiled chicken breast was found to be statistically significant (P < 0.05) with TVC growth. These findings highlight the possibility of analyzing the combination of 3 selected spoilage markers: EtOH, 1But-3M, and C2 as rapid evaluation for poultry quality testing using SPME-GC-MS.

  11. Matrix metalloproteinases regulate the formation of dendritic spine head protrusions during chemically induced long-term potentiation.

    Directory of Open Access Journals (Sweden)

    Zsuzsanna Szepesi

    Full Text Available Dendritic spines are are small membranous protrusions that extend from neuronal dendrites and harbor the majority of excitatory synapses. Increasing evidence has shown that matrix metalloproteinases (MMPs, a family of extracellularly acting and Zn(2+-dependent endopeptidases, are able to rapidly modulate dendritic spine morphology. Spine head protrusions (SHPs are filopodia-like processes that extend from the dendritic spine head, representing a form of postsynaptic structural remodeling in response to altered neuronal activity. Herein, we show that chemically induced long-term potentiation (cLTP in dissociated hippocampal cultures upregulates MMP-9 activity that controls the formation of SHPs. Blocking of MMPs activity or microtubule dynamics abolishes the emergence of SHPs. In addition, autoactive recombinant MMP-9, promotes the formation of SHPs in organotypic hippocampal slices. Furthermore, spines with SHPs gained postsynaptic α-amino-3-hydroxyl-5-methyl-4-isoxazole propionic acid (AMPA receptors upon cLTP and the synaptic delivery of AMPA receptors was controlled by MMPs. The present results strongly imply that MMP-9 is functionally involved in the formation of SHPs and the control of postsynaptic receptor distribution upon cLTP.

  12. Network evolution induced by the dynamical rules of two populations

    Science.gov (United States)

    Platini, Thierry; Zia, R. K. P.

    2010-10-01

    We study the dynamical properties of a finite dynamical network composed of two interacting populations, namely extrovert (a) and introvert (b). In our model, each group is characterized by its size (Na and Nb) and preferred degree (κa and \\kappa_b\\ll \\kappa_a ). The network dynamics is governed by the competing microscopic rules of each population that consist of the creation and destruction of links. Starting from an unconnected network, we give a detailed analysis of the mean field approach which is compared to Monte Carlo simulation data. The time evolution of the restricted degrees langkbbrang and langkabrang presents three time regimes and a non-monotonic behavior well captured by our theory. Surprisingly, when the population sizes are equal Na = Nb, the ratio of the restricted degree θ0 = langkabrang/langkbbrang appears to be an integer in the asymptotic limits of the three time regimes. For early times (defined by t introverts remains constant while the number of connections increases linearly in the extrovert population. Finally, due to the competing dynamics, the network presents a frustrated stationary state characterized by a ratio θ0 = 3.

  13. Electron-induced dynamics of heptathioeter ß-cyclodextrin molecules

    NARCIS (Netherlands)

    Kumar, A.; Heimbuch, R.U.; Wimbush, K.S.; Atesci, H.; Acun, A.; Reinhoudt, D.N.; Velders, A.H.; Zandvliet, H.J.W.

    2012-01-01

    Variable-temperature scanning tunneling microscopy (STM) and spectroscopy (STS) measurements are performed on heptathioether β-cyclodextrin (β-CD) self-assembled monolayers (SAMs) on Au. The β-CD molecules exhibit very rich dynamical behavior, which is not apparent in ensemble-averaged studies. The

  14. Current-induced magnetization dynamics in disordered itinerant ferromagnets

    NARCIS (Netherlands)

    Tserkovnyak, Y.; Skadsem, H.J.; Brataas, A.; Bauer, G.E.W.

    2006-01-01

    Current-driven magnetization dynamics in ferromagnetic metals is studied in a self-consistent adiabatic local-density approximation in the presence of spin-conserving and spin-dephasing impurity scattering. Based on a quantum kinetic equation, we derive Gilbert damping and spin-transfer torques ente

  15. Macroscopic lamellae orientations of diblock copolymer induced by dynamic shear

    Institute of Scientific and Technical Information of China (English)

    张红东; 杨玉良

    1997-01-01

    Computer simulation based on the coupled map lattices has been carried out for morphologies of the diblock copolymeric system under applied periodic shear deformation.The main effort is concentrated on the influence of pre-annenling history on the lamellae orientations in dynamically sheared diblock copolymers.It is found that whatever the quenching temperature is,the perpendicular orientation (i.e.the lamellae normal is parallel to the vorticity axis) is always observed if the dynamic shear deformation with shear amplitude F=1.0 and reduced shear frequency=0.005 is applied during annealing.In contrast to that,the parallel orientation (i.e.the lamellae normal is parallel to the velocity gradient direction) is observed if the dynamic shear with the same amplitude and frequency is applied to a thoroughly annealed (with the annealing time t>4 000) diblock copolymer.Therefore,it is pointed out that the selection of lamellar orientations in dynamically sheared diblock copolymers is not solely dependent on th

  16. Current-induced atomic dynamics, instabilities, and Raman signals

    DEFF Research Database (Denmark)

    Lu, Jing Tao; Brandbyge, Mads; Hedegard, Per

    2012-01-01

    We derive and employ a semiclassical Langevin equation obtained from path integrals to describe the ionic dynamics of a molecular junction in the presence of electrical current. The electronic environment serves as an effective nonequilibrium bath. The bath results in random forces describing Jou...... of these in the Raman signals....

  17. Oscillations and multiscale dynamics in a closed chemical reaction system: second law of thermodynamics and temporal complexity.

    Science.gov (United States)

    Li, Yongfeng; Qian, Hong; Yi, Yingfei

    2008-10-21

    We investigate the oscillatory reaction dynamics in a closed isothermal chemical system: the reversible Lotka-Volterra model. The second law of thermodynamics dictates that the system ultimately reaches an equilibrium. Quasistationary oscillations are analyzed while the free energy of the system serves as a global Lyapunov function of the dissipative dynamics. A natural distinction between regions near and far from equilibrium in terms of the free energy can be established. The dynamics is analogous to a nonlinear mechanical system with time-dependent increasing damping. Near equilibrium, no oscillation is possible as dictated by Onsager's reciprocal symmetry relation. We observe that while the free energy decreases in the closed system's dynamics, it does not follow the steepest descending path.

  18. The imprint of satellite accretion on the chemical and dynamical properties of disc galaxies

    Science.gov (United States)

    Ruiz-Lara, T.; Few, C. G.; Gibson, B. K.; Pérez, I.; Florido, E.; Minchev, I.; Sánchez-Blázquez, P.

    2016-02-01

    Aims: We study the effects of the cosmological assembly history on the chemical and dynamical properties of the discs of spiral galaxies as a function of radius. Methods: We made use of the simulated Milky Way mass, fully-cosmological discs from Ramses Disc Environment Study (RaDES). We analysed their assembly history by examining the proximity of satellites to the galactic disc, instead of their merger trees, to better gauge which satellites impact the disc. We presented stellar age and metallicity profiles, age-metallicity relation (AMR), age-velocity dispersion relation (AVR), and stellar age distribution (SAD) in several radial bins for the simulated galaxies. Results: Assembly histories can be divided into three different stages: i) a merger dominated phase, when a large number of mergers with mass ratios of ~1:1 take place (lasting ~3.2 ± 0.4 Gyr on average); ii) a quieter phase, when ~1:10 mergers take place (lasting ~4.4 ± 2.0 Gyr); and iii) a secular phase where the few mergers that take place have mass ratios below 1:100, which do not affect the disc properties (lasting ~5.5 ± 2.0 Gyr). The first two phases are able to kinematically heat the disc and produce a disc that is chemically mixed over its entire radial extension. Phase 2 ends with a final merger event (at time tjump) marking the onset of important radial differences in the AMR, AVR, and SAD. Conclusions: Inverted AMR trends in the outer parts of discs, for stars younger than tjump, are found as the combined effect of radial motions and star formation in satellites temporarily located in these outer parts. U-shaped stellar age profiles change to an old plateau (~10 Gyr) in the outer discs for the entire RaDES sample. This shape is a consequence of inside-out growth of the disc, radial motions of disc stars (inwards and outwards), and the accretion of old stars from satellites. We see comparable age profiles even when ignoring the influence of stellar migration due to the presence of early in

  19. Capsaicin-induced corneal lesions in mice and the effects of chemical sympathectomy.

    Science.gov (United States)

    Shimizu, T; Izumi, K; Fujita, S; Koja, T; Sorimachi, M; Ohba, N; Fukuda, T

    1987-11-01

    Effects of chemical sympathectomy on corneal changes induced in mice by a s.c. injection of capsaicin were investigated. Pretreatment with a s.c. injection of 6-hydroxydopamine (6-OHDA) on the 1st and 2nd postnatal day or on the 14th and 15th postnatal day led to a marked suppression of the capsaicin-induced corneal lesions. This suppressive effect also was evident in case of administration after capsaicin treatment. Intraventricular injection of 6-OHDA had a slight, transient effect. DSP4 [N-(2-chloroethyl)-N-ethyl-2-bromobenzylamine], another potent substance used for sympathetic denervation, had a suppressive effect similar to that of 6-OHDA. The concentration of capsaicin in tissues of the head was unaltered with 6-OHDA. The content of substance P (SP) in the ocular anterior segments was decreased, dose-dependently, with capsaicin administration. Neonatal administration of 6-OHDA decreased the rate of capsaicin-induced reduction of SP. However, this effect of 6-OHDA was too slight to explain the suppression of the corneal lesions, as the intensity score of lesions with a large dose of capsaicin after 6-OHDA was lower than that with a small dose of capsaicin without 6-OHDA, whereas SP content in the former was still much lower than that in the latter. On the other hand, the content of norepinephrine in the ocular tissues was decreased in the presence of 6-OHDA but not capsaicin. These results suggest that the corneal changes induced by capsaicin are largely inhibited by a decreased activity in the peripheral sympathetic system.

  20. Chemical communication and dynamics of droplet emulsions in networks of Belousov-Zhabotinsky micro-oscillators produced by microfluidics.

    Science.gov (United States)

    Torbensen, Kristian; Rossi, Federico; Ristori, Sandra; Abou-Hassan, Ali

    2017-03-29

    Chemical communication leading to synchronization and collective behaviour of dynamic elements, such as cell colonies, is a widespread phenomenon with biological, physical and chemical importance. Such synchronization between elements proceeds via chemical communication by emmision, interdiffusion and reception of specific messenger molecules. On a lab scale, these phenomena can be modeled by encapsulating an oscillating chemical reaction, which serves as a signal (information) sender/receiver element, inside microcompartments such as droplet emulsions, liposomes and polymersomes. Droplets can thus be regarded as single units, able to generate chemical messengers that diffuse in the environment and hence can interact with other compartments. The Belousov-Zhabotinsky (BZ) reaction is a well-known chemical oscillator largely used as a model for complex nonlinear phenomena, including chemical, physical and biological examples. When the BZ-reaction is encapsulated inside microcompartments, its chemical intermediates can serve as messengers by diffusing among different microcompartments, to trigger specific reactions leading to a collective behavior between the elements. The geometry and constitution of the diffusion pathways play an important role in governing the collective behaviour of the system. In this context, microfluidics is not only a versatile tool for mastering the encapsulation process of the BZ-reaction in monodisperse microcompartments, but also for creating geometries and networks with well defined boundaries. The individual compartments can be engineered with selected properties using different surfactants in the case of simple emulsions, or with specific membrane properties in the case of liposomes. Furthermore, it enables the arrangement of these microcompartments in various geometric configurations, where the diffusive coupling pathways between individual compartments are both spatially and chemically well-defined. In this tutorial paper, we review a

  1. Dynamics of the induced acrosome reaction in boar sperm evaluated by flow cytometry

    DEFF Research Database (Denmark)

    Birck, Anders; Labouriau, Rodrigo; Christensen, Preben

    2009-01-01

    The present study investigated the dynamics of the in vitro induced acrosome reaction (AR) in boar sperm in response to medium composition, incubation time and ionophore concentration. The AR is a prerequisite for normal sperm fertilizing capability and can be studied in vitro following induction...... induced AR. A detailed description of the dynamics of sperm viability and acrosomal status of boar sperm following in vitro induction of the AR has to our knowledge not previously been conducted. In the present study, a triple color flow cytometric detection technique was used, which gave simultaneous...... information on sperm viability and acrosomal status. The ionophore induced AR was dependent on extracellular Ca2+, but could be easily induced in boar sperm without capacitation. Capacitation-associated plasma membrane phospholipid scrambling was assessed and a medium specific ability to induce these membrane...

  2. Attribution of ozone changes to dynamical and chemical processes in CCMs and CTMs

    Directory of Open Access Journals (Sweden)

    H. Garny

    2011-01-01

    Full Text Available Chemistry-climate models (CCMs are commonly used to simulate the past and future development of Earth's ozone layer. The fully coupled chemistry schemes calculate the chemical production and destruction of ozone interactively and ozone is transported by the simulated atmospheric flow. Due to the complexity of the processes acting on ozone it is not straightforward to disentangle the influence of individual processes on the temporal development of ozone concentrations. A method is introduced here that quantifies the influence of chemistry and transport on ozone concentration changes and that is easily implemented in CCMs and chemistry-transport models (CTMs. In this method, ozone tendencies (i.e. the time rate of change of ozone are partitioned into a contribution from ozone production and destruction (chemistry and a contribution from transport of ozone (dynamics. The influence of transport on ozone in a specific region is further divided into export of ozone out of that region and import of ozone from elsewhere into that region. For this purpose, a diagnostic is used that disaggregates the ozone mixing ratio field into 9 separate fields according to in which of 9 predefined regions of the atmosphere the ozone originated. With this diagnostic the ozone mass fluxes between these regions are obtained. Furthermore, this method is used here to attribute long-term changes in ozone to chemistry and transport. The relative change in ozone from one period to another that is due to changes in production or destruction rates, or due to changes in import or export of ozone, are quantified. As such, the diagnostics introduced here can be used to attribute changes in ozone on monthly, interannual and long-term time-scales to the responsible mechanisms. Results from a CCM simulation are shown here as examples, with the main focus of the paper being on introducing the method.

  3. Protective role of food supplement Spirulina fusiformis in chemical induced hepatotoxicity: A Bromobenzene model in rats

    Directory of Open Access Journals (Sweden)

    Evan Prince Sabina

    2014-03-01

    Full Text Available The present study evaluated the efficacy of Spirulina fusiformis in protecting against chemical induced hepatotoxicity in rats using Bromobenzene as the candidate toxin. A single oral dose of bromobenzene (BB (10mmol/kg b.w. resulted in significant (p< 0.05 decrease in antioxidant levels (catalase, superoxide dismutase, glutathione-S-transferase, glutathione peroxidese, total reduced glutathione and total protein, and significant (p< 0.05 increase in the levels of serum bilirubin, liver enzymes (alanine transaminase, aspartate transaminase and alkaline phosphatase indicating the induction of hepatotoxicity. Spirulina fusiformis (400 mg/kg b.w was orally administered for 8 days prior to the administration of BB and was seen to protect the above parameters from significant changes upon challenge with bromobenzene. This was also confirmed by the histological examination of liver tissues after sacrifice. The protective effect of Spirulina fusiformis was comparable to that of the standard hepatoprotective drug sylimarin.

  4. Al-Induced Crystallization Growth of Si Films by Inductively Coupled Plasma Chemical Vapour Deposition

    Institute of Scientific and Technical Information of China (English)

    LI Jun-Shuai; WANG Jin-Xiao; YIN Min; GAO Ping-Qi; HE De-Yan

    2006-01-01

    Polycrystalline Si (poly-Si) films are in situ grown on Al-coated glass substrates by inductively coupled plasma chemical vapour deposition at a temperature as low as 350 C. Compared to the traditional annealing crystallization of amorphous Si/Al-layer structures, no layer exchange is observed and the resultant poly-Si film is much thicker than Al layer. By analysing the depth profiles of the elemental composition, no remains of Al atoms are detected in Si layer within the limit (< 0.01 at. %) of the used evaluations. It is indicated that the poly-Si material obtained by Al-induced crystallization growth has more potential applications than that prepared by annealing the amorphous Si/Al-layer structures.

  5. Heuristic model of chemically induced electron spin polarization in two dimensions

    Science.gov (United States)

    Adrian, Frank J.

    2010-11-01

    A heuristic model of chemically induced electron spin polarization (CIDEP) that breaks the polarization mechanism into its component steps, with each step governed by an appropriate solution of the diffusion equation, is extended from a three to a two-dimensional system. The required solution of the 2D diffusion equation is provided by a relatively simple analytic approximation to the usual infinite series solution. The model yields the polarization and its time development for weak to strong singlet-triplet mixing in the radical pairs, whereas previous models are limited to very weak or very strong mixing. Its results agree with a variational solution of an integral equation of Monchick and are encouraging for observation of CIDEP in dimensionally restricted systems. The method also may be applicable to other diffusion-controlled, spin-dependent chemistry in spatially restricted environments.

  6. High Fidelity Tape Transfer Printing Based On Chemically Induced Adhesive Strength Modulation

    Science.gov (United States)

    Sim, Kyoseung; Chen, Song; Li, Yuhang; Kammoun, Mejdi; Peng, Yun; Xu, Minwei; Gao, Yang; Song, Jizhou; Zhang, Yingchun; Ardebili, Haleh; Yu, Cunjiang

    2015-11-01

    Transfer printing, a two-step process (i.e. picking up and printing) for heterogeneous integration, has been widely exploited for the fabrication of functional electronics system. To ensure a reliable process, strong adhesion for picking up and weak or no adhesion for printing are required. However, it is challenging to meet the requirements of switchable stamp adhesion. Here we introduce a simple, high fidelity process, namely tape transfer printing(TTP), enabled by chemically induced dramatic modulation in tape adhesive strength. We describe the working mechanism of the adhesion modulation that governs this process and demonstrate the method by high fidelity tape transfer printing several types of materials and devices, including Si pellets arrays, photodetector arrays, and electromyography (EMG) sensors, from their preparation substrates to various alien substrates. High fidelity tape transfer printing of components onto curvilinear surfaces is also illustrated.

  7. Artificial Force Induced Reaction (AFIR) Method for Exploring Quantum Chemical Potential Energy Surfaces.

    Science.gov (United States)

    Maeda, Satoshi; Harabuchi, Yu; Takagi, Makito; Taketsugu, Tetsuya; Morokuma, Keiji

    2016-10-01

    In this account, a technical overview of the artificial force induced reaction (AFIR) method is presented. The AFIR method is one of the automated reaction-path search methods developed by the authors, and has been applied extensively to a variety of chemical reactions, such as organocatalysis, organometallic catalysis, and photoreactions. There are two modes in the AFIR method, i.e., a multicomponent mode and a single-component mode. The former has been applied to bimolecular and multicomponent reactions and the latter to unimolecular isomerization and dissociation reactions. Five numerical examples are presented for an Aldol reaction, a Claisen rearrangement, a Co-catalyzed hydroformylation, a fullerene structure search, and a nonradiative decay path search in an electronically excited naphthalene molecule. Finally, possible applications of the AFIR method are discussed.

  8. Improving analytical methods for protein-protein interaction through implementation of chemically inducible dimerization

    DEFF Research Database (Denmark)

    Andersen, Tonni Grube; Nintemann, Sebastian; Marek, Magdalena

    2016-01-01

    into the widely used split ubiquitin-, bimolecular fluorescence complementation (BiFC)- and Forster resonance energy transfer (FRET)-based methods and investigated different protein-protein interactions in yeast and plants. We demonstrate the functionality of this concept by the analysis of weakly interacting......When investigating interactions between two proteins with complementary reporter tags in yeast two-hybrid or split GFP assays, it remains troublesome to discriminate true-from false-negative results and challenging to compare the level of interaction across experiments. This leads to decreased...... sensitivity and renders analysis of weak or transient interactions difficult to perform. In this work, we describe the development of reporters that can be chemically induced to dimerize independently of the investigated interactions and thus alleviate these issues. We incorporated our reporters...

