WorldWideScience

Sample records for chemical dynamics studies

  1. 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.

  2. 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...

  3. 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.

  4. Theoretical studies of the dynamics of chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    Wagner, A.F. [Argonne National Laboratory, IL (United States)

    1993-12-01

    Recent research effort has focussed on several reactions pertinent to combustion. The formation of the formyl radical from atomic hydrogen and carbon monoxide, recombination of alkyl radicals and halo-alkyl radicals with halogen atoms, and the thermal dissociation of hydrogen cyanide and acetylene have been studied by modeling. In addition, the inelastic collisions of NCO with helium have been investigated.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  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. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Dynamic Passive Dosing for Studying the Biotransformation of Hydrophobic Organic Chemicals: Microbial Degradation as an Example

    DEFF Research Database (Denmark)

    Smith, Kilian E. C.; Rein, Arno; Trapp, Stefan

    2012-01-01

    and defined dissolved concentration range, and enables high compound turnover even at low concentrations to simplify end point measurement. As a case study, the biodegradation kinetics of two model HOCs by the bacterium Sphingomonas paucimobilis EPA505 were measured at defined dissolved concentrations ranging...... also similar for both PAHs, but decreased by around 2 orders of magnitude with increasing dissolved concentrations. Dynamic passive dosing is a useful tool for measuring biotransformation kinetics at realistically low and defined dissolved HOC concentrations....

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Study of features of physical and chemical properties of household chemicals on population dynamics of Blattella Germanica (L. in Kyiv

    Directory of Open Access Journals (Sweden)

    Георгій Васильович Кобеньок

    2015-11-01

    Full Text Available The importance of studying the ecology of premises is to study the negative impact on the domestic environment some environmental factors of anthropogenic origin. In the article the possibility of using the method of biological indication is considered to analyze environmental risks emerging in the artificial environment of modern premises. For example of Blattella Germanica (L. it is investigated the possible effect of the toxic properties of synthetic detergents to negative fluctuations in the population of this species of insects-sinanthropus

  3. Mechanism resulting in chemical imbalance due to cellular damage associated with mechanoporation: A molecular dynamics study

    Science.gov (United States)

    Sliozberg, Yelena R.; Chantawansri, Tanya L.

    2016-05-01

    To elucidate the mechanism of ion transport through a transmembrane pore, all-atom molecular dynamics simulations were employed. A model membrane where a pore connects the intra- and extra-cellular compartment was considered. Pores with radii of 1.5 nm or less exhibited resealing over the course of 135 ns simulations, and ionic disturbance is minimal. Ion transport through a larger pore (2 nm radius) leads to a substantial change in the intra- and extra-cellular ionic concentrations. The influx of Na+ and Cl- ions down their concentration gradients is greater than the efflux of K+ leading to an osmotic influx of water.

  4. 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.

  5. Chemical Industry Bandwidth Study

    Energy Technology Data Exchange (ETDEWEB)

    none,

    2006-12-01

    The Chemical Bandwidth Study provides a snapshot of potentially recoverable energy losses during chemical manufacturing. The advantage of this study is the use of "exergy" analysis as a tool for pinpointing inefficiencies.

  6. The Dart estuary, Devon, UK: a case study of chemical dynamics and pollutant mobility

    Directory of Open Access Journals (Sweden)

    2007-01-01

    Full Text Available Water, sediments and gill and digestive gland tissues of adult common shore crab (Carcinus maenas, collected at Noss Marina, Sandquay (Britannia Royal Naval College, the Dartmouth Pier, Warfleet Cove and Sugary Cove in the Dart estuary, Devon, UK, were analysed for major, minor and trace elements in spring 2004. Total acid-available measurements analysed included the truly dissolved component and acid-available sediments. Trace metal concentrations are associated largely with particulate and micro-particulate/colloidal phases, the latter being able to pass through standard filter papers. Wide ranges of chemical concentrations were found in the water, sediments and tissues at all the locations. In the water column, 48% of the variance is linked to the sea-salt component (Cl, Na, K, Ca, Mg, B, Li and Sr and the sediment-associated acid-available fractions are linked to Fe-rich lithogenous materials (Ba, Co, Cu, Fe, Mn, V and Zn. In the sediments, trace elements of Cd, Co, Cr, Fe, Pb, Mn, Ni and V are correlated with the sea salts and associated with the fraction of fine sediments within the total sediment. In the gills and the digestive gland tissues of crabs, high concentrations of Al, Cu and Fe are found and there are correlations between acid-available trace metals of Cu, Cr, Fe, Mn, Ni, Sr and Zn. The relationships between trace metal contaminants, their site-specific concentrations, their temporal and spatial variability and the effects of human activities, such as moorland/agriculture with historic mining and recreational activities in the lower Dart estuary, are discussed.