  9. Silencing of Inducible Immunoproteasome Subunit Expression by Chemically Modified siRNA and shRNA.

    Science.gov (United States)

    Gvozdeva, Olga V; Prassolov, Vladimir S; Zenkova, Marina A; Vlassov, Valentin V; Chernolovskaya, Elena L

    2016-08-01

    Overexpression of inducible subunits of immunoproteasome is related to pathogenesis of some chronic diseases. Specific inhibition of the immunosubunits may be used for the treatment of these diseases and RNA interference is one of the potent methods used in this area. We designed 2'-O-methyl modified siRNAs with selectively protected nuclease-sensitive sites, which efficiently silence LMP2, LMP7, and MECL-1 genes expression. To provide stable long-lasting inhibition of target genes, short-hairpin RNAs (shRNA) expressed by lentiviral vectors were constructed. Our results demonstrated that chemically modified siRNAs inhibited the expression of target genes with similar efficiency or with efficiency exceeding that of corresponding shRNAs and provide silencing effect for 5 days.

  10. Nonlinear Hamiltonian mechanics applied to molecular dynamics theory and computational methods for understanding molecular spectroscopy and chemical reactions

    CERN Document Server

    Farantos, Stavros C

    2014-01-01

    This brief presents numerical methods for describing and calculating invariant phase space structures, as well as solving the classical and quantum equations of motion for polyatomic molecules. Examples covered include simple model systems to realistic cases of molecules spectroscopically studied. Vibrationally excited and reacting molecules are nonlinear dynamical systems, and thus, nonlinear mechanics is the proper theory to elucidate molecular dynamics by investigating invariant structures in phase space. Intramolecular energy transfer, and the breaking and forming of a chemical bond have now found a rigorous explanation by studying phase space structures.

  11. 1H NMR study of the solvent THF concerning their structural and dynamical properties in chemically Li-intercalated SWNT

    KAUST Repository

    Schmid, Marc R.

    2011-09-01

    Structural and dynamical properties of the THF solvent in single-walled carbon nanotubes intercalated with lithium are investigated by NMR. 1H NMR experiments reveal the existence of two types of inequivalent THF solvent molecules with different chemical environments and dynamical behavior. At low temperatures THF molecules perpendicularly arranged in between adjacent SWNT presumably exhibit a restricted rotation around their dipolar axis. At higher temperatures THF molecules are isotropically rotating and diffusing along the interstitial channels of the SWNT bundles. © 2011 Elsevier B.V. All rights reserved.

  12. Critical role of surface chemical modifications induced by length shortening on multi-walled carbon nanotubes-induced toxicity

    Directory of Open Access Journals (Sweden)

    Bussy Cyrill

    2012-11-01

    Full Text Available Abstract Given the increasing use of carbon nanotubes (CNT in composite materials and their possible expansion to new areas such as nanomedicine which will both lead to higher human exposure, a better understanding of their potential to cause adverse effects on human health is needed. Like other nanomaterials, the biological reactivity and toxicity of CNT were shown to depend on various physicochemical characteristics, and length has been suggested to play a critical role. We therefore designed a comprehensive study that aimed at comparing the effects on murine macrophages of two samples of multi-walled CNT (MWCNT specifically synthesized following a similar production process (aerosol-assisted CVD, and used a soft ultrasonic treatment in water to modify the length of one of them. We showed that modification of the length of MWCNT leads, unavoidably, to accompanying structural (i.e. defects and chemical (i.e. oxidation modifications that affect both surface and residual catalyst iron nanoparticle content of CNT. The biological response of murine macrophages to the two different MWCNT samples was evaluated in terms of cell viability, pro-inflammatory cytokines secretion and oxidative stress. We showed that structural defects and oxidation both induced by the length reduction process are at least as responsible as the length reduction itself for the enhanced pro-inflammatory and pro-oxidative response observed with short (oxidized compared to long (pristine MWCNT. In conclusion, our results stress that surface properties should be considered, alongside the length, as essential parameters in CNT-induced inflammation, especially when dealing with a safe design of CNT, for application in nanomedicine for example.

  13. Chemically induced hepatotoxicity in human stem cell-induced hepatocytes compared with primary hepatocytes and HepG2.

    Science.gov (United States)

    Kang, Seok-Jin; Lee, Hyuk-Mi; Park, Young-Il; Yi, Hee; Lee, Hunjoo; So, ByungJae; Song, Jae-Young; Kang, Hwan-Goo

    2016-10-01

    Stem cell-induced hepatocytes (SC-iHeps) have been suggested as a valuable model for evaluating drug toxicology. Here, human-induced pluripotent stem cells (QIA7) and embryonic stem cells (WA01) were differentiated into hepatocytes, and the hepatotoxic effects of acetaminophen (AAP) and aflatoxin B1 (AFB1) were compared with primary hepatocytes (p-Heps) and HepG2. In a cytotoxicity assay, the IC50 of SC-iHeps was similar to that in p-Heps and HepG2 in the AAP groups but different from that in p-Heps of the AFB1 groups. In a multi-parameter assay, phenotypic changes in mitochondrial membrane potential, calcium influx and oxidative stress were similar between QIA7-iHeps and p-Heps following AAP and AFB1 treatment but relatively low in WA01-iHeps and HepG2. Most hepatic functional markers (hepatocyte-specific genes, albumin/urea secretion, and the CYP450 enzyme activity) were decreased in a dose-dependent manner following AAP and AFB1 treatment in SC-iHeps and p-Heps but not in HepG2. Regarding CYP450 inhibition, the cell viability of SC-iHeps and p-Heps was increased by ketoconazole, a CYP3A4 inhibitor. Collectively, SC-iHeps and p-Heps showed similar cytotoxicity and hepatocyte functional effects for AAP and AFB1 compared with HepG2. Therefore, SC-iHeps have phenotypic characteristics and sensitivity to cytotoxic chemicals that are more similar to p-Heps than to HepG2 cells.

  14. Dynamics of water and nutrients for potted plants induced by flooded bench fertigation: experiments and simulation.

    NARCIS (Netherlands)

    Otten, W.

    1994-01-01

    Dynamics of water and nutrients as affected by physical and chemical characteristics of a substrate, fertigation method and schedule, and plant uptake were studied for a flooded bench fertigation system for potted plants, through a detailed experimental study of the root environment and a simulation

  15. Two-step spacetime deformation-induced dynamical torsion

    Energy Technology Data Exchange (ETDEWEB)

    Ter-Kazarian, G, E-mail: gago-50@yahoo.com [Byurakan Astrophysical Observatory, Byurakan 378433, Aragatsotn District (Armenia)

    2011-03-07

    We extend the geometrical ideas of the spacetime deformations to study the physical foundation of the post-Riemannian geometry. To this aim, we construct the theory of two-step spacetime deformation as a guiding principle. We address the theory of teleparallel gravity and construct a consistent Einstein-Cartan (EC) theory with the dynamical torsion. We show that the equations of the standard EC theory, in which the equation defining torsion is the algebraic type and, in fact, no propagation of torsion is allowed, can be equivalently replaced by the set of modified EC equations in which the torsion, in general, is dynamical. The special physical constraint imposed upon the spacetime deformations yields the short-range propagating spin-spin interaction.

  16. Two-step spacetime deformation induced dynamical torsion

    CERN Document Server

    Ter-Kazarian, G

    2011-01-01

    We extend the geometrical ideas of the spacetime deformations to study the physical foundation of the post-Riemannian geometry. To this aim, we construct the theory of 'two-step spacetime deformation' as a guiding principle. We address the theory of teleparallel gravity and construct a consistent Einstein-Cartan (EC) theory with the 'dynamical torsion'. We show that the equations of the standard EC theory, in which the equation defining torsion is the algebraic type and, in fact, no propagation of torsion is allowed, can be equivalently replaced by the set of 'modified EC equations' in which the torsion, in general, is dynamical. The special physical constraint imposed upon the spacetime deformations yields the short-range propagating spin-spin interaction.

  17. Antioxidant Activity of Caffeic Acid against Iron-Induced Free Radical Generation--A Chemical Approach.

    Directory of Open Access Journals (Sweden)

    Thiago C Genaro-Mattos

    Full Text Available Caffeic acid (CA is a phenolic compound widely found in coffee beans with known beneficial effects in vivo. Many studies showed that CA has anti-inflammatory, anti-mutagenic, antibacterial and anti-carcinogenic properties, which could be linked to its antioxidant activity. Taking in consideration the reported in vitro antioxidant mechanism of other polyphenols, our working hypothesis was that the CA antioxidant activity could be related to its metal-chelating property. With that in mind, we sought to investigate the chemical antioxidant mechanism of CA against in vitro iron-induced oxidative damage under different assay conditions. CA was able to prevent hydroxyl radical formation promoted by the classical Fenton reaction, as determined by 2-deoxyribose (2-DR oxidative degradation and DMPO hydroxylation. In addition to its ability to prevent hydroxyl radical formation, CA had a great inhibition of membrane lipid peroxidation. In the lipid peroxidation assays CA acted as both metal-chelator and as hydrogen donor, preventing the deleterious action promoted by lipid-derived peroxyl and alkoxyl radicals. Our results indicate that the observed antioxidant effects were mostly due to the formation of iron-CA complexes, which are able to prevent 2-DR oxidation and DMPO hydroxylation. Noteworthy, the formation of iron-CA complexes and prevention of oxidative damage was directly related to the pH of the medium, showing better antioxidant activity at higher pH values. Moreover, in the presence of lipid membranes the antioxidant potency of CA was much higher, indicating its enhanced effectiveness in a hydrophobic environment. Overall, our results show that CA acts as an antioxidant through an iron chelating mechanism, preventing the formation of free hydroxyl radicals and, therefore, inhibiting Fenton-induced oxidative damage. The chemical properties of CA described here--in association with its reported signaling effects--could be an explanation to its

  18. Antioxidant Activity of Caffeic Acid against Iron-Induced Free Radical Generation—A Chemical Approach

    Science.gov (United States)

    Genaro-Mattos, Thiago C.; Maurício, Ângelo Q.; Rettori, Daniel; Alonso, Antonio; Hermes-Lima, Marcelo

    2015-01-01

    Caffeic acid (CA) is a phenolic compound widely found in coffee beans with known beneficial effects in vivo. Many studies showed that CA has anti-inflammatory, anti-mutagenic, antibacterial and anti-carcinogenic properties, which could be linked to its antioxidant activity. Taking in consideration the reported in vitro antioxidant mechanism of other polyphenols, our working hypothesis was that the CA antioxidant activity could be related to its metal-chelating property. With that in mind, we sought to investigate the chemical antioxidant mechanism of CA against in vitro iron-induced oxidative damage under different assay conditions. CA was able to prevent hydroxyl radical formation promoted by the classical Fenton reaction, as determined by 2-deoxyribose (2-DR) oxidative degradation and DMPO hydroxylation. In addition to its ability to prevent hydroxyl radical formation, CA had a great inhibition of membrane lipid peroxidation. In the lipid peroxidation assays CA acted as both metal-chelator and as hydrogen donor, preventing the deleterious action promoted by lipid-derived peroxyl and alkoxyl radicals. Our results indicate that the observed antioxidant effects were mostly due to the formation of iron-CA complexes, which are able to prevent 2-DR oxidation and DMPO hydroxylation. Noteworthy, the formation of iron-CA complexes and prevention of oxidative damage was directly related to the pH of the medium, showing better antioxidant activity at higher pH values. Moreover, in the presence of lipid membranes the antioxidant potency of CA was much higher, indicating its enhanced effectiveness in a hydrophobic environment. Overall, our results show that CA acts as an antioxidant through an iron chelating mechanism, preventing the formation of free hydroxyl radicals and, therefore, inhibiting Fenton-induced oxidative damage. The chemical properties of CA described here—in association with its reported signaling effects—could be an explanation to its beneficial effects

  19. The Chemopreventive Effect of Tamoxifen Combined with Celecoxib on DMBA chemically-Induced Breast Cancer

    Institute of Scientific and Technical Information of China (English)

    Xiaoxu Liu; Huafeng Kang; Xijing Wang; Zhijun Dai; Fengjie Xue; Xinghuan Xue

    2007-01-01

    Objective: To investigate the chemopreventive effect of tamoxifen combined with a COX-2 selective inhibitor, celecoxib, on breast cancer in rats chemically induced by 7,12-dimethylben (a)anthracene (DMBA). Methods:DMBA was irrigated into the stomaches of SD female rats to build breast cancer model. A total of 120 rats were divided into four groups: control group, tamoxifen group, celecoxib group and combined group. The incidence rate, latent period, number and volume of breast cancer were detected and analyzed. Results:The tumor incidence rate of tamoxifen group (48.15%, 13/27) and celecoxib group (50.00%,14/28) were lower than that of control group (85.71%, 24/28), but higher than that of combined group (21.43%, 6/28). The tumor's latent period of tamoxifen group (97.54±1.85 d) and celecoxib group (96.79±2.89 d) were longer than that of control group (89.50±5.99 d), but shorter than that of combined group (103.67±3.39 d). The average tumor number of tamoxifen group (1.77±0.73) and celecoxib group (1.71±0.61) were less than that of control group (3.50±1.62), but more than that of combined group ( 1.17±0.42 ). The average tumor volume of tamoxifen group (1.78±0.71 cm3) and celecoxib group (2.05±1.04 cm3) were smaller than that of control group (6.42±3.96 cm3), but bigger than that of combined group (0.71±0.96 cm3) (P < 0.05 respectively).Conclusion:Celecoxib and tamoxifen are effective drugs in preventing the occurrence of rat breast cancer chemically induced by DMBA. Furthermore, combination of them has better chemopreventive effect.

  20. Evolution of color vision loss induced by occupational exposure to chemicals.

    Science.gov (United States)

    Gobba, F; Cavalleri, A

    2000-10-01

    The evolution of occupationally induced color vision loss was studied in workers exposed to various chemicals. Exposure was evaluated by biological monitoring or personal air samplers, and color vision using the Lanthony D-15 desaturated panel (D-15 d). The effect of short-term interruption of exposure was studied in 39 Styrene (St) exposed workers: at a first examination a dose-related color vision loss was disclosed; a re-test performed after one month's interruption of exposure did not show any improvement of the effect. The evolution during longer periods was studied in another group of 30 St workers. Exposure and color vision were evaluated, then a follow-up was done 12 months later: the exposure was unmodified or slightly decreased in 20 subjects, and D-15 d outcomes remained unchanged, while St levels had increased and color vision loss progressed in the other 10. Similar results were obtained in 33 PCE exposed dry-cleaners: no change in color perception was observed in 14 workers whose exposure decreased, while in the other 19 a rise in PCE levels was followed by a significant color vision worsening. In 21 Hg exposed workers whose mean urinary excretion of Hg was threefold the BEI proposed by ACGIH, a dose-related impairment in color perception was observed. 12 months after a marked reduction of exposure, an almost complete recovery of the impairment was observed. Our data show that an increase in exposure can induce a worsening in color vision loss. A short interruption in exposure did not reduce the effect. A more prolonged reduction of dose reversed color vision loss in Hg exposed workers, while in solvent-exposed individuals the progression deserves further evaluation. D-15 d proved a useful test for studies on the evolution of color perception in workers exposed to eye-toxic chemicals.

  1. Quinones and aromatic chemical compounds in particulate matter induce mitochondrial dysfunction: implications for ultrafine particle toxicity.

    Science.gov (United States)

    Xia, Tian; Korge, Paavo; Weiss, James N; Li, Ning; Venkatesen, M Indira; Sioutas, Constantinos; Nel, Andre

    2004-10-01

    Particulate pollutants cause adverse health effects through the generation of oxidative stress. A key question is whether these effects are mediated by the particles or their chemical compounds. In this article we show that aliphatic, aromatic, and polar organic compounds, fractionated from diesel exhaust particles (DEPs), exert differential toxic effects in RAW 264.7 cells. Cellular analyses showed that the quinone-enriched polar fraction was more potent than the polycyclic aromatic hydrocarbon (PAH)-enriched aromatic fraction in O2 .- generation, decrease of membrane potential (Delta-Psi m), loss of mitochondrial membrane mass, and induction of apoptosis. A major effect of the polar fraction was to promote cyclosporin A (CsA)-sensitive permeability transition pore (PTP) opening in isolated liver mitochondria. This opening effect is dependent on a direct effect on the PTP at low doses as well as on an effect on Delta-Psi m at high doses in calcium (Ca2+)-loaded mitochondria. The direct PTP effect was mimicked by redox-cycling DEP quinones. Although the aliphatic fraction failed to perturb mitochondrial function, the aromatic fraction increased the Ca2+ retention capacity at low doses and induced mitochondrial swelling and a decrease in Delta-Psi m at high doses. This swelling effect was mostly CsA insensitive and could be reproduced by a mixture of PAHs present in DEPs. These chemical effects on isolated mitochondria could be reproduced by intact DEPs as well as ambient ultrafine particles (UFPs). In contrast, commercial polystyrene nanoparticles failed to exert mitochondrial effects. These results suggest that DEP and UFP effects on the PTP and Delta-Psi m are mediated by adsorbed chemicals rather than the particles themselves.

  2. Secondary Metabolome Variability and Inducible Chemical Defenses in the Mediterranean Sponge Aplysina cavernicola.

    Science.gov (United States)

    Reverter, M; Perez, T; Ereskovsky, A V; Banaigs, B

    2016-01-01

    Secondary metabolites play a crucial role in marine invertebrate chemical ecology. Thus, it is of great importance to understand factors regulating their production and sources of variability. This work aimed to study the variability of the bromotyrosine derivatives in the Mediterranean sponge Aplysina cavernicola, and also to better understand how biotic (reproductive state) and abiotic factors (seawater temperature) could partly explain this variability. Results showed that the A. cavernicola reproductive cycle has little effect on the variability of the sponges' secondary metabolism, whereas water temperature has a significant influence on the production level of secondary metabolites. Temporal variability analysis of the sponge methanolic extracts showed that bioactivity variability was related to the presence of the minor secondary metabolite dienone, which accounted for 50 % of the bioactivity observed. Further bioassays coupled to HPLC extract fractionation confirmed that dienone was the only compound from Aplysina alkaloids to display a strong bioactivity. Both dienone production and bioactivity showed a notable increase in October 2008, after a late-summer warming episode, indicating that A. cavernicola might be able to induce chemical changes to cope with environmental stressors.

  3. Influence of physical, chemical and inducer treatments on menaquinone-7 biosynthesis by Bacillus subtilis MTCC 2756

    Directory of Open Access Journals (Sweden)

    Alka Puri

    2015-06-01

    Full Text Available Effects of physical and chemical treatment on nutrient mobility, their utilization for menaquinone-7 (MK-7 biosynthesis; growth of microbial cells has been investigated in the present research. Bacillus subtilis MTCC 2756 fermented medium was supplied with 1-naphthol and hypoxanthine resulted in a significant increase in MK-7 production. Ultrasonication, electric shock, heat shock, and tween 80 were used for inducer uptake by Bacillus subtilis and menaquinone-7 production. Induction of Bacillus subtilis (at 16 hours of fermentation using 1-naphthol (2 mg/ml, along with tween 80 (0.1% was found to increase the MK-7 production by 3 fold i.e. 14.4 µg/ml as compared to the untreated fermentation medium. The ultrasonicated (ultrasonic power 33 W, treatment time 4 min and frequency 36 KHz microbial cells yielded higher biomass and 2.5 fold increase in the MK-7 production i.e.10.3 µg/ml than control. 1-naphthol along with physical or chemical treatment is required for maximum MK-7 production by Bacillus subtilis.

  4. Network Evolution Induced by the Dynamical Rules of Two Populations

    CERN Document Server

    Platini, T

    2010-01-01

    We study the dynamical properties of a finite dynamical network composed of two interacting populations, namely; extrovert ($a$) and introvert ($b$). In our model, each group is characterized by its size ($N_a$ and $N_b$) and preferred degree ($\\kappa_a$ and $\\kappa_b\\ll\\kappa_a$). The network dynamics is governed by the competing microscopic rules of each population that consist of the creation and destruction of links. Starting from an unconnected network, we give a detailed analysis of the mean field approach which is compared to Monte Carlo simulation data. The time evolution of the restricted degrees $\\moyenne{k_{bb}}$ and $\\moyenne{k_{ab}}$ presents three time regimes and a non monotonic behavior well captured by our theory. Surprisingly, when the population size are equal $N_a=N_b$, the ratio of the restricted degree $\\theta_0=\\moyenne{k_{ab}}/\\moyenne{k_{bb}}$ appears to be an integer in the asymptotic limits of the three time regimes. For early times (defined by $t

  5. How crouch gait can dynamically induce stiff-knee gait.

    Science.gov (United States)

    van der Krogt, Marjolein M; Bregman, Daan J J; Wisse, Martijn; Doorenbosch, Caroline A M; Harlaar, Jaap; Collins, Steven H

    2010-04-01

    Children with cerebral palsy frequently experience foot dragging and tripping during walking due to a lack of adequate knee flexion in swing (stiff-knee gait). Stiff-knee gait is often accompanied by an overly flexed knee during stance (crouch gait). Studies on stiff-knee gait have mostly focused on excessive knee muscle activity during (pre)swing, but the passive dynamics of the limbs may also have an important effect. To examine the effects of a crouched posture on swing knee flexion, we developed a forward-dynamic model of human walking with a passive swing knee, capable of stable cyclic walking for a range of stance knee crouch angles. As crouch angle during stance was increased, the knee naturally flexed much less during swing, resulting in a 'stiff-knee' gait pattern and reduced foot clearance. Reduced swing knee flexion was primarily due to altered gravitational moments around the joints during initial swing. We also considered the effects of increased push-off strength and swing hip flexion torque, which both increased swing knee flexion, but the effect of crouch angle was dominant. These findings demonstrate that decreased knee flexion during swing can occur purely as the dynamical result of crouch, rather than from altered muscle function or pathoneurological control alone.

  6. Nanoscale Chemical Imaging of a Dynamic Molecular Phase Boundary with Ultrahigh Vacuum Tip-Enhanced Raman Spectroscopy.

    Science.gov (United States)

    Jiang, Nan; Chiang, Naihao; Madison, Lindsey R; Pozzi, Eric A; Wasielewski, Michael R; Seideman, Tamar; Ratner, Mark A; Hersam, Mark C; Schatz, George C; Van Duyne, Richard P

    2016-06-08

    Nanoscale chemical imaging of a dynamic molecular phase boundary has broad implications for a range of problems in catalysis, surface science, and molecular electronics. While scanning probe microscopy (SPM) is commonly used to study molecular phase boundaries, its information content can be severely compromised by surface diffusion, irregular packing, or three-dimensional adsorbate geometry. Here, we demonstrate the simultaneous chemical and structural analysis of N-N'-bis(2,6-diisopropylphenyl)-1,7-(4'-t-butylphenoxy)perylene-3,4:9,10-bis(dicarboximide) (PPDI) molecules by UHV tip-enhanced Raman spectroscopy. Both condensed and diffusing domains of PPDI coexist on Ag(100) at room temperature. Through comparison with time-dependent density functional theory simulations, we unravel the orientation of PPDI molecules at the dynamic molecular domain boundary with unprecedented ∼4 nm spatial resolution.

  7. Combination of high performance refractometry and infrared spectroscopy as a probe for chemically induced gelation and vitrification of epoxies

    OpenAIRE

    Müller, Ulrich; Philipp, Martine; Gervais, P. C.; Possart, Prof Dr Wulff; Wehlack, C.; Kieffer, J.; Sanctuary, Roland; Krüger, Jan-Kristian

    2010-01-01

    A combination of infrared spectroscopy and high performance refractometry was used to investigate the chemically induced sol-gel and glass transition during the polymerization of epoxies. Representations of the refractive index versus chemical conversion reveal an interesting insight in the optical properties accompanying gelation and vitrification. Whereas the electronic polarizability of the liquid state of small average molecular mass and the glassy state is dominated by the mass density, ...

  8. Laser-induced chemical reactions. [H + H/sub 2/; F + H/sub 2/; H + HF; Cl + H/sub 2/; H + HCl; H + LiF

    Energy Technology Data Exchange (ETDEWEB)

    Orel, A.E.

    1980-12-01

    A classical model for the interaction of laser radiation with a molecular system is derived. This model is used to study the enhancement of a chemical reaction via a collision induced absorption. It was found that an infrared laser will in general enhance the rate of a chemical reaction, even if the reactants are infrared inactive. Results for an illustrative analytically solvable model are presented, as well as results from classical trajectory studies on a number of systems. The collision induced absorption spectrum in these systems can be written as the Fourier transform of a particular dipole correlation function. This is used to obtain the collision induced absorption spectrum for a state-selected, mono-energetic reactive collision system. Examples treated are a one-dimensional barrier problem, reactive and nonreactive collisions of H + H/sub 2/, and a modified H + H/sub 2/ potential energy surface which leads to a collision intermediate. An extension of the classical model to treat laser-induced electronically nonadiabatic collision processes is constructed. The model treats all degrees of freedom, molecular, electronic and radiation, in a dynamically consistent framework within classical mechanics. Application is made to several systems. Several interesting phenomena are discovered including a Franck-Condon-like effect causing maxima in the reaction probability at energies much below the classical threshold, laser de-enhancement of chemical reactions and an isotope effect. In order to assess the validity of the classical model for electronically nonadiabatic process (without a laser field), a model problem involving energy transfer in a collinear atom-diatom system is studied, and the results compared to the available quantum mechanical calculation. The calculations are in qualitative agreement.

  9. A Coupled Dynamical Model of Redox Flow Battery Based on Chemical Reaction, Fluid Flow, and Electrical Circuit

    OpenAIRE

    Li, Minghua; Hikihara, Takashi

    2008-01-01

    The redox (Reduction-Oxidation) flow battery is one of the most promising rechargeable batteries due to its ability to average loads and output of power sources. The transient characteristics are well known as the remarkable feature of the battery. Then it can also compensate for a sudden voltage drop. The dynamics are governed by the chemical reactions, fluid flow, and electrical circuit of its structure. This causes the difficulty of the analysis at transient state. This paper discusses the...

  10. Prediction of the Chapman–Jouguet chemical equilibrium state in a detonation wave from first principles based reactive molecular dynamics

    OpenAIRE

    Guo, Dezhou; Zybin, Sergey V.; An, Qi; Goddard, William A.; Huang, Fenglei

    2016-01-01

    The combustion or detonation of reacting materials at high temperature and pressure can be characterized by the Chapman–Jouguet (CJ) state that describes the chemical equilibrium of the products at the end of the reaction zone of the detonation wave for sustained detonation. This provides the critical properties and product kinetics for input to macroscale continuum simulations of energetic materials. We propose the ReaxFF Reactive Dynamics to CJ point protocol (Rx2CJ) for predicting the CJ s...

  11. Molecular characterization of chemical mutagenesis induced diversity in elite maize germplasm

    Directory of Open Access Journals (Sweden)

    Christov Nikolai K.

    2004-01-01

    Full Text Available Three classical breeding Iowa Super Stiff Stalk (SSS inbred lines B37, B73 and B84, one Lancaster inbred Oh43 and mutant lines obtained by chemical mutagenesis followed by mutation breeding as follows: two of B37 and four of Oh43 were selected for molecular characterization. The mutant inbred lines were chosen because in addition to the improved GCA and SCA for grain yield, proven by their predominance in the Bulgarian breeding programs, they showed shifts in the flowering time as compared to the initial inbreds. Molecular markers (micro satellites and other PCR-based DNA markers were used for characterization of maize genotypes and determination of the induced by chemical mutagenesis genetic variability in maize germplasm. The tested nine SSR markers (umc 1001, umclO14, umcl057, umcll81, umcl0lS, umc 1029. umcl003, umc 1033 and umcl035 can discriminate between the initial classical breeding inbred lines and the originating mutant inbreds. Allelic diversity was also studied by PCR amplification with specifically de-signed primers in the coding regions and flanking sequence of two genes: dwarf8 (d&: chromosome 1, 198.5 cM, and indeterminate l (id1; chromosome 1. 175.0 cM. These are considered candidate genes for variation in plant height and/or flowering time, based on mutant phenotypes and chromosomal locations near major QTLs. Single nucleotide polymorphisms and indels were detected in the region flanking the SH2 domain of dwarf8 gene in some of the mutant inbreds as a result of SSCP and sequencing analyses. However, these polymorphisms could not be associated with the observed variations in flowering time. PCR analysis of the promoter region dwarf8 showed a variant fragment of about 1 kb in the inbred line Oh43 that was not present in any other initial and mutant in-bred lines included in the study. PCR amplification of the 5' end of the Id1 coding sequence revealed polymorphic bands in the mutant lines XM535, XM521, XM250-l, XM98-8 and XM85

  12. Near-field photochemical and radiation-induced chemical fabrication of nanopatterns of a self-assembled silane monolayer

    Directory of Open Access Journals (Sweden)

    Ulrich C. Fischer

    2014-09-01

    Full Text Available A general concept for parallel near-field photochemical and radiation-induced chemical processes for the fabrication of nanopatterns of a self-assembled monolayer (SAM of (3-aminopropyltriethoxysilane (APTES is explored with three different processes: 1 a near-field photochemical process by photochemical bleaching of a monomolecular layer of dye molecules chemically bound to an APTES SAM, 2 a chemical process induced by oxygen plasma etching as well as 3 a combined near-field UV-photochemical and ozone-induced chemical process, which is applied directly to an APTES SAM. All approaches employ a sandwich configuration of the surface-supported SAM, and a lithographic mask in form of gold nanostructures fabricated through colloidal sphere lithography (CL, which is either exposed to visible light, oxygen plasma or an UV–ozone atmosphere. The gold mask has the function to inhibit the photochemical reactions by highly localized near-field interactions between metal mask and SAM and to inhibit the radiation-induced chemical reactions by casting a highly localized shadow. The removal of the gold mask reveals the SAM nanopattern.

  13. Chemical and biological insights into uranium-induced apoptosis of rat hepatic cell line

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Fang; You, Yong [University of South China, College of Hunan Province, Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang (China); Du, Ke-Jie [University of South China, School of Chemistry and Chemical Engineering, Hengyang (China); Fang, Zhen [Anhui Normal University, College of Chemistry and Materials Science, Wuhu (China); Wen, Ge-Bo [University of South China, College of Hunan Province, Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang (China); University of South China, Laboratory of Protein Structure and Function, Hengyang (China); Lin, Ying-Wu [University of South China, School of Chemistry and Chemical Engineering, Hengyang (China); University of South China, Laboratory of Protein Structure and Function, Hengyang (China)

    2015-05-15

    Uranium release into the environment is a threat to human health, and the mechanisms of cytotoxicity caused by uranium are not well-understood. To improve our understanding in this respect, we herein evaluated the effects of uranium exposure on normal rat hepatic BRL cells. As revealed by scanning electron microscopy and transmission electron microscope analysis, uranyl nitrate was found to be transformed into uranyl phosphate particles in the medium and taken up by BRL cells in an endocytotic uptake manner, which presumably initiates apoptosis of the cell, although soluble uranyl ion may also be toxic. The apoptosis of BRL cells upon uranium exposure was also confirmed by both the acridine orange and ethidium bromide double staining assay and the Annexin V/propidium iodide double staining assay. Further studies revealed that uranium induced the loss of mitochondrial membrane potential in a dose-dependent manner. Moreover, the uranium-induced apoptosis was found to be associated with the activation of caspase-3, caspase-8 and caspase-9, indicating both a mitochondria-dependent signaling pathway and a death receptor pathway by a crosstalk. This study provides new chemical and biological insights into the mechanism of uranium toxicity toward hepatic cells, which will help seek approaches for biological remediation of uranium. (orig.)

  14. Dietary zinc deficiency predisposes mice to the development of preneoplastic lesions in chemically-induced hepatocarcinogenesis.

    Science.gov (United States)

    Romualdo, Guilherme Ribeiro; Goto, Renata Leme; Henrique Fernandes, Ana Angélica; Cogliati, Bruno; Barbisan, Luis Fernando

    2016-10-01

    Although there is a concomitance of zinc deficiency and high incidence/mortality for hepatocellular carcinoma in certain human populations, there are no experimental studies investigating the modifying effects of zinc on hepatocarcinogenesis. Thus, we evaluated whether dietary zinc deficiency or supplementation alter the development of hepatocellular preneoplastic lesions (PNL). Therefore, neonatal male Balb/C mice were submitted to a diethylnitrosamine/2-acetylaminefluorene-induced hepatocarcinogenesis model. Moreover, mice were fed adequate (35 mg/kg diet), deficient (3 mg/kg) or supplemented (180 mg/kg) zinc diets. Mice were euthanized at 12 (early time-point) or 24 weeks (late time-point) after introducing the diets. At the early time-point, zinc deficiency decreased Nrf2 protein expression and GSH levels while increased p65 and p53 protein expression and the number of PNL/area. At the late time-point, zinc deficiency also decreased GSH levels while increased liver genotoxicity, cell proliferation into PNL and PNL size. In contrast, zinc supplementation increased antioxidant defense at both time-points but not altered PNL development. Our findings are the first to suggest that zinc deficiency predisposes mice to the PNL development in chemically-induced hepatocarcinogenesis. The decrease of Nrf2/GSH pathway and increase of liver genotoxicity, as well as the increase of p65/cell proliferation, are potential mechanisms to this zinc deficiency-mediated effect.

  15. Insights from advances in research of chemically induced experimental models of human inflammatory bowel disease

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Inflammatory bowel disease (IBD), the most important being Crohn's disease and ulcerative colitis, results from chronic dysregulation of the mucosal immune system in the gastrointestinal tract. Although the pathogenesis of IBD remains unclear, it is widely accepted that genetic, environmental, and immunological factors are involved. Recent studies suggest that intestinal epithelial defenses are important to prevent inflammation by protecting against microbial pathogens and oxidative stresses. To investigate the etiology of IBD, animal models of experimental colitis have been developed and are frequently used to evaluate new anti-inflammatory treatments for IBD. Several models of experimental colitis that demonstrate various pathophysiological aspects of the human disease have been described. In this manuscript, we review the characteristic features of IBD through a discussion of the various chemically induced experimental models of colitis (e.g. dextran sodium sulfate-, 2,4,6-trinitrobenzene sulfonic acid-, oxazolone-, acetic acid-, and indomethacin-induced models). We also summarize some regulatory and pathogenic factors demonstrated by these models that can, hopefully, be exploited to develop future therapeutic strategies against IBD.

  16. Identification of Differently Expressed Genes in Chemical Carcinogen-induced Rat Bladder Cancers

    Institute of Scientific and Technical Information of China (English)

    Guangfu CHEN; Franky L. CHAN; Xu ZHANG; Peter S.F. CHAN

    2009-01-01

    Possible altered gene expression patterns in bladder turnout carcinogenesis in rat bladder cancers induced by BBN [N-butyl-N-(4-hydroxybutyl)nitrosamine] was examined by cDNA microarray analysis of gene expression profiles.Thirty Sprague-Dawley rats were given drinking water containing 0.05% BBN ad libitum for 24 to 28-weeks.Equal numbers of control rats were given tap water without BBN.After treatment,the rat bladders were excised for RNA extraction and histopathological examinations.Total RNAs were extracted from rat transitional cell carcinoma (TCC) tissues and micro-dissected normal rat bladder epithelia.The atlas glass rat microarray was used,which included oligonucleotides of 1081 rat genes.Some of the up-regulated genes in rat bladder TCCs were further confirmed by Northern blotting.Our results showed that the transcriptions of 30 genes were significantly elevated in the rat bladder TCCs,and these included fly proto-oncogene,Lipocortin 2,COX Ⅳ,COX Ⅴ a,and cathepsin D.Also,15 genes were significantly down-regulated in the rat bladder TCCs and they included B7.1,TNFrl,APOAI and VHL.The resuits of cDNA microarray analysis demonstrated that normal rat bladder epithelia and bladder TCC exhibited different and specific gene statement profiles.The increased expressions of the identified genes may play an important role in the chemically induced bladder carcinogenesis.

  17. Femtosecond laser pulse induced desorption: A molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Lončarić, Ivor, E-mail: ivor.loncaric@gmail.com [Centro de Física de Materiales CFM/MPC (CSIC-UPV/EHU), P. Manuel de Lardizabal 5, 20018 San Sebastián (Spain); Alducin, Maite [Centro de Física de Materiales CFM/MPC (CSIC-UPV/EHU), P. Manuel de Lardizabal 5, 20018 San Sebastián (Spain); Donostia International Physics Center DIPC, P. Manuel de Lardizabal 4, 20018 San Sebastián (Spain); Saalfrank, Peter [Institut für Chemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, D-14476 Potsdam (Germany); Donostia International Physics Center DIPC, P. Manuel de Lardizabal 4, 20018 San Sebastián (Spain); Juaristi, J. Iñaki [Departamento de Física de Materiales, Facultad de Químicas, Universidad del País Vasco (UPV/EHU), Apartado 1072, 20080 San Sebastián (Spain); Centro de Física de Materiales CFM/MPC (CSIC-UPV/EHU), P. Manuel de Lardizabal 5, 20018 San Sebastián (Spain); Donostia International Physics Center DIPC, P. Manuel de Lardizabal 4, 20018 San Sebastián (Spain)

    2016-09-01

    In recent simulations of femtosecond laser induced desorption of molecular oxygen from the Ag(110) surface, it has been shown that depending on the properties (depth and electronic environment) of the well in which O{sub 2} is adsorbed, the desorption can be either induced dominantly by hot electrons or via excitations of phonons. In this work we explore whether the ratios between the desorption yields from different adsorption wells can be tuned by changing initial surface temperature and laser pulse properties. We show that the initial surface temperature is an important parameter, and that by using low initial surface temperatures the electronically mediated process can be favored. In contrast, laser properties seem to have only a modest influence on the results.

  18. Dynamic aerobic exercise induces baroreflex improvement in diabetic rats.

    Science.gov (United States)

    Jorge, Luciana; da Pureza, Demilto Y; da Silva Dias, Danielle; Conti, Filipe Fernandes; Irigoyen, Maria-Cláudia; De Angelis, Kátia

    2012-01-01

    The objective of the present study was to investigate the effects of an acute aerobic exercise on arterial pressure (AP), heart rate (HR), and baroreflex sensitivity (BRS) in STZ-induced diabetic rats. Male Wistar rats were divided into control (n = 8) and diabetic (n = 8) groups. AP, HR, and BRS, which were measured by tachycardic and bradycardic (BR) responses to AP changes, were evaluated at rest (R) and postexercise session (PE) on a treadmill. At rest, STZ diabetes induced AP and HR reductions, associated with BR impairment. Attenuation in resting diabetes-induced AP (R: 103 ± 2 versus PE: 111 ± 3 mmHg) and HR (R: 290 ± 7 versus PE: 328 ± 10 bpm) reductions and BR dysfunction (R: -0.70 ± 0.06 versus PE: -1.21 ± 0.09 bpm/mmHg) was observed in the postexercise period. In conclusion, the hemodynamic and arterial baro-mediated control of circulation improvement in the postexercise period reinforces the role of exercise in the management of cardiovascular risk in diabetes.

  19. Quantum-Gravity Induced Lorentz Violation and Dynamical Mass Generation

    OpenAIRE

    Mavromatos, Nick E.

    2010-01-01

    In Ref. [1] (by J. Alexandre) a minimal extension of (3+1)-dimensional Quantum Electrodynamics has been proposed, which includes Lorentz-Violation (LV) in the form of higher-(spatial)-derivative isotropic terms in the gauge sector, suppressed by a mass scale $M$. The model can lead to dynamical mass generation for charged fermions. In this article I elaborate further on this idea and I attempt to connect it to specific quantum-gravity models, inspired from string/brane theory. Specifically, i...