  7. 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.

  8. 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.

  9. 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).

  10. The reactivation of tabun-inhibited mutant AChE with Ortho-7: steered molecular dynamics and quantum chemical studies.

    Science.gov (United States)

    Lo, Rabindranath; Chandar, Nellore Bhanu; Ghosh, Shibaji; Ganguly, Bishwajit

    2016-04-01

    A highly toxic nerve agent, tabun, can inhibit acetylcholinesterase (AChE) at cholinergic sites, which leads to serious cardiovascular complications, respiratory compromise and death. We have examined the structural features of the tabun-conjugated AChE complex with an oxime reactivator, Ortho-7, to provide a strategy for designing new and efficient reactivators. Mutation of mAChE within the choline binding site by Y337A and F338A and its interaction with Ortho-7 has been investigated using steered molecular dynamics (SMD) and quantum chemical methods. The overall study shows that after mutagenesis (Y337A), the reactivator can approach more freely towards the phosphorylated active site of serine without any significant steric hindrance in the presence of tabun compared to the wild type and double mutant. Furthermore, the poor binding of Ortho-7 with the peripheral residues of mAChE in the case of the single mutant compared to that of the wild-type and double mutant (Y337A/F338A) can contribute to better efficacy in the former case. Ortho-7 has formed a greater number of hydrogen bonds with the active site surrounding residues His447 and Phe295 in the case of the single mutant (Y337A), and that stabilizes the drug molecule for an effective reactivation process. The DFT M05-2X/6-31+G(d) level of theory shows that the binding energy of Ortho-7 with the single mutant (Y337A) is energetically more preferred (-19.8 kcal mol(-1)) than the wild-type (-8.1 kcal mol(-1)) and double mutant (Y337A/F338A) (-16.0 kcal mol(-1)). The study reveals that both the orientation of the oxime reactivator for nucleophilic attack and the stabilization of the reactivator at the active site would be crucial for the design of an efficient reactivator.

  11. 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.

  12. 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

  13. Fe/C interactions during SWNT growth with C2 feedstock molecules: A quantum chemical molecular dynamics study.

    Science.gov (United States)

    Zheng, Guishan; Irle, Stephan; Morokuma, Keiji

    2006-05-01

    We are presenting the first quantum chemical molecular dynamics (QM/MD) model simulations for iron catalyzed single-walled carbon nanotube (SWNT) growth based on the density functional tight binding (DFTB) quantum chemical potential. As model systems, open-ended (10,10) armchair tube fragments were selected with 0, 10, and 20 Fe atoms attached in 1,4-positions on the open rims, and ensembles of randomly oriented C2 molecules were included to simulate carbon plasma feedstock molecules. Isokinetic trajectories at 1500 K to 3000 K show that divalent Fe increases the number of coordination partners with carbon and/or Fe, depending on the Fe concentration. Fe/C interactions weaken the tube sidewall due to electron transfer from Fe into antibonding carbon orbitals, and C2 addition occurs mainly in an Fe-C2-Fe bridge addition mechanism, while growth of polyyne chains characteristic for high-temperature carbon systems is suppressed in the presence of Fe on the rims of the growing SWNT. Our findings are the first quantum chemical evidence for the importance of intermetallic interactions during SWNT growth.

  14. 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.