  20. Theoretical study of ultraviolet induced photodissociation dynamics of sulfuric acid

    Energy Technology Data Exchange (ETDEWEB)

    Murakami, Tatsuhiro; Ohta, Ayumi; Suzuki, Tomoya; Ikeda, Kumiko [Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-Cho, Chiyoda-ku, Tokyo 102-8554 (Japan); Danielache, Sebastian O. [Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-Cho, Chiyoda-ku, Tokyo 102-8554 (Japan); Earth-Life Science Institute (ELSI), Tokyo Institute of Technology (Japan); Department of Environmental Science and Techonology, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Yoohama 226-8502 (Japan); Nanbu, Shinkoh, E-mail: shinkoh.nanbu@sophia.ac.jp [Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-Cho, Chiyoda-ku, Tokyo 102-8554 (Japan)

    2015-05-01

    Highlights: • Photodissociation dynamics of H{sub 2}SO{sub 4} at low-lying electronically excited states were investigated. • Photochemical processes were simulated by on-the-fly ab initio MD. • Sulfuric acid after the excitation to the S{sub 1} state dissociated to HSO{sub 4}(1{sup 2}A″) + H({sup 2}S). • Sulfuric acid after the excitation to the S{sub 2} state dissociated to HSO{sub 4}(2{sup 2}A″) + H({sup 2}S). • The energy region of the UV spectra where NMD fractionation may occur is predicted. - Abstract: Photodissociation dynamics of sulfuric acid after excitation to the first and second excited states (S{sub 1} and S{sub 2}) were studied by an on-the-fly ab initio molecular dynamics simulations based on the Zhu–Nakamura version of the trajectory surface hopping (ZN-TSH). Forces acting on the nuclear motion were computed on-the-fly by CASSCF method with Dunning’s augmented cc-pVDZ basis set. It was newly found that the parent molecule dissociated into two reaction-channels (i) HSO{sub 4}(1{sup 2}A″) + H({sup 2}S) by S{sub 1}-excitation, and (ii) HSO{sub 4}(2{sup 2}A″) + H({sup 2}S) by S{sub 2}-excitation. The direct dissociation dynamics yield products different from the SO{sub 2} + 2OH fragments often presented in the literature. Both channels result in the same product and differs only in the electronic state of the HSO{sub 4} fragment{sub .} The trajectories running on S{sub 2} do not hop with S{sub 0} and a nonadiabatic transition happens at the S{sub 2}–S{sub 1} conical intersection located at a longer OH bond-length than the S{sub 1}–S{sub 0} intersection producing an electronic excited state (2{sup 2}A″) of HSO{sub 4} product.

  1. Tension-induced vesicle fusion: pathways and pore dynamics

    DEFF Research Database (Denmark)

    Shillcock, Julian C.

    2008-01-01

    and eventually opens a pore to complete the fusion process. In pathway II, at higher tension, a stalk is formed during the fusion process that is then transformed by transmembrane pore formation into a fusion pore. Whereas the latter pathway II resembles stalk pathways as observed in other simulation studies...... fusion time on membrane tension implies that the fusion process is completed by overcoming two energy barriers with scales of 13kBT and 11kBT. The fusion pore radius as a function of time has also been extracted from the simulations, and provides a quantitative measure of the fusion dynamics which...

  2. Unpredictability induced by unfocused games in evolutionary game dynamics.

    Science.gov (United States)

    Hashimoto, Koh

    2006-08-07

    Evolutionary game theory is a basis of replicator systems and has applications ranging from animal behavior and human language to ecosystems and other hierarchical network systems. Most studies in evolutionary game dynamics have focused on a single game, but, in many situations, we see that many games are played simultaneously. We construct a replicator equation with plural games by assuming that a reward of a player is a simple summation of the reward of each game. Even if the numbers of the strategies of the games are different, its dynamics can be described in one replicator equation. We here show that when players play several games at the same time, the fate of a single game cannot be determined without knowing the structures of the whole other games. The most absorbing fact is that even if a single game has a ESS (evolutionary stable strategy), the relative frequencies of strategies in the game does not always converge to the ESS point when other games are played simultaneously.

  3. Dynamic effects induced transition of droplets on biomimetic superhydrophobic surfaces.

    Science.gov (United States)

    Jung, Yong Chae; Bhushan, Bharat

    2009-08-18

    Superhydrophobic surfaces have considerable technological potential for various applications because of their extreme water-repellent properties. Dynamic effects, such as the bouncing and vibration of a droplet, can destroy the composite solid-air-liquid interface. The impact pressure of a bouncing droplet and the inertia force of a vibrating droplet affect the transition from a solid-air-liquid interface to a solid-liquid interface. Therefore, it is necessary to study the dynamic effect of droplets under various system parameters (impact velocity and frequency and amplitude of vibration). A new model for the prediction of the wetting and dewetting process during droplet vibration based on the relationship between the adhesion force and the inertia force of a droplet is proposed. To investigate whether micro-, nano-, and hierarchical structures can resist the destabilizing factors responsible for the transition, a study of bouncing and vibration of a water droplet is systematically conducted on various surfaces. The physics of wetting phenomena for water droplet studies is of fundamental importance in the geometrical design of superhydrophobic surfaces.

  4. The Influence of Seasonal Changes and Headwaters on Physico-chemical Dynamics of Temengor Reservoir, Malaysia%The Influence of Seasonal Changes and Headwaters on Physico-chemical Dynamics of Temengor Reservoir,Malaysia

    Institute of Scientific and Technical Information of China (English)

    Zarul Hazrin Hashim; Asmah Patiroi; Mashhor Mansor; Shahml Anuar Md. Sah; Donald C. Jackson

    2011-01-01

    A study on physico-chemical dynamics of Temengor Reservoir was conducted to determine whether headwaters and seasonal changes play a major role in regulating physico-chemical dynamics of Temengor Reservoir.Temengor Reservoir receives water from its surrounding water catchments and headwaters.Then,the water flows into a series of hydroelectric dams,namely the Bersia,Kenering and Chenderoh dams.Generally,water quality in Temengot Reservoir can be classified as Class I.Physico-chemical trends showed that water quality in euphoric zone of Temengor Reservoir is stable and consistent.Two-way ANOVA analyses showed that seasonal variations only affected water temperature,Secchi disc's depth and nitrate-nitrogen.Based on Tukey' s post-hoc test,all three headwaters in this study exert no influence to the reservoir's water quality.These insignificant differences were probably due to water temperature and the size of the headwaters and the reservoir itself.In situ parameters profiling showed that the epilirrmion zone in Temengor Reservoir is from the surface to 6 m depth,the metalirrmion zone is from 6 m to 12 m depth and the hypolimnion zone is from 12 m depth onwards to the bottom of the reservoir.Thus,continuous water profiling monitoring that covers high and low water levels need to be conducted to determine characteristics of the physico-chemical dynamics in the water column and also to analyse changes in reservoir layers.Through these studies,discontinuity trends in the Perak River could be determined and suggestions to the respective agencies could be made to conserve and to sustain downstream biodiversity.

  5. Nonlinear magnetization dynamics of antiferromagnetic spin resonance induced by intense terahertz magnetic field

    CERN Document Server

    Mukai, Y; Yamamoto, T; Kageyama, H; Tanaka, K

    2016-01-01

    We report on the nonlinear magnetization dynamics of a HoFeO3 crystal induced by a strong terahertz magnetic field resonantly enhanced with a split ring resonator and measured with magneto-optical Kerr effect microscopy. The terahertz magnetic field induces a large change (~40%) in the spontaneous magnetization. The frequency of the antiferromagnetic resonance decreases in proportion to the square of the magnetization change. A modified Landau-Lifshitz-Gilbert equation with a phenomenological nonlinear damping term quantitatively reproduced the nonlinear dynamics.

  6. The multiscale simulation of metal organic chemical vapor deposition growth dynamics of GaInP thin film

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    As a Group III–V compound, GaInP is a high-efficiency luminous material. Metal organic chemical vapor deposition (MOCVD) technology is a very efficient way to uniformly grow multi-chip, multilayer and large-area thin film. By combining the computational fluid dynamics (CFD) and the kinetic Monte Carlo (KMC) methods with virtual reality (VR) technology, this paper presents a multiscale simulation of fluid dynamics, thermodynamics, and molecular dynamics to study the growth process of GaInP thin film in a vertical MOCVD reactor. The results of visualization truly and intuitively not only display the distributional properties of the gas’ thermal and flow fields in a MOCVD reactor but also display the process of GaInP thin film growth in a MOCVD reactor. The simulation thus provides us with a fundamental guideline for optimizing GaInP MOCVD growth.

  7. Ultrafast infrared studies of chemical reaction dynamics in room-temperature liquids

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Haw [Univ. of California, Berkeley, CA (United States)

    1999-11-01

    Femtosecond infrared spectroscopy provides sufficient spectral and temporal resolution to support a detailed investigation of the early events of a photochemical reaction. Previously unreported transient species that arise as intermediates during the course of a reaction may have lifetimes that are too short for conventional characterization. For these species, quantum-mechanical (density functional theoretical and ab initio) electronic structure calculations provide invaluable insight into chemical properties including molecular structure and energetic. With the combination of experimental and theoretical results, it is possible to assemble a comprehensive picture of the reaction dynamics of a system that is intricately influenced by the surrounding solvent molecules. The mechanisms of several important organometallic reactions, such as alkane C– H bond activation by η3-Tp*Rh(CO), silane Si–H bond activation by η5-CpMn(CO)2 and η5-CpRe(CO)2, as well as chlorinated methane C–Cl bond cleavage by the Re(CO)5 radical are elucidated. The results demonstrate the importance of molecular morphology change (C–H and Si–H act ivat ion), solvent rearrangement (Si–H activation), intersystem crossing (Si–H activation), and solvent caging (C–Cl cleavage) in understanding the reactivity of the organometallic species, The nature of the apparent free-energy barrier for C–H, Si–H, and C–Cl bond activation reaction is found to be- cleavage of an alkane C–H bond, rearrangement of a silane molecule HSiR3 (R = alkyl group) from a nonreactive alkyl site to the reactive Si–H bond, and Cl atom transfer from a chlorinated methane molecule to Re(CO)5, respectively. These results support previous d initio calculations for C–H and Si–H bond activation reaction profiles which suggest that cleavage of an alkane C–H bond by a transition metal center, unlike that of a silane

  8. Microbial dynamics during and after in situ chemical oxidation of chlorinated solvents

    NARCIS (Netherlands)

    Sutton, N.B.; Atashgahi, S.; Wal, van der J.; Wijn, G.; Grotenhuis, J.T.C.; Smidt, H.; Rijnaarts, H.

    2015-01-01

    In situ chemical oxidation (ISCO) followed by a bioremediation step is increasingly being considered as an effective biphasic technology. Information on the impact of chemical oxidants on organohalide respiring bacteria (OHRB), however, is largely lacking. Therefore, we used quantitative PCR (qPCR)

  9. Noise-induced temporal dynamics in Turing systems

    KAUST Repository

    Schumacher, Linus J.

    2013-04-25

    We examine the ability of intrinsic noise to produce complex temporal dynamics in Turing pattern formation systems, with particular emphasis on the Schnakenberg kinetics. Using power spectral methods, we characterize the behavior of the system using stochastic simulations at a wide range of points in parameter space and compare with analytical approximations. Specifically, we investigate whether polarity switching of stochastic patterns occurs at a defined frequency. We find that it can do so in individual realizations of a stochastic simulation, but that the frequency is not defined consistently across realizations in our samples of parameter space. Further, we examine the effect of noise on deterministically predicted traveling waves and find them increased in amplitude and decreased in speed. © 2013 American Physical Society.

  10. Dynamical architectures of planetary systems induced by orbital migration

    CERN Document Server

    Szuszkiewicz, Ewa

    2009-01-01

    The aim of this talk is to present the most recent advances in establishing plausible planetary system architectures determined by the gravitational tidal interactions between the planets and the disc in which they are embedded during the early epoch of planetary system formation. We concentrate on a very well defined and intensively studied process of the disc-planet interaction leading to the planet migration. We focus on the dynamics of the systems in which low-mass planets are present. Particular attention is devoted to investigation of the role of resonant configurations. Our studies, apart from being complementary to the fast progress occurring just now in observing the whole variety of planetary systems and uncovering their structure and origin, can also constitute a valuable contribution in support of the missions planned to enhance the number of detected multiple systems.

  11. Shock induced chemistry in liquids studied with ultrafast dynamic ellipsometry and visible transient absorption spectroscopy.

    Science.gov (United States)

    Dang, N C; Bolme, C A; Moore, D S; McGrane, S D

    2012-10-25

    The response to ultrafast laser shock loading of nine liquids was monitored in an effort to reveal evidence of chemical changes occurring during the first 350 ps following the shock front. In an effort to compare molecular structures possessing a variety of common bonding patterns, data were acquired for the liquids: cyclohexane, cyclohexene, 1,3-cyclohexadiene, benzene, water, acetonitrile, acrylonitrile, tert-butylacetylene, and phenylacetylene. Transient absorption spectra were measured in the spectral region from 440 to 780 nm over shock stress states from 7 to 20 GPa. Ultrafast dynamic ellipsometry was used to measure the shock and particle velocity as well as the shocked refractive index. Significant transient absorption attributed to chemical reaction was observed for shocked phenylacetylene and acrylonitrile. Evidence of volume decreasing chemical reactions was also observed in the ultrafast dynamic ellipsometry data for phenylacetylene and acrylonitrile. The liquid 1,3-cyclohexadiene exhibited volume decreasing reaction in the ultrafast dynamic ellipsometry data but did not exhibit an increase in the transient absorption spectra. There was no evidence of chemical reaction in cyclohexane, cyclohexene, benzene, water, acetonitrile, or tert-butylacetylene in the first 350 ps, despite the application of shock stress that was in many cases well above the reaction threshold observed at microsecond time scales.

  12. Brain activity correlates with emotional perception induced by dynamic avatars.

    Science.gov (United States)

    Goldberg, Hagar; Christensen, Andrea; Flash, Tamar; Giese, Martin A; Malach, Rafael

    2015-11-15

    An accurate judgment of the emotional state of others is a prerequisite for successful social interaction and hence survival. Thus, it is not surprising that we are highly skilled at recognizing the emotions of others. Here we aimed to examine the neuronal correlates of emotion recognition from gait. To this end we created highly controlled dynamic body-movement stimuli based on real human motion-capture data (Roether et al., 2009). These animated avatars displayed gait in four emotional (happy, angry, fearful, and sad) and speed-matched neutral styles. For each emotional gait and its equivalent neutral gait, avatars were displayed at five morphing levels between the two. Subjects underwent fMRI scanning while classifying the emotions and the emotional intensity levels expressed by the avatars. Our results revealed robust brain selectivity to emotional compared to neutral gait stimuli in brain regions which are involved in emotion and biological motion processing, such as the extrastriate body area (EBA), fusiform body area (FBA), superior temporal sulcus (STS), and the amygdala (AMG). Brain activity in the amygdala reflected emotional awareness: for visually identical stimuli it showed amplified stronger response when the stimulus was perceived as emotional. Notably, in avatars gradually morphed along an emotional expression axis there was a parametric correlation between amygdala activity and emotional intensity. This study extends the mapping of emotional decoding in the human brain to the domain of highly controlled dynamic biological motion. Our results highlight an extensive level of brain processing of emotional information related to body language, which relies mostly on body kinematics.

  13. Cellular proton dynamics in Elodea canadensis leaves induced by cadmium.

    Science.gov (United States)

    Tariq Javed, M; Lindberg, Sylvia; Greger, Maria

    2014-04-01

    Our earlier investigations showed that Elodea canadensis shoots, grown in the presence of cadmium (Cd), caused basification of the surrounding medium. The present study was aimed to examine the proton dynamics of the apoplastic, cytosolic and vacuolar regions of E. canadensis leaves upon Cd exposure and to establish possible linkage between cellular pH changes and the medium basification. The changes in cytosolic calcium [Ca(2+)]cyt was also investigated as the [Ca(2+)]cyt and [pH]cyt homeostasis are closely linked. The cellular H(+) and Ca(2+) concentrations were monitored by fluorescence microscopy and ion-specific fluorescent dyes. Cadmium concentration of leaf-cell walls was measured after plant cultivation at different fixed levels of starting pH. The protoplasts from E. canadensis leaves were isolated by use of a newly developed enzymatic method. Upon Cd addition, both cytosolic and vacuolar pH of leaf protoplasts increased with a concomitant rise in the cytosolic Ca(2+) concentration. Time course studies revealed that changes in [Ca(2+)]cyt and [pH]cyt followed similar dynamics. Cadmium (0.5 μM) exposure decreased the apoplastic pH by 0.85 units. The maximum cell wall bound Cd-contents were obtained in plants grown at low starting pH. It is concluded that Cd treatment causes apoplastic acidosis in E. canadensis leaves associated with enhanced Cd binding to the cell walls and, consequently, reduced Cd influx into the cytosol.

  14. Laser Induced C60 Cage Opening Studied by Semiclassical Dynamics Simulation

    Directory of Open Access Journals (Sweden)

    Yusheng Dou

    2011-01-01

    Full Text Available Laser induced opening of the C60 cage is studied by a semiclassical electron-radiation-ion dynamics technique. The simulation results indicate that the C60 cage is abruptly opened immediately after laser excitation. The opening of the C60 cage induces a quick increase in kinetic energy and a sharp decrease in electronic energy, suggesting that the breaking of the C60 cage efficiently heats up the cluster and enhances the thermal fragmentation of C60 fullerene.

  15. From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors

    OpenAIRE

    Ana Zafra Ruano; Elisa Cilia; Couceiro, José R.; Javier Ruiz Sanz; Joost Schymkowitz; Frederic Rousseau; Irene Luque; Tom Lenaerts

    2016-01-01

    Src Homology 3 domains are ubiquitous small interaction modules known to act as docking sites and regulatory elements in a wide range of proteins. Prior experimental NMR work on the SH3 domain of Src showed that ligand binding induces long-range dynamic changes consistent with an induced fit mechanism. The identification of the residues that participate in this mechanism produces a chart that allows for the exploration of the regulatory role of such domains in the activity of the encompassing...

  16. Crystallization-induced dynamic resolution R-epimer from 25-OCH3-PPD epimeric mixture.

    Science.gov (United States)

    Zhang, Sainan; Tang, Yun; Cao, Jiaqing; Zhao, Chen; Zhao, Yuqing

    2015-11-15

    25-OCH3-PPD is a promising antitumor dammarane sapogenin isolated from the total saponin-hydrolyzed extract of Panax ginseng berry and Panax notoginseng leaves. 20(R)-25-OCH3-PPD was more potent as an anti-cancer agent than 20(S)-25-OCH3-PPD and epimeric mixture of 25-OCH3-PPD. This paper describes the rapid separation process of the R-epimer of 25-OCH3-PPD from its epimeric mixture by crystallization-induced dynamic resolution (CIDR). The optimized CIDR process was based on single factor analysis and nine well-planned orthogonal design experiments (OA9 matrix). A rapid and sensitive reverse phase high-performance liquid chromatographic (HPLC) method with evaporative light-scattering detector (ELSD) was developed and validated for the quantitation of 25-OCH3-PPD epimeric mixture and crystalline product. Separation and quantitation were achieved with a silica column using a mobile phase consisting of methanol and water (87:13, v/v) at a flow rate of 1.0mL/min. The ELSD detection was performed at 50°C and 3L/min. Under conditions involving 3mL of 95% ethanol, 8% HCl, and a hermetically sealed environment for 72h, the maximum production of 25(R)-OCH3-PPD was achieved with a chemical purity of 97% and a total yield of 87% through the CIDR process. The 25(R)-OCH3-PPD was nearly completely separated from the 220mg 25-OCH3-PPD epimeric mixture. Overall, a simple and steady small-batch purification process for the large-scale production of 25(R)-OCH3-PPD from 25-OCH3-PPD epimeric mixture was developed.

  17. Pulse and quench induced dynamical phase transition in a chiral multiferroic spin chain

    Science.gov (United States)

    Azimi, M.; Sekania, M.; Mishra, S. K.; Chotorlishvili, L.; Toklikishvili, Z.; Berakdar, J.

    2016-08-01

    Quantum dynamics of magnetic order in a chiral multiferroic chain is studied. We consider two different scenarios: ultrashort terahertz excitations or a sudden electric field quench. Performing analytical and numerical exact diagonalization calculations, we trace the pulse induced spin dynamics and extract quantities that are relevant to quantum information processing. In particular, we analyze the dynamics of the system chirality, the von Neumann entropy, and the pairwise and many-body entanglement. If the characteristic frequencies of the generated states are noncommensurate, then a partial loss of pair concurrence occurs. Increasing the system size, this effect becomes even more pronounced. Many-particle entanglement and chirality are robust and persist in the incommensurate phase. To analyze the dynamical quantum transitions for the quenched and pulsed dynamics we combined the Weierstrass factorization technique for entire functions and the Lanczos exact diagonalization method. For a small system we obtained analytical results including the rate function of the Loschmidt echo. Exact numerical calculations for a system up to 40 spins confirm phase transition. Quench-induced dynamical transitions have been extensively studied recently. Here we show that related dynamical transitions can be achieved and controlled by appropriate electric field pulses.

  18. Dynamics of chemical vapor sensing with MoS2 using 1T/2H phase contacts/channel

    Science.gov (United States)

    Friedman, Adam L.; Perkins, F. Keith; Hanbicki, Aubrey T.; Culbertson, James C.; Campbell, Paul M.

    2016-06-01

    Ultra-thin transition metal dichalcogenides (TMDs) films show remarkable potential for use in chemical vapor sensing devices. Electronic devices fabricated from TMD films are inexpensive, inherently flexible, low-power, amenable to industrial-scale processing because of emergent growth techniques, and have shown high sensitivity and selectivity to electron donor analyte molecules important for explosives and nerve gas detection. However, for devices reported to date, the conductance response to chemical vapors is dominated by Schottky contacts, to the detriment of the sensitivity, selectivity, recovery, and obscuring their intrinsic behavior. Here, we use contact engineering to transition the contacts in a MoS2 FET-based chemical vapor sensor to the 1T conducting phase, while leaving the channel in the 2H semiconducting state, and thus providing Ohmic contacts to the film. We demonstrate that the resultant sensors have much improved electrical characteristics, are more selective, and recover fully after chemical vapor exposure--all major enhancements to previously MoS2 sensor devices. We identify labile nitrogen-containing electron donors as the primary species that generate a response in MoS2, and we study the dynamics of the sensing reactions, identifying two possible qualitative models for the chemical sensing reaction.

  19. Local chemical reaction of benzene on Cu110 via STM-induced excitation.

    Science.gov (United States)

    Komeda, T; Kim, Y; Fujita, Y; Sainoo, Y; Kawai, Maki

    2004-03-15

    We have investigated the mechanism of the chemical reaction of the benzene molecule adsorbed on Cu(110) surface induced by the injection of tunneling electrons using scanning tunneling microscopy (STM). With the dosing of tunneling electrons of the energy 2-5 eV from the STM tip to the molecule, we have detected the increase of the height of the benzene molecule by 40% in the STM image and the appearance of the vibration feature of the nu(C-H) mode in the inelastic tunneling spectroscopy (IETS) spectrum. It can be understood with a model in which the dissociation of C-H bonds occurs in a benzene molecule that induces a bonding geometry change from flat-lying to up-right configuration, which follows the story of the report of Lauhon and Ho on the STM-induced change of benzene on the Cu(100) surface. [L. J. Lauhon and W. Ho, J. Phys. Chem. A 104, 2463 (2000)]. The reaction probability shows a sharp rise at the sample bias voltage at 2.4 V, which saturates at 3.0 V, which is followed by another sharp rise at the voltage of 4.3 V. No increase of the reaction yield is observed for the negative sample voltage up to 5 eV. In the case of a fully deuterated benzene molecule, it shows the onset at the same energy of 2.4 eV, but the reaction probability is 10(3) smaller than the case of the normal benzene molecule. We propose a model in which the dehydrogenation of the benzene molecule is induced by the formation of the temporal negative ion due to the trapping of the electrons at the unoccupied resonant states formed by the pi orbitals. The existence of the resonant level close to the Fermi level ( approximately 2.4 eV) and multiple levels in less than approximately 5 eV from the Fermi level, indicates a fairly strong interaction of the Cu-pi(*) state of the benzene molecule. We estimated that the large isotope effect of approximately 10(3) can be accounted for with the Menzel-Gomer-Redhead (MGR) model with an assumption of a shallow potential curve for the excited state. (c

  20. Apoptosis is an early event during phthalocyanine photodynamic therapy-induced ablation of chemically induced squamous papillomas in mouse skin.

    Science.gov (United States)

    Agarwal, R; Korman, N J; Mohan, R R; Feyes, D K; Jawed, S; Zaim, M T; Mukhtar, H

    1996-04-01

    Photodynamic therapy (PDT) is a promising new modality to treat malignant neoplasms including superficial skin cancers. In our search for an ideal photosensitizer for PDT, Pc 4, a silicon phthalocyanine, has shown promising results both in in vitro assays and in implanted tumors. In this study we assessed the efficacy of Pc 4 PDT in the ablation of murine skin tumors; and the evidence for apoptosis during tumor ablation was also obtained. The Pc 4 was administered through tail vein injection to SENCAR mice bearing chemically induced squamous papillomas, and 24 h later the lesions were illuminated with an argon ion-pumped dye laser tuned at 675 nm for a total light dose of 135 J/cm2. Within 72-96 h, almost complete tumor shrinkage occurred; no tumor regrowth was observed up to 90 days post-PDT. As evident by nucleosome-size DNA fragmentation, appearance of apoptotic bodies in hematoxylin and eosin staining and direct immunoperoxidase detection of digoxigenin-labeled genomic DNA in sections, apoptosis was clearly evident 6 h post-PDT at which time tumor shrinkage was less than 30%. The apoptotic bodies, as evident by the condensation of chromatin material around the periphery of the nucleus and increased vacuolization of the cytoplasm, were also observed in electron microscopic studies of the tumor tissues following Pc 4 PDT. The extent of apoptosis was greater at 15 h than at 6 and 10 h post-PDT. Taken together, our results clearly show that Pc 4 may be an effective photosensitizer for PDT of nonmelanoma skin cancer, and that apoptosis is an early event during this process.

  1. Epigenetic alterations induced by genotoxic occupational and environmental human chemical carcinogens: A systematic literature review.

    Science.gov (United States)

    Chappell, Grace; Pogribny, Igor P; Guyton, Kathryn Z; Rusyn, Ivan

    2016-01-01

    Accumulating evidence suggests that epigenetic alterations play an important role in chemically-induced carcinogenesis. Although the epigenome and genome may be equally important in carcinogenicity, the genotoxicity of chemical agents and exposure-related transcriptomic responses have been more thoroughly studied and characterized. To better understand the evidence for epigenetic alterations of human carcinogens, and the potential association with genotoxic endpoints, we conducted a systematic review of published studies of genotoxic carcinogens that reported epigenetic endpoints. Specifically, we searched for publications reporting epigenetic effects for the 28 agents and occupations included in Monograph Volume 100F of the International Agency for the Research on Cancer (IARC) that were classified as "carcinogenic to humans" (Group 1) with strong evidence of genotoxic mechanisms of carcinogenesis. We identified a total of 158 studies that evaluated epigenetic alterations for 12 of these 28 carcinogenic agents and occupations (1,3-butadiene, 4-aminobiphenyl, aflatoxins, benzene, benzidine, benzo[a]pyrene, coke production, formaldehyde, occupational exposure as a painter, sulfur mustard, and vinyl chloride). Aberrant DNA methylation was most commonly studied, followed by altered expression of non-coding RNAs and histone changes (totaling 85, 59 and 25 studies, respectively). For 3 carcinogens (aflatoxins, benzene and benzo[a]pyrene), 10 or more studies reported epigenetic effects. However, epigenetic studies were sparse for the remaining 9 carcinogens; for 4 agents, only 1 or 2 published reports were identified. While further research is needed to better identify carcinogenesis-associated epigenetic perturbations for many potential carcinogens, published reports on specific epigenetic endpoints can be systematically identified and increasingly incorporated in cancer hazard assessments. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Load and Time Dependence of Interfacial Chemical Bond-Induced Friction at the Nanoscale

    Science.gov (United States)

    Tian, Kaiwen; Gosvami, Nitya N.; Goldsby, David L.; Liu, Yun; Szlufarska, Izabela; Carpick, Robert W.

    2017-02-01

    Rate and state friction (RSF) laws are widely used empirical relationships that describe the macroscale frictional behavior of a broad range of materials, including rocks found in the seismogenic zone of Earth's crust. A fundamental aspect of the RSF laws is frictional "aging," where friction increases with the time of stationary contact due to asperity creep and/or interfacial strengthening. Recent atomic force microscope (AFM) experiments and simulations found that nanoscale silica contacts exhibit aging due to the progressive formation of interfacial chemical bonds. The role of normal load (and, thus, normal stress) on this interfacial chemical bond-induced (ICBI) friction is predicted to be significant but has not been examined experimentally. Here, we show using AFM that, for nanoscale ICBI friction of silica-silica interfaces, aging (the difference between the maximum static friction and the kinetic friction) increases approximately linearly with the product of the normal load and the log of the hold time. This behavior is attributed to the approximately linear dependence of the contact area on the load in the positive load regime before significant wear occurs, as inferred from sliding friction measurements. This implies that the average pressure, and thus the average bond formation rate, is load independent within the accessible load range. We also consider a more accurate nonlinear model for the contact area, from which we extract the activation volume and the average stress-free energy barrier to the aging process. Our work provides an approach for studying the load and time dependence of contact aging at the nanoscale and further establishes RSF laws for nanoscale asperity contacts.

  3. Earth's Inner Core dynamics induced by the Lorentz force

    CERN Document Server

    Lasbleis, M; Cardin, P; Labrosse, S

    2015-01-01

    Seismic studies indicate that the Earth's inner core has a complex structure and exhibits a strong elastic anisotropy with a cylindrical symmetry. Among the various models which have been proposed to explain this anisotropy, one class of models considers the effect of the Lorentz force associated with the magnetic field diffused within the inner core. In this paper we extend previous studies and use analytical calculations and numerical simulations to predict the geometry and strength of the flow induced by the poloidal component of the Lorentz force in a neutrally or stably stratified growing inner core, exploring also the effect of different types of boundary conditions at the inner core boundary (ICB). Unlike previous studies, we show that the boundary condition that is most likely to produce a significant deformation and seismic anisotropy is impermeable, with negligible radial flow through the boundary. Exact analytical solutions are found in the case of a negligible effect of buoyancy forces in the inne...

  4. Chemical stress induced by heliotrope (Heliotropium europaeum L.) allelochemicals and increased activity of antioxidant enzymes.

    Science.gov (United States)

    Abdulghader, Kalantar; Nojavan, Majid; Naghshbandi, Nabat

    2008-03-15

    The aims of this study were to evaluate the allelopathic potential of heliotrope on some biochemical processes of dodder. The preliminary experiments revealed that the effect of aqueous extract of leaves of heliotrope is higher than its seeds and roots. So, the aqueous extract of leaves was used in remaining experiments. Leaf extracts of 5 g powder per 100 mL H2O inhibited the germination of dodder seeds up to 95% and that of radish up to 100%. While, the aqueous extract of vine leaves which is a non-allelopathic plant did not have any inhibitory effect on these seeds. Vine leaf was used as a control to show that the inhibitory effect of heliotrope is due to an inhibitory compound but not due to the concentration. The leaf extract of heliotrope at 0.0, 0.1, 1.0, 2, 3, 4 and 5 g powder per 100 mL H2O reduced the radish seedling growth from 14 cm to about 0.5 cm and that of dodder from 7.5 cm to about 0.25 cm. The effects of heliotrope allelochemicals on some physiological and biochemical processes of radish was also Investigated. The activity of auxin oxidase increased in leaves and roots of radish. Suggesting that the reduced radish growth is due to the decreased active auxin levels in its leaves and roots. The activity of alpha-amylase was reduced, so reduction of starch degradation and lack of respiratory energy is the prime reason of germination inhibition in dodder and radish seeds. The level of soluble sugars increased. This is an indication of reduction of the activity of some respiratory enzymes and reduced consumption of these sugars. Proline levels were also increased, indicating that, the chemical stress is induced by leaf extract. Finally, the activities of GPX and CAT which are antioxidant enzymes were increased, along with increased extract concentration. These finding shows that the chemical stress induced by leaf extract produces super oxide (O2*) and H2O2, which is neutralized to H2O and O2 by these enzymes.

  5. What is the Role of the Transition State in Soret and Chemical Diffusion Induced Isotopic Fractionation?

    Science.gov (United States)

    Dominguez, G.

    2013-12-01

    For over six decades, Urey's (1) statistical mechanical model of isotopic fractionation based on partition functions with quantized energy levels have enjoyed enormous success in quantitatively explaining equilibrium isotopic fractionation in a wide variety of geochemical systems For example, the interpretation of oxygen isotopic variations in carbonate systems (e.g. foraminiferas), in terms of partition functions with quantized energy levels, forms the basis for paleothermometry (2). Recent observations of isotopic fractionation from chemical and thermal (Soret) diffusion (3-7) appear to challenge our theoretical understanding of mass-transport and isotopic fractionation (8, 9). For example, a recently proposed quantum mechanical model of Soret diffusion, which correctly predicts the isotopic fractionation in thermal gradients for isotopes of Mg, Ca, Fe, Si, and possibly oxygen, was critiqued as being unphysical. First, it was argued that the zero point energies needed to explain the magnitude of isotopic fractionation in basalt melts were unrealistically high based on infrared spectra of these melts. Second, it was argued that the chemical diffusion isotopic fractionation (beta) factors expected from these zero-point energies were also unphysical (10). A recently proposed collision-momentum transfer model partially explains observed fractionation factors, although it fails miserably (by a factor of 3) to account for the isotopic fractionation of Mg isotopes (11). In this presentation, I will review recent observations and models of isotopic fractionation in geochemical melts with thermal gradients and expand upon previous work (8, 12) to show how transition state theory can simultaneously explain mass-transport induced isotopic fractionation, including kinetic, equilibrium, and Soret isotopic fractionation. I show this by providing a few example calculations of the kinetic fractionation factors (a.k.a. beta factors) expected in chemical diffusion as well as

  6. Influence of dietary low histamine diets in the development of chemical kindling induced by pentylenetetrazole in Sprague Dawley rats

    Institute of Scientific and Technical Information of China (English)

    JinChun-lei; ZhangLi-san; XuLi-sa; YanaiKazuhiko; ChenZhong

    2004-01-01

    A role for dietary low histamine diets (LH) on the seizure development of pentylenetetrazole (PTZ)-induced kindling and excitatory behavior was examined in rats. The chemical kindling started after 14 days of dietary treatment with LH( containing 0.145mol/g of histamine) . As compared with the basal histamine diets (BH, containing 7.28 mol/g of histamine)

  7. In vivo photo-detection of chemically induced premalignant lesions and squamous cell carcinoma of the rat palatal mucosa

    NARCIS (Netherlands)

    Nauta, JM; Speelman, OC; vanLeengoed, HLLM; Nikkels, PGJ; Roodenburg, JLN; Witjes, MJH; Vermey, A

    1997-01-01

    Photo-detection using in vivo fluorescence was studied for different stages of chemically induced premalignant lesions and squamous cell carcinoma (SCC) of the Wistar rat palatal mucosa. It was found that the epithelial dysplasia (numerically expressed in the epithelial atypia index (EAI)) of the ra

  8. Influence of chemical structure on hypersensitivity reactions induced by antiepileptic drugs: the role of the aromatic ring.

    NARCIS (Netherlands)

    Handoko, K.B.; Puijenbroek, E.P. van; Bijl, A.H.; Hermens, W.A.; Rijkom, JE Zwart-van; Hekster, Y.A.; Egberts, T.C.G.

    2008-01-01

    OBJECTIVE: Antiepileptic drugs (AEDs) can cause various 'idiosyncratic' hypersensitivity reactions, i.e. the mechanism by which AEDs induce hypersensitivity is unknown. The aim of this study was to assess whether the presence of an aromatic ring as a commonality in chemical structures of AEDs can ex

  9. Influence of chemical structure on hypersensitivity reactions induced by antiepileptic drugs : the role of the aromatic ring

    NARCIS (Netherlands)

    Handoko, Kim B; van Puijenbroek, Eugène P; Bijl, Annemarie H; Hermens, Walter A J J; Zwart-van Rijkom, Jeannette E F; Hekster, Yechiel A; Egberts, Toine C G

    2008-01-01

    OBJECTIVE: Antiepileptic drugs (AEDs) can cause various 'idiosyncratic' hypersensitivity reactions, i.e. the mechanism by which AEDs induce hypersensitivity is unknown. The aim of this study was to assess whether the presence of an aromatic ring as a commonality in chemical structures of AEDs can ex

  10. The dynamics of climate-induced deglacial ice stream acceleration

    Science.gov (United States)

    Robel, A.; Tziperman, E.

    2015-12-01

    Geological observations indicate that ice streams were a significant contributor to ice flow in the Laurentide Ice Sheet during the Last Glacial Maximum. Conceptual and simple model studies have also argued that the gradual development of ice streams increases the sensitivity of large ice sheets to weak climate forcing. In this study, we use an idealized configuration of the Parallel Ice Sheet Model to explore the role of ice streams in rapid deglaciation. In a growing ice sheet, ice streams develop gradually as the bed warms and the margin expands outward onto the continental shelf. Then, a weak change in equilibrium line altitude commensurate with Milankovitch forcing results in a rapid deglacial response, as ice stream acceleration leads to enhanced calving and surface melting at low elevations. We explain the dynamical mechanism that drives this ice stream acceleration and its broader applicability as a feedback for enhancing ice sheet decay in response to climate forcing. We show how our idealized ice sheet simulations match geomorphological observations of deglacial ice stream variability and previous model-data analyses. We conclude with observations on the potential for interaction between ice streams and other feedback mechanisms within the earth system.

  11. Inducing mutations in the mouse genome with the chemical mutagen ethylnitrosourea

    Directory of Open Access Journals (Sweden)

    S.M.G. Massironi

    2006-09-01

    Full Text Available When compared to other model organisms whose genome is sequenced, the number of mutations identified in the mouse appears extremely reduced and this situation seriously hampers our understanding of mammalian gene function(s. Another important consequence of this shortage is that a majority of human genetic diseases still await an animal model. To improve the situation, two strategies are currently used: the first makes use of embryonic stem cells, in which one can induce knockout mutations almost at will; the second consists of a genome-wide random chemical mutagenesis, followed by screening for mutant phenotypes and subsequent identification of the genetic alteration(s. Several projects are now in progress making use of one or the other of these strategies. Here, we report an original effort where we mutagenized BALB/c males, with the mutagen ethylnitrosourea. Offspring of these males were screened for dominant mutations and a three-generation breeding protocol was set to recover recessive mutations. Eleven mutations were identified (one dominant and ten recessives. Three of these mutations are new alleles (Otop1mlh, Foxn1sepe and probably rodador at loci where mutations have already been reported, while 4 are new and original alleles (carc, eqlb, frqz, and Sacc. This result indicates that the mouse genome, as expected, is far from being saturated with mutations. More mutations would certainly be discovered using more sophisticated phenotyping protocols. Seven of the 11 new mutant alleles induced in our experiment have been localized on the genetic map as a first step towards positional cloning.