  15. Chemical Imaging and Dynamical Studies of Reactivity and Emergent Behavior in Complex Interfacial Systems. Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    Sibener, Steven J. [University of Chicago, IL (United States)

    2014-03-11

    This research program explored the efficacy of using molecular-level manipulation, imaging and scanning tunneling spectroscopy in conjunction with supersonic molecular beam gas-surface scattering to significantly enhance our understanding of chemical processes occurring on well-characterized interfaces. One program focus was on the spatially-resolved emergent behavior of complex reaction systems as a function of the local geometry and density of adsorbate-substrate systems under reaction conditions. Another focus was on elucidating the emergent electronic and related reactivity characteristics of intentionally constructed single and multicomponent atom- and nanoparticle-based materials. We also examined emergent chirality and self-organization in adsorbed molecular systems where collective interactions between adsorbates and the supporting interface lead to spatial symmetry breaking. In many of these studies we combined the advantages of scanning tunneling (STM) and atomic force (AFM) imaging, scanning tunneling local electronic spectroscopy (STS), and reactive supersonic molecular beams to elucidate precise details of interfacial reactivity that had not been observed by more traditional surface science methods. Using these methods, it was possible to examine, for example, the differential reactivity of molecules adsorbed at different bonding sites in conjunction with how reactivity is modified by the local configuration of nearby adsorbates. At the core of this effort was the goal of significantly extending our understanding of interfacial atomic-scale interactions to create, with intent, molecular assemblies and materials with advanced chemical and physical properties. This ambitious program addressed several key topics in DOE Grand Challenge Science, including emergent chemical and physical properties in condensed phase systems, novel uses of chemical imaging, and the development of advanced reactivity concepts in combustion and catalysis including carbon

  16. 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.

  17. Chiral recognition of Propranolol enantiomers by β-Cyclodextrin: Quantum chemical calculation and molecular dynamics simulation studies

    Energy Technology Data Exchange (ETDEWEB)

    Ghatee, Mohammad Hadi, E-mail: ghatee@susc.ac.ir; Sedghamiz, Tahereh

    2014-12-05

    Highlights: • Enantiomeric recognition of Propranolol studied by β-Cyclodextrin complexations. • Complexes characterized by PM3 and molecular dynamics (MD) simulation methods. • Results support more stability of R-enantiomer complex in gas and in aqueous solution phases. • Gas phase complexes are unlikely free-energy-wise, though solution phase’s are more likely. • Higher molecular diffusion in aqueous solution phase is inherent to S-enantiomer. - Abstract: Enantiomeric recognition of Propranolol by complexation with β-Cyclodextrin was studied by PM3 method and molecular dynamics (MD) simulation. Gas phase results show that the R-enantiomer complex is more stable than the S-enantiomer complex by 8.54 kJ/mol (Hartree–Fock energy). Using polarized continuum model, solution phase of R-enantiomer complex was found to be more stable than S-enantiomer complex by 25.95 kJ/mol. Both complexes hardly occur at room temperature free-energy-wise, though, complexation with R-enantiomer is more favorable than with S-enantiomer enthalpy-wise. Also, complexes were studied by molecular dynamics simulation in gas and solution phases. More stability of R-enantiomer complex in gas phase is confirmed by MD van der Waals energy (5.04 kJ/mol) and closely by the counterpart PM3 binding energy (8.54 kJ/mol). Simulation in solution phase indicates more stability of R-enantiomer complex. Finally, simulated transport property provides insight into the high anisotropic atoms motion according to which S-Propranolol found possessing significantly higher dynamics.

  18. Chiral recognition of Propranolol enantiomers by β-Cyclodextrin: Quantum chemical calculation and molecular dynamics simulation studies

    Science.gov (United States)