  12. Evaluation of the chemical model of vestibular lesions induced by arsanilate in rats

    Energy Technology Data Exchange (ETDEWEB)

    Vignaux, G. [INSERM, ERI27, Caen, F-14000 (France); Univ Caen, Caen, F-14000 (France); Chabbert, C.; Gaboyard-Niay, S.; Travo, C. [INSERM U1051, Institut des Neurosciences de Montpellier, Montpellier, F-34090,France (France); Machado, M.L. [INSERM, ERI27, Caen, F-14000 (France); Univ Caen, Caen, F-14000 (France); Denise, P. [INSERM, ERI27, Caen, F-14000 (France); Univ Caen, Caen, F-14000 (France); CHRU Caen, Explorations Fonctionnelles, Caen, F-14000 (France); Comoz, F. [CHRU Caen, Laboratoire d' anatomopathologie, Caen, F-14000 (France); Hitier, M. [CHRU Caen, Service d' Otorhinolaryngologie, Caen, F-14000,France (France); Landemore, G. [CHRU Caen, Laboratoire d' anatomopathologie, Caen, F-14000 (France); Philoxène, B. [INSERM, ERI27, Caen, F-14000 (France); Univ Caen, Caen, F-14000 (France); CHRU Caen, Explorations Fonctionnelles, Caen, F-14000 (France); Besnard, S., E-mail: besnard-s@phycog.org [INSERM, ERI27, Caen, F-14000 (France); Univ Caen, Caen, F-14000 (France); CHRU Caen, Explorations Fonctionnelles, Caen, F-14000 (France)

    2012-01-01

    Several animal models of vestibular deficits that mimic the human pathology phenotype have previously been developed to correlate the degree of vestibular injury to cognate vestibular deficits in a time-dependent manner. Sodium arsanilate is one of the most commonly used substances for chemical vestibular lesioning, but it is not well described in the literature. In the present study, we used histological and functional approaches to conduct a detailed exploration of the model of vestibular lesions induced by transtympanic injection of sodium arsanilate in rats. The arsanilate-induced damage was restricted to the vestibular sensory organs without affecting the external ear, the oropharynx, or Scarpa's ganglion. This finding strongly supports the absence of diffusion of arsanilate into the external ear or Eustachian tubes, or through the eighth cranial nerve sheath leading to the brainstem. One of the striking observations of the present study is the complete restructuring of the sensory epithelia into a non sensory epithelial monolayer observed at 3 months after arsanilate application. This atrophy resembles the monolayer epithelia observed postmortem in the vestibular epithelia of patients with a history of lesioned vestibular deficits such as labyrinthectomy, antibiotic treatment, vestibular neuritis, or Ménière's disease. In cases of Ménière's disease, aminoglycosides, and platinum-based chemotherapy, vestibular hair cells are destroyed, regardless of the physiopathological process, as reproduced with the arsanilate model of vestibular lesion. These observations, together with those presented in this study of arsanilate vestibular toxicity, suggest that this atrophy process relies on a common mechanism of degeneration of the sensory epithelia.

  13. Complex Langevin dynamics for dynamical QCD at nonzero chemical potential: a comparison with multi-parameter reweighting

    CERN Document Server

    Fodor, Z; Sexty, D; Török, C

    2015-01-01

    We study lattice QCD at non-vanishing chemical potential using the complex Langevin equation. We compare the results with multi-parameter reweighting both from $\\mu=0$ and phase quenched ensembles. We find a good agreement for lattice spacings below $\\approx$0.15 fm. On coarser lattices the complex Langevin approach breaks down. Four flavors of staggered fermions are used on $N_t=4, 6$ and 8 lattices. For one ensemble we also use two flavors to investigate the effects of rooting.

  14. Quantitative chemical tagging, stellar ages and the chemo-dynamical evolution of the Galactic disc

    CERN Document Server

    Mitschang, A W; Zucker, D B; Anguiano, B; Bensby, T; Feltzing, S

    2013-01-01

    The early science results from the new generation of high-resolution stellar spectroscopic surveys, such as GALAH and the Gaia-ESO survey, will represent major milestones in the quest to chemically tag the Galaxy. Yet this technique to reconstruct dispersed coeval stellar groups has remained largely untested until recently. We build on previous work that developed an empirical chemical tagging probability function, which describes the likelihood that two field stars are conatal, that is, they were formed in the same cluster environment. In this work we perform the first ever blind chemical tagging experiment, i.e., tagging stars with no known or otherwise discernable associations, on a sample of 714 disc field stars with a number of high quality high resolution homogeneous metal abundance measurements. We present evidence that chemical tagging of field stars does identify coeval groups of stars, yet these groups may not represent distinct formation sites, e.g. as in dissolved open clusters, as previously thou...

  15. Temporal dynamics of distinct CA1 cell populations during unconscious state induced by ketamine.

    Directory of Open Access Journals (Sweden)

    Hui Kuang

    Full Text Available Ketamine is a widely used dissociative anesthetic which can induce some psychotic-like symptoms and memory deficits in some patients during the post-operative period. To understand its effects on neural population dynamics in the brain, we employed large-scale in vivo ensemble recording techniques to monitor the activity patterns of simultaneously recorded hippocampal CA1 pyramidal cells and various interneurons during several conscious and unconscious states such as awake rest, running, slow wave sleep, and ketamine-induced anesthesia. Our analyses reveal that ketamine induces distinct oscillatory dynamics not only in pyramidal cells but also in at least seven different types of CA1 interneurons including putative basket cells, chandelier cells, bistratified cells, and O-LM cells. These emergent unique oscillatory dynamics may very well reflect the intrinsic temporal relationships within the CA1 circuit. It is conceivable that systematic characterization of network dynamics may eventually lead to better understanding of how ketamine induces unconsciousness and consequently alters the conscious mind.

  16. Tracing Dynamics and Clonal Heterogeneity of Cbx7-Induced Leukemic Stem Cells by Cellular Barcoding

    NARCIS (Netherlands)

    Klauke, Karin; Broekhuis, Mathilde J. C.; Weersing, Ellen; Dethmers-Ausema, Albertina; Ritsema, Martha; Gonzalez, Marta Vila; Zwart, Erik; Bystrykh, Leonid V.; de Haan, Gerald

    2015-01-01

    Accurate monitoring of tumor dynamics and leukemic stem cell (LSC) heterogeneity is important for the development of personalized cancer therapies. In this study, we experimentally induced distinct types of leukemia in mice by enforced expression of Cbx7. Simultaneous cellular barcoding allowed for

  17. Recurring dynamically induced thinning during 1985 to 2010 on Upernavik Isstrøm, West Greenland

    Science.gov (United States)

    Khan, Shfaqat Abbas; KjæR, Kurt H.; Korsgaard, Niels J.; Wahr, John; Joughin, Ian R.; Timm, Lars H.; Bamber, Jonathan L.; Broeke, Michiel R.; Stearns, Leigh A.; Hamilton, Gordon S.; Csatho, Bea M.; Nielsen, Karina; Hurkmans, Ruud; Babonis, Greg

    2013-03-01

    Many glaciers along the southeast and northwest coasts of Greenland have accelerated, increasing the ice sheet's contribution to global sea-level rise. In this article, we map elevation changes on Upernavik Isstrøm (UI), West Greenland, during 2003to 2009 using high-resolution ice, cloud and land elevation satellite laser altimeter data supplemented with altimeter surveys from NASA's Airborne Topographic Mapper during 2002 to 2010. To assess thinning prior to 2002, we analyze aerial photographs from 1985. We document at least two distinct periods of dynamically induced ice loss during 1985 to 2010 characterized by a rapid retreat of the calving front, increased ice speed, and lowering of the ice surface. The first period occurred before 1991, whereas the latter occurred during 2005 to 2009. Analyses of air and sea-surface temperature suggest a combination of relatively warm air and ocean water as a potential trigger for the dynamically induced ice loss. We estimate a total catchment-wide ice-mass loss of UI caused by the two events of 72.3 ± 15.8 Gt during 1985 to 2010, whereas the total melt-induced ice-mass loss during this same period is 19.8 ± 2.8 Gt. Thus, 79% of the total ice-mass loss of the UI catchment was caused by ice dynamics, indicating the importance of including dynamically induced ice loss in the total mass change budget of the Greenland ice sheet.

  18. Changes in the anisotropy of oriented membrane dynamics induced by myelin basic protein

    Science.gov (United States)

    Natali, F.; Gliozzi, A.; Rolandi, R.; Relini, A.; Cavatorta, P.; Deriu, A.; Fasano, A.; Riccio, P.

    We report recent results showing the evidence of the effect induced by physiological amounts of myelin basic protein (MBP) on the dynamics of dimyristoyl L-a-phosphatidic acid (DMPA) membranes. Incoherent elastic neutron scattering scans, performed over a wide temperature range, have shown that the anisotropy of motions in oriented membranes is significantly enhanced by the presence of MBP.

  19. Changes in the anisotropy of oriented membrane dynamics induced by myelin basic protein

    Energy Technology Data Exchange (ETDEWEB)

    Natali, F. [OGG-INFM, Grenoble (France); Gliozzi, A.; Rolandi, R.; Relini, A. [Dipartimento di Fisica and Istituto Nazionale per la Fisica della Materia, Universita di Genova (Italy); Cavatorta, P.; Deriu, A. [Dipartimento di Fisica and Istituto Nazionale per la Fisica della Materia, Universita di Parma (Italy); Fasano, A. [Dipartimento di Biochimica e Biologia Molecolare, Universita di Bari (Italy); Riccio, P. [Dipartimento di Biologia D.B.A.F., Universita della Basilicata, Potenza (Italy)

    2002-07-01

    We report recent results showing the evidence of the effect induced by physiological amounts of myelin basic protein (MBP) on the dynamics of dimyristoyl L-a-phosphatidic acid (DMPA) membranes. Incoherent elastic neutron scattering scans, performed over a wide temperature range, have shown that the anisotropy of motions in oriented membranes is significantly enhanced by the presence of MBP. (orig.)

  20. Dynamics of the wetting-induced nanowire reconstruction of Au/Ge(001)

    NARCIS (Netherlands)

    Safaei, A.; van Houselt, Arie; Poelsema, Bene; Zandvliet, Henricus J.W.; van Gastel, Raoul

    2013-01-01

    We have used low-energy electron microscopy and scanning tunneling microscopy to visualize the dynamics of the formation of one-dimensional Au-induced nanowires on a Ge(001) substrate. At low temperature, the growth of nanowire domains is limited by the diffusion of Au. A wetting-dewetting

  1. Death, dynamics and disorder: Terminating reentry in excitable media by dynamically-induced inhomogeneities

    Indian Academy of Sciences (India)

    Johannes Breur; Sitabhra Sinha

    2005-04-01

    Formation of feedback loops of excitation waves (reentrant circuit) around non-conducting ventricular scar tissue is a common cause of cardiac arrhythmias, such as ventricular tachycardia, often leading to death. This is typically treated by rapid stimulation from an implantable device (ICD). However, the mechanisms of reentry termination success and, more importantly, failure, are poorly understood. To study such mechanisms, we simulated pacing termination of reentry in a model of cardiac tissue having significant restitution and dispersion properties. Our results show that rapid pacing dynamically generates conduction inhomogeneities in the reentrant circuit, leading to successful pacing termination of tachycardia. The study suggests that more effective pacing algorithms can be designed by taking into account the role of such dynamical inhomogeneities.

  2. Ejection Dynamics in Vibration-Induced Droplet Atomization

    Science.gov (United States)

    Vukasinovic, Bojan; Smith, Marc K.; Glezer, Ari

    2001-11-01

    A primary sessile liquid drop is atomized into a fine spray of secondary droplets using vibration-induced atomization (VIDA) resulting from forced waves on a free surface of the primary drop. The mechanism of free surface breakup during the VIDA process is investigated using high-speed imaging and laser vibrometry. Secondary droplets result from a localized collapse of surface troughs and the ejection and ultimate breakup of momentary liquid spikes. The characteristic breakup time of these liquid spikes scales with the vibration period and the spike length initially varies like t0.5. The breakup begins with a capillary pinch-off from the tip of the spike that can be followed by additional pinching of liquid droplets. For relatively low-viscosity liquid (e.g., water) a capillary-wave instability of a jet is observed in some cases, while in very viscous liquid (e.g., glycerin-water solution) the first breakup occurs near the stem of the jet. The mechanisms of secondary droplet ejection and the influence of the operating parameters and fluid properties are discussed.

  3. Investigation of biphasic tumor oxygen dynamics induced by hyperoxic gas intervention: the dynamic phantom approach

    Science.gov (United States)

    Kim, Jae G.; Liu, Hanli

    2008-01-01

    We have developed dynamic tumor vascular phantoms and utilized them to investigate the biphasic behavior of increases in light absorption, which is directly associated with oxygenated hemoglobin concentration that was observed in vivo from rat breast tumor experiments during carbogen/oxygen inhalation. The experimental setup for the phantom study included a continuous-wave, multichannel, near-infrared spectroscopy (NIRS) system and syringe pumps to drive the simulated blood through the dynamic vascular phantoms. The results from such phantom experiments clearly show that the two time constants observed in tumor oxygenation dynamics in vivo can result from two different perfusion rates or two different blood flow velocities. We provide experimental support for our previous hypothesis: the biphasic tumor hemodynamic feature stems from a well-perfused and poorly perfused region that could be detected with the two time constants of the NIRS signals. With a multichannel approach, noninvasive NIRS measurements may have useful and prognostic values to quantify the therapeutic effects of cancer treatments.

  4. Determination of the Orientation and Dynamics of Ergosterol in Model Membranes Using Uniform 13C Labeling and Dynamically Averaged 13C Chemical Shift Anisotropies as Experimental Restraints

    Science.gov (United States)

    Soubias, O.; Jolibois, F.; Massou, S.; Milon, A.; Réat, V.

    2005-01-01

    A new strategy was established to determine the average orientation and dynamics of ergosterol in dimyristoylphosphatidylcholine model membranes. It is based on the analysis of chemical shift anisotropies (CSAs) averaged by the molecular dynamics. Static 13C CSA tensors were computed by quantum chemistry, using the gauge-including atomic-orbital approach within Hartree-Fock theory. Uniformly 13C-labeled ergosterol was purified from Pichia pastoris cells grown on labeled methanol. After reconstitution into dimyristoylphosphatidylcholine lipids, the complete 1H and 13C assignment of ergosterol's resonances was performed using a combination of magic-angle spinning two-dimensional experiments. Dynamically averaged CSAs were determined by standard side-band intensity analysis for isolated 13C resonances (C3 and ethylenic carbons) and by off-magic-angle spinning experiments for other carbons. A set of 18 constraints was thus obtained, from which the sterol's molecular order parameter and average orientation could be precisely defined. The validity of using computed CSAs in this strategy was verified on cholesterol model systems. This new method allowed us to quantify ergosterol's dynamics at three molar ratios: 16 mol % (Ld phase), 30 mol % (Lo phase), and 23 mol % (mixed phases). Contrary to cholesterol, ergosterol's molecular diffusion axis makes an important angle (14°) with the inertial axis of the rigid four-ring system. PMID:15923221

  5. Role of tip chemical reactivity on atom manipulation process in dynamic force microscopy.

    Science.gov (United States)

    Sugimoto, Yoshiaki; Yurtsever, Ayhan; Abe, Masayuki; Morita, Seizo; Ondráček, Martin; Pou, Pablo; Pérez, Ruben; Jelínek, Pavel

    2013-08-27

    The effect of tip chemical reactivity on the lateral manipulation of intrinsic Si adatoms toward a vacancy site on a Si(111)-(7 × 7) surface has been investigated by noncontact atomic force microscopy at room temperature. Here we measure the atom-hopping probabilities associated with different manipulation processes as a function of the tip-surface distance by means of constant height scans with chemically different types of tips. The interactions between different tips and Si atoms are evaluated by force spectroscopic measurements. Our results demonstrate that the ability to manipulate Si adatoms depends extremely on the chemical nature of the tip apex and is correlated with the maximal attractive force measured over Si adatoms. We rationalize the observed dependence of the atom manipulation process on tip-apex chemical reactivity by means of density functional theory calculations. The results of these calculations suggest that the ability to reduce the energy barrier associated with the Si adatom movement depends profoundly on tip chemical reactivity and that the level of energy barrier reduction is higher with tips that exhibit high chemical reactivity with Si adatoms. The results of this study provide a better way to control the efficiency of the atomic manipulation process for chemisorption systems.

  6. Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text.

    Science.gov (United States)

    Bravo, Àlex; Li, Tong Shu; Su, Andrew I; Good, Benjamin M; Furlong, Laura I

    2016-01-01

    Drug toxicity is a major concern for both regulatory agencies and the pharmaceutical industry. In this context, text-mining methods for the identification of drug side effects from free text are key for the development of up-to-date knowledge sources on drug adverse reactions. We present a new system for identification of drug side effects from the literature that combines three approaches: machine learning, rule- and knowledge-based approaches. This system has been developed to address the Task 3.B of Biocreative V challenge (BC5) dealing with Chemical-induced Disease (CID) relations. The first two approaches focus on identifying relations at the sentence-level, while the knowledge-based approach is applied both at sentence and abstract levels. The machine learning method is based on the BeFree system using two corpora as training data: the annotated data provided by the CID task organizers and a new CID corpus developed by crowdsourcing. Different combinations of results from the three strategies were selected for each run of the challenge. In the final evaluation setting, the system achieved the highest Recall of the challenge (63%). By performing an error analysis, we identified the main causes of misclassifications and areas for improving of our system, and highlighted the need of consistent gold standard data sets for advancing the state of the art in text mining of drug side effects.Database URL: https://zenodo.org/record/29887?ln¼en#.VsL3yDLWR_V.

  7. Changes in chemical interactions and protein conformation during heat-induced wheat gluten gel formation.

    Science.gov (United States)

    Wang, Kai-Qiang; Luo, Shui-Zhong; Zhong, Xi-Yang; Cai, Jing; Jiang, Shao-Tong; Zheng, Zhi

    2017-01-01

    In order to elucidate the heat-induced wheat gluten gel formation mechanism, changes in chemical interactions and protein conformation were investigated during gelation. The contribution of ionic and hydrogen bonds were found to decrease from 0.746 and 4.133g/L to 0.397 and 2.733g/L, respectively, as the temperature increased from 25 to 90°C. Moreover, the free SH content remarkably decreased from 37.91 to 19.79μmol/g during gelation. Ultraviolet absorption spectra and intrinsic fluorescence spectra suggested that wheat gluten unfolded during the heating process. In addition, wheat gluten gels treated at 80 and 90°C exhibited a "steric hindrance" effect, which can be attributed to the formation of aggregates. Fourier transform infrared spectra suggested that the random coil content increased at low temperatures (40 and 50°C), whereas the content of intermolecular β-sheets due to protein aggregation increased from 38.10% to 44.28% when the gelation temperature was 90°C.

  8. Pressure-induced changes in interdiffusivity and compressive stress in chemically strengthened glass.

    Science.gov (United States)

    Svenson, Mouritz N; Thirion, Lynn M; Youngman, Randall E; Mauro, John C; Rzoska, Sylwester J; Bockowski, Michal; Smedskjaer, Morten M

    2014-07-09

    Glass exhibits a significant change in properties when subjected to high pressure because the short- and intermediate-range atomic structures of glass are tunable through compression. Understanding the link between the atomic structure and macroscopic properties of glass under high pressure is an important scientific problem because the glass structures obtained via quenching from elevated pressure may give rise to properties unattainable under standard ambient pressure conditions. In particular, the chemical strengthening of glass through K(+)-for-Na(+) ion exchange is currently receiving significant interest due to the increasing demand for stronger and more damage-resistant glass. However, the interplay among isostatic compression, pressure-induced changes in alkali diffusivity, compressive stress generated through ion exchange, and the resulting mechanical properties are poorly understood. In this work, we employ a specially designed gas pressure chamber to compress bulk glass samples isostatically up to 1 GPa at elevated temperature before or after the ion exchange treatment of a commercial sodium-magnesium aluminosilicate glass. Compression of the samples prior to ion exchange leads to a decreased Na(+)-K(+) interdiffusivity, increased compressive stress, and slightly increased hardness. Compression after the ion exchange treatment changes the shape of the potassium-sodium diffusion profiles and significantly increases glass hardness. We discuss these results in terms of the underlying structural changes in network-modifier environments and overall network densification.

  9. Mapping the chemical potential dependence of current-induced spin polarization in a topological insulator

    Science.gov (United States)

    Lee, Joon Sue; Richardella, Anthony; Hickey, Danielle Reifsnyder; Mkhoyan, K. Andre; Samarth, Nitin

    2015-10-01

    We report electrical measurements of the current-induced spin polarization of the surface current in topological insulator devices where contributions from bulk and surface conduction can be disentangled by electrical gating. The devices use a ferromagnetic tunnel junction (permalloy/Al 2O3 ) as a spin detector on a back-gated (Bi,Sb ) 2Te3 channel. We observe hysteretic voltage signals as the magnetization of the detector ferromagnet is switched parallel or antiparallel to the spin polarization of the surface current. The amplitude of the detected voltage change is linearly proportional to the applied dc bias current in the (Bi,Sb ) 2Te3 channel. As the chemical potential is tuned from the bulk bands into the surface state band, we observe an enhancement of the spin-dependent voltages up to 300% within the range of the electrostatic gating. Using a simple model, we extract the spin polarization near charge neutrality (i.e., the Dirac point).