    Ghatee, Mohammad Hadi; Sedghamiz, Tahereh

    2014-12-01

    Enantiomeric recognition of Propranolol by complexation with β-Cyclodextrin was studied by PM3 method and molecular dynamics (MD) simulation. Gas phase results show that the R-enantiomer complex is more stable than the S-enantiomer complex by 8.54 kJ/mol (Hartree-Fock energy). Using polarized continuum model, solution phase of R-enantiomer complex was found to be more stable than S-enantiomer complex by 25.95 kJ/mol. Both complexes hardly occur at room temperature free-energy-wise, though, complexation with R-enantiomer is more favorable than with S-enantiomer enthalpy-wise. Also, complexes were studied by molecular dynamics simulation in gas and solution phases. More stability of R-enantiomer complex in gas phase is confirmed by MD van der Waals energy (5.04 kJ/mol) and closely by the counterpart PM3 binding energy (8.54 kJ/mol). Simulation in solution phase indicates more stability of R-enantiomer complex. Finally, simulated transport property provides insight into the high anisotropic atoms motion according to which S-Propranolol found possessing significantly higher dynamics.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. Insight into the effect of inhibitor resistant S130G mutant on physico-chemical properties of SHV type beta-lactamase: a molecular dynamics study.

    Directory of Open Access Journals (Sweden)

    Mohd Hassan Baig

    Full Text Available Bacterial resistance is a serious threat to human health. The production of β-lactamase, which inactivates β-lactams is most common cause of resistance to the β-lactam antibiotics. The Class A enzymes are most frequently encountered among the four β-lactamases in the clinic isolates. Mutations in class A β-lactamases play a crucial role in substrate and inhibitor specificity. SHV and TEM type are known to be most common class A β-lactamases. In the present study, we have analyzed the effect of inhibitor resistant S130G point mutation of SHV type Class-A β-lactamase using molecular dynamics and other in silico approaches. Our study involved the use of different in silico methods to investigate the affect of S130G point mutation on the major physico-chemical properties of SHV type class A β-lactamase. We have used molecular dynamics approach to compare the dynamic behaviour of native and S130G mutant form of SHV β-lactamase by analyzing different properties like root mean square deviation (RMSD, H-bond, Radius of gyration (Rg and RMS fluctuation of mutation. The results clearly suggest notable loss in the stability of S130G mutant that may further lead to decrease in substrate specificity of SHV. Molecular docking further indicates that S130G mutation decreases the binding affinity of all the three inhibitors in clinical practice.

  7. 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.

  8. 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.

  9. 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,

  10. 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.

  11. 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.

  12. Novel serine-based gemini surfactants as chemical permeation enhancers of local anesthetics: A comprehensive study on structure-activity relationships, molecular dynamics and dermal delivery.

    Science.gov (United States)

    Teixeira, Raquel S; Cova, Tânia F G G; Silva, Sérgio M C; Oliveira, Rita; do Vale, M Luísa C; Marques, Eduardo F; Pais, Alberto A C C; Veiga, Francisco J B

    2015-06-01

    This work aims at studying the efficacy of a series of novel biocompatible, serine-based surfactants as chemical permeation enhancers for two different local anesthetics, tetracaine and ropivacaine, combining an experimental and computational approach. The surfactants consist of gemini molecules structurally related, but with variations in headgroup charge (nonionic vs. cationic) and in the hydrocarbon chain lengths (main and spacer chains). In vitro permeation and molecular dynamics studies combined with cytotoxicity profiles were performed to investigate the permeation of both drugs, probe skin integrity, and rationalize the interactions at molecular level. Results show that these enhancers do not have significant deleterious effects on the skin structure and do not cause relevant changes on cell viability. Permeation across the skin is clearly improved using some of the selected serine-based gemini surfactants, namely the cationic ones with long alkyl chains and shorter spacer. This is noteworthy in the case of ropivacaine hydrochloride, which is not easily administered through the stratum corneum. Molecular dynamics results provide a mechanistic view of the surfactant action on lipid membranes that essentially corroborate the experimental observations. Overall, this study suggests the viability of these serine-based surfactants as suitable and promising delivery agents in pharmaceutical formulations.

  13. 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.

  14. 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...

  15. 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.

  16. 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.

  17. 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.