  10. Water chemical evolution in Underground Pumped Storage Hydropower plants and induced consequences

    Science.gov (United States)

    Pujades, Estanislao; Orban, Philippe; Jurado, Anna; Ayora, Carlos; Brouyère, Serge; Dassargues, Alain

    2017-04-01

    Underground Pumped Storage Hydropower (UPSH) using abandoned mines is an alternative to manage the electricity production in flat regions. UPSH plants consist of two reservoirs; the upper reservoir is located at the surface or at shallow depth, while the lower reservoir is underground. These plants have potentially less constraints that the classical Pumped Storage Hydropower plants because more sites are available and impacts on landscape, land use, environment and society seem lower. Still, it is needed to consider the consequences of the groundwater exchanges occurring between the underground reservoir and surrounding porous media. Previous studies have been focused on the influence of these groundwater exchanges on the efficiency and on groundwater flow impacts. However, hydrochemical variations induced by the surface exposure of pumped water and their consequences have not been yet addressed. The objective of this work is to evaluate the hydrochemical evolution of the water in UPSH plants and its effects on the environment and on the UPSH efficiency. The problem is studied numerically by means of reactive transport modelling. Different scenarios are considered varying the chemical properties of the surrounding porous medium and groundwater. Results show that the dissolution and/or precipitation of some compounds may affect (1) the groundwater quality, and (2) the efficiency and the useful life of the used pumps and turbines of the UPSH system.

  11. Chemically induced graft copolymerization of 2-hydroxyethyl methacrylate onto polyurethane surface for improving blood compatibility

    Science.gov (United States)

    He, Chunli; Wang, Miao; Cai, Xianmei; Huang, Xiaobo; Li, Li; Zhu, Haomiao; Shen, Jian; Yuan, Jiang

    2011-11-01

    To improve hydrophilicity and blood compatibility properties of polyurethane (PU) film, we chemically induced graft copolymerization of 2-hydroxyethyl methacrylate (HEMA) onto the surface of polyurethane film using benzoyl peroxide as an initiator. The effects of grafting temperature, grafting time, monomer and initiator concentrations on the grafting yields were studied. The maximum grafting yield value was obtained 0.0275 g/cm2 for HEMA. Characterization of the films was carried out by attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR), water contact angle measurements. ATR-FTIR data showed that HEMA was successfully grafted onto the PU films surface. Water contact angle measurement demonstrated the grafted films possessed a relatively hydrophilic surface. The blood compatibility of the grafted films was preliminarily evaluated by a platelet-rich plasma adhesion test and hemolysis test. The results of platelet adhesion experiment showed that polyurethane grafted polymerization with monomer of 2-hydroxyethyl methacrylate had good blood compatibility featured by the low platelet adhesion. Hemolysis rate of the PU-g-PHEMA films was dramatically decreased than the ungrafted PU films. This kind of new biomaterials grafted with HEMA monomers might have a potential usage for biomedical applications.

  12. Chemical reactions induced by oscillating external fields in weak thermal environments

    CERN Document Server

    Craven, Galen T; Hernandez, Rigoberto

    2015-01-01

    Chemical reaction rates must increasingly be determined in systems that evolve under the control of external stimuli. In these systems, when a reactant population is induced to cross an energy barrier through forcing from a temporally varying external field, the transition state that the reaction must pass through during the transformation from reactant to product is no longer a fixed geometric structure, but is instead time-dependent. For a periodically forced model reaction, we develop a recrossing-free dividing surface that is attached to a transition state trajectory [T. Bartsch, R. Hernandez, and T. Uzer, Phys. Rev. Lett. 95, 058301 (2005)]. We have previously shown that for single-mode sinusoidal driving, the stability of the time-varying transition state directly determines the reaction rate [G. T. Craven, T. Bartsch, and R. Hernandez, J. Chem. Phys. 141, 041106 (2014)]. Here, we extend our previous work to the case of multi-mode driving waveforms. Excellent agreement is observed between the rates pred...

  13. A mint purified extract protects human keratinocytes from short-term, chemically induced oxidative stress.

    Science.gov (United States)

    Berselli, Patrizia Valeria Rita; Zava, Stefania; Montorfano, Gigliola; Corsetto, Paola Antonia; Krzyzanowska, Justyna; Oleszek, Wieslaw; Berra, Bruno; Rizzo, Angela Maria

    2010-11-10

    Oxidative stress is strictly correlated to the pathogenesis of many diseases, and a diet rich in fruits and vegetables, or adequately integrated, is currently considered to be a protective and preventive factor. This study aimed to analyze the efficacy of a 1 h preincubation with the highest nontoxic dose of a characterized Mentha longifolia extract (80 μg/mL) in protecting human keratinocytes (NCTC2544) from chemically induced oxidative stress (500 μM H2O2 for 2, 16, and 24 h). As reference synthetic pure compounds rosmarinic acid (360.31 μg/mL), a major mint phenolic constituent, and resveratrol (31.95 mg/mL), a well-known antioxidant, were used. Cellular viability was significantly protected by mint, which limited protein and DNA damage, decreased lipid peroxidation, and preserved glutathione and superoxide dismutase activity in the shorter phases of oxidative stress induction, in extents comparable to or better than those of pure compounds. These data suggest that mint use as only a flavoring has to be revised, taking into consideration its enrichment in foodstuff and cosmetics.

  14. A comparative study of laser-induced demagnetization dynamics in Fe, Co, and Ni

    Science.gov (United States)

    Gopalakrishnan, Maithreyi; Gentry, Christian; Zusin, Dmitriy; Grychtol, Patrik; Knut, Ronny; Shaw, Justin; Nembach, Hans; Mathias, Stefan; Aeschlimann, Martin; Oppeneer, Peter; Schneider, Claus; Kapteyn, Henry; Murnane, Margaret

    Even twenty years after the discovery of ultrafast demagnetization of ferromagnetic materials induced by a femtosecond laser pulse there is still an ongoing debate about the mechanisms that drive the process. Surprisingly, a comprehensive study that compares demagnetization dynamics in different materials on equal footing is lacking. Yet, the scientific community would greatly benefit from such study. We fill this gap by performing a systematic comparison of ultrafast demagnetization behavior in Iron, Cobalt and Nickel, the simplest itinerant ferromagnets, under a wide range of pump fluences. In this experiment, we utilize a tabletop broadband extreme ultraviolet source to probe magnetization dynamics at the M2,3 absorption edges of these three elements using the transverse magneto-optical Kerr effect. The obtained data can be used to inform theory and, thereby, assist in resolving the remaining questions about the micro- and macroscopic mechanisms behind ultrafast laser-induced magnetization dynamics in materials.

  15. Acetylation dynamics of human nuclear proteins during the ionizing radiation-induced DNA damage response

    DEFF Research Database (Denmark)

    Bennetzen, Martin; Andersen, J.S.; Lasen, D.H.

    2013-01-01

    -dependent posttranslational modifications (PT Ms). To complement our previous analysis of IR-induced temporal dynamics of nuclear phosphoproteome, we now identify a range of human nuclear proteins that are dynamically regulated by acetylation, and predominantly deacetylation, during IR-induced DDR by using mass spectrometry......-based proteomic approaches. Apart from cataloging acetylation sites through SILAC proteomic analyses before IR and at 5 and 60 min after IR exposure of U2OS cells, we report that: (1) key components of the transcriptional machinery, such as EP 300 and CREBBP, are dynamically acetylated; (2) that nuclear...... to assess lysine acetylation status and thereby validate the mass spectrometry data. We thus present evidence that nuclear proteins, including those known to regulate cellular functions via epigenetic modifications of histones, are regulated by (de)acetylation in a timely manner upon cell's exposure...

  16. AKT1E¹⁷K Is Oncogenic in Mouse Lung and Cooperates with Chemical Carcinogens in Inducing Lung Cancer.

    Science.gov (United States)

    Malanga, Donatella; Belmonte, Stefania; Colelli, Fabiana; Scarfò, Marzia; De Marco, Carmela; Oliveira, Duarte Mendes; Mirante, Teresa; Camastra, Caterina; Gagliardi, Monica; Rizzuto, Antonia; Mignogna, Chiara; Paciello, Orlando; Papparella, Serenella; Fagman, Henrik; Viglietto, Giuseppe

    2016-01-01

    The hotspot AKT1E17K mutation in the pleckstrin homology domain of AKT1 occurs in approximately 0.6-2% of human lung cancers. Recently, we have demonstrated that AKT1E17K transforms immortalized human bronchial cells. Here by use of a transgenic Cre-inducible murine strain in the wild type Rosa26 (R26) locus (R26-AKT1E17K mice) we demonstrate that AKT1E17K is a bona-fide oncogene and plays a role in the development of lung cancer in vivo. In fact, we report that mutant AKT1E17K induces bronchial and/or bronchiolar hyperplastic lesions in murine lung epithelium, which progress to frank carcinoma at very low frequency, and accelerates tumor formation induced by chemical carcinogens. In conclusion, AKT1E17K induces hyperplasia of mouse lung epithelium in vivo and cooperates with urethane to induce the fully malignant phenotype.

  17. Ligand induced conformational changes of the human serotonin transporter revealed by molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Heidi Koldsø

    Full Text Available The competitive inhibitor cocaine and the non-competitive inhibitor ibogaine induce different conformational states of the human serotonin transporter. It has been shown from accessibility experiments that cocaine mainly induces an outward-facing conformation, while the non-competitive inhibitor ibogaine, and its active metabolite noribogaine, have been proposed to induce an inward-facing conformation of the human serotonin transporter similar to what has been observed for the endogenous substrate, serotonin. The ligand induced conformational changes within the human serotonin transporter caused by these three different types of ligands, substrate, non-competitive and competitive inhibitors, are studied from multiple atomistic molecular dynamics simulations initiated from a homology model of the human serotonin transporter. The results reveal that diverse conformations of the human serotonin transporter are captured from the molecular dynamics simulations depending on the type of the ligand bound. The inward-facing conformation of the human serotonin transporter is reached with noribogaine bound, and this state resembles a previously identified inward-facing conformation of the human serotonin transporter obtained from molecular dynamics simulation with bound substrate, but also a recently published inward-facing conformation of a bacterial homolog, the leucine transporter from Aquifex Aoelicus. The differences observed in ligand induced behavior are found to originate from different interaction patterns between the ligands and the protein. Such atomic-level understanding of how an inhibitor can dictate the conformational response of a transporter by ligand binding may be of great importance for future drug design.

  18. Ligand induced conformational changes of the human serotonin transporter revealed by molecular dynamics simulations.

    Science.gov (United States)

    Koldsø, Heidi; Autzen, Henriette Elisabeth; Grouleff, Julie; Schiøtt, Birgit

    2013-01-01

    The competitive inhibitor cocaine and the non-competitive inhibitor ibogaine induce different conformational states of the human serotonin transporter. It has been shown from accessibility experiments that cocaine mainly induces an outward-facing conformation, while the non-competitive inhibitor ibogaine, and its active metabolite noribogaine, have been proposed to induce an inward-facing conformation of the human serotonin transporter similar to what has been observed for the endogenous substrate, serotonin. The ligand induced conformational changes within the human serotonin transporter caused by these three different types of ligands, substrate, non-competitive and competitive inhibitors, are studied from multiple atomistic molecular dynamics simulations initiated from a homology model of the human serotonin transporter. The results reveal that diverse conformations of the human serotonin transporter are captured from the molecular dynamics simulations depending on the type of the ligand bound. The inward-facing conformation of the human serotonin transporter is reached with noribogaine bound, and this state resembles a previously identified inward-facing conformation of the human serotonin transporter obtained from molecular dynamics simulation with bound substrate, but also a recently published inward-facing conformation of a bacterial homolog, the leucine transporter from Aquifex Aoelicus. The differences observed in ligand induced behavior are found to originate from different interaction patterns between the ligands and the protein. Such atomic-level understanding of how an inhibitor can dictate the conformational response of a transporter by ligand binding may be of great importance for future drug design.

  19. Fluid patterns and dynamics induced by vibrations in microgravity conditions

    Science.gov (United States)

    Porter, Jeff; Tinao Perez-Miravete, Ignacio; Laverón-Simavilla, Ana

    Understanding the effects of vibrations is extremely important in microgravity environments where residual acceleration, or g-jitter, is easily generated by crew manoeuvring or machinery, and can have a significant impact on material processing systems and on-board experiments. Indeed, vibrations can dramatically affect fluid behaviour whether gravity is present or not, inducing instability in some cases while suppressing it in others. We will describe the results of investigations being conducted at the ESA affiliated Spanish User Support and Operations Centre (E-USOC) on the effect of vibrations on fluids interfaces, most notably with the forcing oriented parallel to the fluid surface. Pattern formation properties will be described in detail, and the importance of symmetry constraints and mean flows will be considered. Current exper-imental results are intriguing and have challenged existing assumptions in the field, particularly with regard to the parametric instability underlying subharmonic cross-waves. They suggest an intimate connection between Faraday waves, which are observed in vertically vibrated systems, and cross-waves, which are found in horizontally forced systems. Concurrent theoretical work, based on the analysis of reduced models, and on numerical simulations, will then be described. Finally, this research will be placed in a microgravity context and used to motivate the defini-tion of a proposed set of experiments on the International Space Station (ISS). The experiments would be in the large-aspect-ratio-limit, requiring relatively high frequency but low amplitude vibrations, where comparatively little microgravity research has been done. The interest of such a microgravity experiment will be discussed, with emphasis on fluid management and the potential of vibrations to act as a kind of artificial gravity by orienting surfaces (or density contours) perpendicular to the axis of vibration.

  20. Novel quantitative methods for characterization of chemical induced functional alteration in developing neuronal cultures

    Science.gov (United States)

    ABSTRACT BODY: Thousands of chemicals lack adequate testing for adverse effects on nervous system development, stimulating research into alternative methods to screen chemicals for potential developmental neurotoxicity. Microelectrode arrays (MEA) collect action potential spiking...

  1. A new route to nanoscale tomographic chemical analysis: Focused ion beam-induced auger electron spectrosocpy

    Science.gov (United States)

    Parvaneh, Hamed

    This research project is aimed to study the application of ion-induced Auger electron spectroscopy (IAES) in combination with the characteristics of focused ion beam (FIB) microscopy for performing chemical spectroscopy and further evaluate its potential for 3-dimensional chemical tomography applications. The mechanism for generation of Auger electrons by bombarding ions is very different from its electron induced counterpart. In the conventional electron-induced Auger electron spectroscopy (EAES), an electron beam with energy typically in the range 1-10kV is used to excite inner-shell (core) electrons of the solid. An electron from a higher electron energy state then de-excites to fill the hole and the extra energy is then transferred to either another electron, i.e. the Auger electron, or generation of an X-ray (photon). In both cases the emitting particles have charac-teristic energies and could be used to identify the excited target atoms. In IAES, however, large excitation cross sections can occur by promotion of in-ner shell electrons through crossing of molecular orbitals. Originally such phenomenological excitation processes were first proposed [3] for bi-particle gas phase collision systems to explain the generation of inner shell vacancies in violent collisions. In addition to excitation of incident or target atoms, due to a much heavier mass of ions compared to electrons, there would also be a substantial momentum transfer from the incident to the target atoms. This may cause the excited target atom to recoil from the lattice site or alternatively sputter off the surface with the possibility of de-excitation while the atom is either in motion in the matrix or traveling in vacuum. As a result, one could expect differences between the spectra induced by incident electrons and ions and interpretation of the IAE spectra requires separate consideration of both excitation and decay processes. In the first stage of the project, a state-of-the-art mass

  2. Hybrid molecular dynamics simulation for plasma induced damage analysis

    Science.gov (United States)

    Matsukuma, Masaaki

    2016-09-01

    In order to enable further device size reduction (also known as Moore's law) and improved power performance, the semiconductor industry is introducing new materials and device structures into the semiconductor fabrication process. Materials now include III-V compounds, germanium, cobalt, ruthenium, hafnium, and others. The device structure in both memory and logic has been evolving from planar to three dimensional (3D). One such device is the FinFET, where the transistor gate is a vertical fin made either of silicon, silicon-germanium or germanium. These changes have brought renewed interests in the structural damages caused by energetic ion bombardment of the fin sidewalls which are exposed to the ion flux from the plasma during the fin-strip off step. Better control of the physical damage of the 3D devices requires a better understanding of the damage formation mechanisms on such new materials and structures. In this study, the damage formation processes by ion bombardment have been simulated for Si and Ge substrate by Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid simulations and compared to the results from the classical molecular dynamics (MD) simulations. In our QM/MM simulations, the highly reactive region in which the structural damage is created is simulated with the Density Functional based Tight Binding (DFTB) method and the region remote from the primary region is simulated using classical MD with the Stillinger-Weber and Moliere potentials. The learn on the fly method is also used to reduce the computational load. Hence our QM/MM simulation is much faster than the full QC-MD simulations and the original QM/MM simulations. The amorphous layers profile simulated with QM/MM have obvious differences in their thickness for silicon and germanium substrate. The profile of damaged structure in the germanium substrate is characterized by a deeper tail then in silicon. These traits are also observed in the results from the mass selected ion beam

  3. Stochastic dynamics and non-equilibrium thermodynamics of a bistable chemical system: the Schlögl model revisited.

    Science.gov (United States)

    Vellela, Melissa; Qian, Hong

    2009-10-06

    Schlögl's model is the canonical example of a chemical reaction system that exhibits bistability. Because the biological examples of bistability and switching behaviour are increasingly numerous, this paper presents an integrated deterministic, stochastic and thermodynamic analysis of the model. After a brief review of the deterministic and stochastic modelling frameworks, the concepts of chemical and mathematical detailed balances are discussed and non-equilibrium conditions are shown to be necessary for bistability. Thermodynamic quantities such as the flux, chemical potential and entropy production rate are defined and compared across the two models. In the bistable region, the stochastic model exhibits an exchange of the global stability between the two stable states under changes in the pump parameters and volume size. The stochastic entropy production rate shows a sharp transition that mirrors this exchange. A new hybrid model that includes continuous diffusion and discrete jumps is suggested to deal with the multiscale dynamics of the bistable system. Accurate approximations of the exponentially small eigenvalue associated with the time scale of this switching and the full time-dependent solution are calculated using Matlab. A breakdown of previously known asymptotic approximations on small volume scales is observed through comparison with these and Monte Carlo results. Finally, in the appendix section is an illustration of how the diffusion approximation of the chemical master equation can fail to represent correctly the mesoscopically interesting steady-state behaviour of the system.

  4. Phase Diagram of Dynamical Twisted Mass Wilson Fermions at Finite Isospin Chemical Potential

    CERN Document Server

    Janssen, Oliver; Splittorff, K; Verbaarschot, Jacobus J M; Zafeiropoulos, Savvas

    2015-01-01

    We consider the phase diagram of twisted mass Wilson fermions of two-flavor QCD in the parameter space of the quark mass, the isospin chemical potential, the twist angle and the lattice spacing. This work extends earlier studies in the continuum and those at zero chemical potential. We evaluate the phase diagram as well as the spectrum of the (pseudo-)Goldstone bosons using the chiral Lagrangian for twisted mass Wilson fermions at non-zero isospin chemical potential. The phases are obtained from a mean field analysis. At zero twist angle we find that already an infinitesimal isospin chemical potential destroys the Aoki phase. The reason is that in this phase we have massless Goldstone bosons with a non-zero isospin charge. At finite twist angle only two different phases are present, one phase which is continuously connected to the Bose condensed phase at non-zero chemical potential and another phase which is continuously connected to the normal phase. For either zero or maximal twist the phase diagram is more...

  5. Chemical Dynamic Thermodynamic Resolution and S/R Interconversion of Unprotected Unnatural Tailor-made α-Amino Acids.

    Science.gov (United States)

    Wang, Shuni; Zhou, Shengbin; Wang, Jiang; Nian, Yong; Kawashima, Aki; Moriwaki, Hiroki; Aceña, José L; Soloshonok, Vadim A; Liu, Hong

    2015-10-16

    Described here is an advanced, general method for purely chemical dynamic thermodynamic resolution and S/R interconversion of unprotected tailor-made α-amino acids (α-AAs) through intermediate formation of the corresponding nickel(II)-chelated Schiff bases. The method features virtually complete stereochemical outcome, broad substrate generality (35 examples), and operationally convenient conditions allowing for large-scale preparation of the target α-AAs in enantiomerically pure form. Furthermore, the new type of nonracemizable axially chiral ligands can be quantitatively recycled and reused, rendering the whole process economically and synthetically attractive.

  6. High-power supersonic chemical lasers: gas-dynamic problems of operation of mobile systems with PRS

    Science.gov (United States)

    Boreysho, A. S.; Malkov, V. M.; Savin, A. V.

    2008-10-01

    Supersonic chemical lasers, such as HF /DF and COIL, have always been in the focus of special interest as the most powerful sources of continuous wave generation. Presently, autonomous mobile laser complexes (both air- and landbased) are being developed on the basis of SCL [1-3]. It is commonly accepted that SCL appeared, conditionally speaking, at the crossroads of a number of sciences: of physics - quantum electronics and physical kinetics; chemistry - combustion theory and chemical kinetics; classic optics - theory of resonators, aero-optics, and gas dynamics (there is a supersonic flow in the SCL channel). Due to this fact, all tasks and problems which could be resolved in the course of SCL development have complex character and could be considered as the next stage of complexity in comparison with the well known similar tasks which had been considered earlier. This is why they should be resolved anew with consideration of the specific aspects of the SCL processes. This is true for the gas-dynamic problems: new parameter areas, non-traditional channel geometry, consideration of new phenomena, etc.Supersonic chemical lasers, such as HF /DF and COIL, have always been in the focus of special interest as the most powerful sources of continuous wave generation. Presently, autonomous mobile laser complexes (both air- and landbased) are being developed on the basis of SCL [1-3]. It is commonly accepted that SCL appeared, conditionally speaking, at the crossroads of a number of sciences: of physics - quantum electronics and physical kinetics; chemistry - combustion theory and chemical kinetics; classic optics - theory of resonators, aero-optics, and gas dynamics (there is a supersonic flow in the SCL channel). Due to this fact, all tasks and problems which could be resolved in the course of SCL development have complex character and could be considered as the next stage of complexity in comparison with the well known similar tasks which had been considered earlier

  7. Probing the Gas-Phase Dynamics of Graphene Chemical Vapour Deposition using in-situ UV Absorption Spectroscopy

    DEFF Research Database (Denmark)

    Shivayogimath, Abhay; Mackenzie, David; Luo, Birong

    2017-01-01

    of multilayer nucleation when backstreaming is suppressed. These results point to an important and previously undescribed mechanism for multilayer nucleation, wherein higher-order gas-phase carbon species play an integral role. Our work highlights the importance of gas-phase dynamics in understanding......The processes governing multilayer nucleation in the chemical vapour deposition (CVD) of graphene are important for obtaining high-quality monolayer sheets, but remain poorly understood. Here we show that higher-order carbon species in the gas-phase play a major role in multilayer nucleation...

  8. Cytological and comparative proteomic analyses on male sterility in Brassica napus L. induced by the chemical hybridization agent monosulphuron ester sodium.

    Directory of Open Access Journals (Sweden)

    Yufeng Cheng

    Full Text Available Male sterility induced by a chemical hybridization agent (CHA is an important tool for utilizing crop heterosis. Monosulphuron ester sodium (MES, a new acetolactate synthase-inhibitor herbicide belonging to the sulphonylurea family, has been developed as an effective CHA to induce male sterility in rapeseed (Brassica napus L.. To understand MES-induced male sterility in rapeseed better, comparative cytological and proteomic analyses were conducted in this study. Cytological analysis indicated that defective tapetal cells and abnormal microspores were gradually generated in the developing anthers of MES-treated plants at various development stages, resulting in unviable microspores and male sterility. A total of 141 differentially expressed proteins between the MES-treated and control plants were revealed, and 131 of them were further identified by MALDI-TOF/TOF MS. Most of these proteins decreased in abundance in tissues of MES-treated rapeseed plants, and only a few increased. Notably, some proteins were absent or induced in developing anthers after MES treatment. These proteins were involved in several processes that may be crucial for tapetum and microspore development. Down-regulation of these proteins may disrupt the coordination of developmental and metabolic processes, resulting in defective tapetum and abnormal microspores that lead to male sterility in MES-treated plants. Accordingly, a simple model of CHA-MES-induced male sterility in rapeseed was established. This study is the first cytological and dynamic proteomic investigation on CHA-MES-induced male sterility in rapeseed, and the results provide new insights into the molecular events of male sterility.

  9. Trans-generational radiation-induced chromosomal instability in the female enhances the action of chemical mutagens

    Energy Technology Data Exchange (ETDEWEB)

    Camats, Nuria [Institut de Biotecnologia i Biomedicina (IBB), Universitat Autonoma de Barcelona, 08193 Barcelona (Spain); Departament de Biologia Cel.lular, Fisiologia i Immunologia, Universitat Autonoma de Barcelona, 08193 Barcelona (Spain); Garcia, Francisca [Institut de Biotecnologia i Biomedicina (IBB), Universitat Autonoma de Barcelona, 08193 Barcelona (Spain); Parrilla, Juan Jose [Servicio de Ginecologia y Obstetricia, Hospital Universitario Virgen de la Arrixaca, 30120 El Palmar, Murcia (Spain); Calaf, Joaquim [Servei de Ginecologia i Obstetricia, Hospital Universitari de la Santa Creu i Sant Pau, 08025 Barcelona (Spain); Martin, Miguel [Departament de Pediatria, d' Obstetricia i Ginecologia i de Medicina Preventiva, Universitat Autonoma de Barcelona, 08193 Barcelona (Spain); Caldes, Montserrat Garcia [Institut de Biotecnologia i Biomedicina (IBB), Universitat Autonoma de Barcelona, 08193 Barcelona (Spain); Departament de Biologia Cel.lular, Fisiologia i Immunologia, Universitat Autonoma de Barcelona, 08193 Barcelona (Spain)], E-mail: Montserrat.Garcia.Caldes@uab.es

    2008-04-02

    Genomic instability can be produced by ionising radiation, so-called radiation-induced genomic instability, and chemical mutagens. Radiation-induced genomic instability occurs in both germinal and somatic cells and also in the offspring of irradiated individuals, and it is characterised by genetic changes including chromosomal rearrangements. The majority of studies of trans-generational, radiation-induced genomic instability have been described in the male germ line, whereas the authors who have chosen the female as a model are scarce. The aim of this work is to find out the radiation-induced effects in the foetal offspring of X-ray-treated female rats and, at the same time, the possible impact of this radiation-induced genomic instability on the action of a chemical mutagen. In order to achieve both goals, the quantity and quality of chromosomal damage were analysed. In order to detect trans-generational genomic instability, a total of 4806 metaphases from foetal tissues from the foetal offspring of X-irradiated female rats (5 Gy, acute dose) were analysed. The study's results showed that there is radiation-induced genomic instability: the number of aberrant metaphases and the breaks per total metaphases studied increased and were found to be statistically significant (p {<=} 0.05), with regard to the control group. In order to identify how this trans-generational, radiation-induced chromosomal instability could influence the chromosomal behaviour of the offspring of irradiated rat females in front of a chemical agent (aphidicolin), a total of 2481 metaphases were studied. The observed results showed that there is an enhancement of the action of the chemical agent: chromosomal breaks per aberrant metaphases show significant differences (p {<=} 0.05) in the X-ray- and aphidicolin-treated group as regards the aphidicolin-treated group. In conclusion, our findings indicate that there is trans-generational, radiation-induced chromosomal instability in the foetal

  10. Modelling static and dynamic behaviour of proton exchange membrane fuel cells on the basis of electro-chemical description

    Science.gov (United States)

    Ceraolo, M.; Miulli, C.; Pozio, A.

    A simplified dynamical model of a fuel cell of the proton exchange membrane (PEM) type, based on physical-chemical knowledge of the phenomena occurring inside the cell has been developed by the authors. The model has been implemented in the MATLAB/SIMULINK environment. Lab tests have been carried out at ENEA's laboratories; and a good agreement has been found between tests and simulations, both in static and dynamic conditions. In a previous study [M. Ceraolo, R. Giglioli, C. Miulli, A. Pozio, in: Proceedings of the 18th International Electric Fuel Cell and Hybrid Vehicle Symposium (EVS18), Berlin, 20-24 October 2001, p. 306] the basic ideas of the model, as well as its experimental validation have been published. In the present paper, the full implementation of the model is reported in detail. Moreover, a procedure for evaluating all the needed numerical parameters is presented.

  11. NATO Advanced Research Workshop on The Theory of Chemical Reaction Dynamics

    CERN Document Server

    1986-01-01

    The calculation of cross sections and rate constants for chemical reactions in the gas phase has long been a major problem in theoretical chemistry. The need for reliable and applicable theories in this field is evident when one considers the significant recent advances that have been made in developing experimental techniques, such as lasers and molecular beams, to probe the microscopic details of chemical reactions. For example, it is now becoming possible to measure cross sections for chemical reactions state selected in the vibrational­ rotational states of both reactants and products. Furthermore, in areas such as atmospheric, combustion and interstellar chemistry, there is an urgent need for reliable reaction rate constant data over a range of temperatures, and this information is often difficult to obtain in experiments. The classical trajectory method can be applied routinely to simple reactions, but this approach neglects important quantum mechanical effects such as tunnelling and resonances. For al...

  12. Molecular beam studies of unimolecular and bimolecular chemical reaction dynamics using VUV synchrotron radiation as a product probe

    Energy Technology Data Exchange (ETDEWEB)

    Blank, David Andrew [Univ. of California, Berkeley, CA (United States)

    1997-08-01

    This dissertation describes the use of a new molecular beam apparatus designed to use tunable VUV synchrotron radiation for photoionization of the products from scattering experiments. The apparatus was built at the recently constructed Advanced Light Source at Lawrence Berkeley National Laboratory, a third generation 1-2 GeV synchrotron radiation source. The new apparatus is applied to investigations of the dynamics of unimolecular reactions, photodissociation experiments, and bimolecular reactions, crossed molecular beam experiments. The first chapter describes the new apparatus and the VUV radiation used for photoionization. This is followed by a number of examples of the many advantages provided by using VUV photoionization in comparison with the traditional technique of electron bombardment ionization. At the end of the chapter there is a discussion of the data analysis employed in these scattering experiments. The remaining four chapters are complete investigations of the dynamics of four chemical systems using the new apparatus and provide numerous additional examples of the advantages provided by VUV photoionizaiton of the products. Chapters 2-4 are photofragment translational spectroscopy studies of the photodissociation dynamics of dimethyl sulfoxide, acrylonitrile, and vinyl chloride following absorption at 193 mn. All of these systems have multiple dissociation channels and provide good examples of the ability of the new apparatus to unravel the complex UV photodissociation dynamics that can arise in small polyatomic molecules.

  13. Vascularization of the dorsal root ganglia and peripheral nerve of the mouse: Implications for chemical-induced peripheral sensory neuropathies

    Directory of Open Access Journals (Sweden)

    Melemedjian Ohannes K

    2008-03-01

    Full Text Available Abstract Although a variety of industrial chemicals, as well as several chemotherapeutic agents used to treat cancer or HIV, preferentially induce a peripheral sensory neuropathy what remains unclear is why these agents induce a sensory vs. a motor or mixed neuropathy. Previous studies have shown that the endothelial cells that vascularize the dorsal root ganglion (DRG, which houses the primary afferent sensory neurons, are unique in that they have large fenestrations and are permeable to a variety of low and high molecular weight agents. In the present report we used whole-mount preparations, immunohistochemistry, and confocal laser scanning microscopy to show that the cell body-rich area of the L4 mouse DRG has a 7 fold higher density of CD31+ capillaries than cell fiber rich area of the DRG or the distal or proximal aspect of the sciatic nerve. This dense vascularization, coupled with the high permeability of these capillaries, may synergistically contribute, and in part explain, why many potentially neurotoxic agents preferentially accumulate and injure cells within the DRG. Currently, cancer survivors and HIV patients constitute the largest and most rapidly expanding groups that have chemically induced peripheral sensory neuropathy. Understanding the unique aspects of the vascularization of the DRG and closing the endothelial fenestrations of the rich vascular bed of capillaries that vascularize the DRG before intravenous administration of anti-neoplastic or anti-HIV therapies, may offer a mechanism based approach to attenuate these chemically induced peripheral neuropathies in these patients.

  14. Comparison of two chemically-induced colitis-models in adult zebrafish, using optical projection tomography and novel transcriptional markers

    DEFF Research Database (Denmark)

    Haarder, Simon; Kania, Per Walter; Holm, Thomas

    2016-01-01

    of proinflammatory cytokines, acute-phase reactants and metalloprotease 9 in both chemical models, primarily after 72 hours. In comparison, transcription factors and cytokines associated with Th1 and Th17 (Crohn’s) and Th2 (ulcerative colitis) were mainly not affected in this acute setting. However, elevated...... zebrafish. In conclusion, a distinct acute inflammatory reaction was induced in both chemical models. Further, oxazolone and TNBS did not result in clear-cut Th2 and Th1/Th17 pathway signaling at this early timepoint, but the applied molecular tools may provide further insight to the IBD pathogenesis...

  15. Combination of high-performance refractometry and infrared spectroscopy as a probe for chemically induced gelation and vitrification of epoxies

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, U; Philipp, M; Gervais, P-C; Sanctuary, R; Krueger, J K [Laboratoire de Physique des Materiaux, Universite du Luxembourg, 162A avenue de la faiencerie, L-1511 Luxembourg (Luxembourg); Possart, W; Wehlack, C [Fachbereich Werkstoffwissenschaften, Universitaet des Saarlandes, D-66123 Saarbruecken (Germany); Kieffer, J, E-mail: ulrich.mueller@uni.l [Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI (United States)

    2010-08-15

    A combination of infrared spectroscopy and high-performance refractometry was used to investigate the chemically induced sol-gel and glass transition during the polymerization of epoxies. Representations of the refractive index versus chemical conversion reveal an interesting insight into the optical properties accompanying gelation and vitrification. Whereas the electronic polarizability of the liquid state of small average molecular mass and the glassy state is dominated by the mass density, an unexpected excess polarizability observed during the gelation is attributed to cooperative dipole-dipole interactions.

  16. In-Situ Chemical Dynamics and Phase Mapping Under Steep Thermal Gradients Using Time-Resolved and Spatially Resolved X-Ray Diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Wong, J.; Larson, E.M.; Holt, J.B.; Ressler, T.; Elmer, J.W.

    1999-09-17

    Time-resolved and spatially-resolved diffraction techniques have been developed recently to perform materials dynamics study in-situ extending into the time and spatial domain in high temperature processes. The applications of these methods to investigate the chemical dynamics of solid combustion reactions and to map phases and their transformation in fusion welds are exemplified in this paper.

  17. Electron dynamics upon ionization: Control of the timescale through chemical substitution and effect of nuclear motion

    Energy Technology Data Exchange (ETDEWEB)

    Vacher, Morgane; Bearpark, Michael J.; Robb, Michael A. [Department of Chemistry, Imperial College London, London SW7 2AZ (United Kingdom); Mendive-Tapia, David [Laboratoire CEISAM - UMR CNR 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3 (France)

    2015-03-07

    Photoionization can generate a non-stationary electronic state, which leads to coupled electron-nuclear dynamics in molecules. In this article, we choose benzene cation as a prototype because vertical ionization of the neutral species leads to a Jahn-Teller degeneracy between ground and first excited states of the cation. Starting with equal populations of ground and first excited states, there is no electron dynamics in this case. However, if we add methyl substituents that break symmetry but do not radically alter the electronic structure, we see charge migration: oscillations in the spin density that we can correlate with particular localized electronic structures, with a period depending on the gap between the states initially populated. We have also investigated the effect of nuclear motion on electron dynamics using a complete active space self-consistent field (CASSCF) implementation of the Ehrenfest method, most previous theoretical studies of electron dynamics having been carried out with fixed nuclei. In toluene cation for instance, simulations where the nuclei are allowed to move show significant differences in the electron dynamics after 3 fs, compared to simulations with fixed nuclei.

  18. Non-steady state mass action dynamics without rate constants: dynamics of coupled reactions using chemical potentials

    Science.gov (United States)

    Cannon, William R.; Baker, Scott E.

    2017-10-01

    Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in scope and application by the fact that the determination of enzyme rate constants is laborious and low throughput. We present a statistical thermodynamic formulation of the law of mass action for coupled reactions at both steady states and non-stationary states. The formulation uses chemical potentials instead of rate constants. When used to model deterministic systems, the method corresponds to a rescaling of the time dependent reactions in such a way that steady states can be reached on the same time scale but with significantly fewer computational steps. The relationships between reaction affinities, free energy changes and generalized detailed balance are central to the discussion. The significance for applications in systems biology are discussed as is the concept and assumption of maximum entropy production rate as a biological principle that links thermodynamics to natural selection.

  19. Characterizations of Dynamic Strain-induced Transformation in Low Carbon Steel

    Institute of Scientific and Technical Information of China (English)

    Luhan Hao; Mingyue Sun; Namin Xiao; Dianzhong Li

    2012-01-01

    Dynamic strain-induced transformation of the low carbon steel Q(235) at 770℃ and 850℃ leads to fine ferrite grains. The microstructure characterization and mechanism of the fine ferrite grain were studied by scanning electron microscopy (SEM), transmission electron microscopy (TEM) and electron backscattered diffraction (EBSD) technique. The results show that strain-induced microstructure is the mixed microstructure of ferrite and pearlite, with cementite randomly distributed on ferrite grain boundaries and the grains interiors. EBSD images of grain boundaries demonstrate that high angle grain boundaries (HAGBs) are dominant in both of the deformation induced microstructures occurring below and above A(e3) , with only a few low angle grain boundaries (LAGBs) existing in the grain interiors. It implies that the dynamic strain-induced transformation (DSIT) happens above and below A(e3) temperature and has the same phase transition mechanisms. The refinement of ferrite is the cooperative effect of DSIT and continuous dynamic recrystallization (CDRX) of ferrite. Besides, DSIT is deemed as an incomplete carbon diffusion phase transition through the analysis of microstructure and the previous simulated results. The strengths of the Q(235) steel with refined ferrite and pearlite structure get doubled than the initial state without treated by DSIT and the residual stress in the refined structure is partly responsible for the ductility loss.

  20. Developing a multimedia model of chemical dynamics in an urban area.

    Science.gov (United States)

    Diamond, M L; Priemer, D A; Law, N L

    2001-09-01

    A multimedia model has been developed to account for the movement of semi-volatile organic compounds (SOCs) in an urban environment. The model, based on a Level III fugacity model of D. Mackay (Multimedia Environmental Models: The Fugacity Approach, Lewis Publishers, Boca Raton, FL, 1991), consists of six compartments: air, surface water, sediment, soil, vegetation, and an organic film that coats impervious surfaces. The latter is a newly identified compartment into which gas-phase SOCs partition and particle-phase SOCs are believed to be efficiently captured (M.L. Diamond, S.E. Gingrich, K. Fertuck, B.E. McCarry, G.A. Stern, B. Billeck, B. Grift, D. Brooker, T.D. Yager, Environ. Sci. Technol., 34 (2000a), 2900-2908). The model, parameterized for downtown Toronto, Ontario, Canada, and run with an illustrative emission rate for selected polycyclic aromatic hydrocarbons and homologues of polychlorinated dibenzodioxins, indicates that the film achieves the highest concentrations among media but that soils are the greatest sink for all but the least hydrophobic chemicals. The film "reflects" the more volatile chemicals into air, facilitates removal to surface waters by wash-off, and provides a surface on which photolytic degradation can occur. As such, the film is a transient sink that increases chemical mobility in urban areas by increasing air concentrations and the cycling of these compounds between air and urban surfaces and increasing water concentrations. Vegetation also accumulates SOCs, a portion of which is transferred to soil that reduces chemical mobility.