  18. Structure of N'-(adamantan-2-ylidene)benzohydrazide, a potential antibacterial agent, in solution: Molecular dynamics simulations, quantum chemical calculations and Ultraviolet–visible spectroscopy studies

    Indian Academy of Sciences (India)

    ALEXANDER M ANDRIANOV; IVAN A KASHYN; VIKTOR M ANDRIANOV; MAKSIM B SHUNDALAU; ANTON V HLINISTY; SERGEY V GAPONENKO; ELENA V SHABUNYA -KLYACHKOVSKAYA; ANNA MATSUKOVICH; ABDUL-MALEK S AL- TAMIMI; ALI A EL- EMAM

    2016-12-01

    The molecular dynamics simulations of the structure of the N'-(adamantan-2-ylidene)benzohydrazide followed by the quantum chemical calculations at the DFT level of theory have identified four stable conformers of this potential antibacterial agent in solution: one “central” cis- and three (“central”, “left” and “right”) trans-conformers. The UV-Vis absorption spectrum in the 220–320 nm region in the ethanol solution reveals two bands that can be primarily explained based on the ab initio calculations of the spectral characteristics of the “side” trans-conformers at the MRPT level of theory. However, the close energy values for thecalculated cis- S₁ ← S₀ and “side” trans- S₂ ← S₀ transitions cannot exclude the presence of cis-conformer in solution. Therefore, the data obtained show that the coexistence of both trans-conformers and cis-conformer should be taken into consideration when studying the pharmaceutical properties of the title molecule.

  19. The study and applications of photochemical-dynamical gravity wave model Ⅱ-- The effects of stable gravity wave on chemical species distribution in mesosphere

    Institute of Scientific and Technical Information of China (English)

    XU; Jiyao(徐寄遥); MA; Ruiping(马瑞平); A.K.Smith

    2002-01-01

    A nonlinear, compressible, non-isothermal gravity wave model that involves photochemistry is used to study the effects of gravity wave on atmospheric chemical species distributions in this paper. The changes in the distributions of oxygen compound and hydrogen compound density induced by gravity wave propagation are simulated. The results indicate that when a gravity wave propagates through a mesopause region, even if it does not break, it can influence the background distributions of chemical species. The effect of gravity wave on chemical species at night is larger than in daytime.

  20. 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.

  1. 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.

  2. Quantum chemical study on influence of intermolecular hydrogen bonding on the geometry, the atomic charges and the vibrational dynamics of 2,6-dichlorobenzonitrile.

    Science.gov (United States)

    Agarwal, Parag; Bee, Saba; Gupta, Archana; Tandon, Poonam; Rastogi, V K; Mishra, Soni; Rawat, Poonam

    2014-01-01

    FT-IR (4000-400 cm(-1)) and FT-Raman (4000-200 cm(-1)) spectral measurements on solid 2,6-dichlorobenzonitrile (2,6-DCBN) have been done. The molecular geometry, harmonic vibrational frequencies and bonding features in the ground state have been calculated by density functional theory at the B3LYP/6-311++G (d,p) level. A comparison between the calculated and the experimental results covering the molecular structure has been made. The assignments of the fundamental vibrational modes have been done on the basis of the potential energy distribution (PED). To investigate the influence of intermolecular hydrogen bonding on the geometry, the charge distribution and the vibrational spectrum of 2,6-DCBN; calculations have been done for the monomer as well as the tetramer. The intermolecular interaction energies corrected for basis set superposition error (BSSE) have been calculated using counterpoise method. Based on these results, the correlations between the vibrational modes and the structure of the tetramer have been discussed. Molecular electrostatic potential (MEP) contour map has been plotted in order to predict how different geometries could interact. The Natural Bond Orbital (NBO) analysis has been done for the chemical interpretation of hyperconjugative interactions and electron density transfer between occupied (bonding or lone pair) orbitals to unoccupied (antibonding or Rydberg) orbitals. UV spectrum was measured in methanol solution. The energies and oscillator strengths were calculated by Time Dependent Density Functional Theory (TD-DFT) and matched to the experimental findings. TD-DFT method has also been used for theoretically studying the hydrogen bonding dynamics by monitoring the spectral shifts of some characteristic vibrational modes involved in the formation of hydrogen bonds in the ground and the first excited state. The (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the Gauge independent atomic orbital

  3. 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...

  4. All-atom Molecular Dynamic Simulations Combined with the Chemical Shifts Study on the Weak Interactions of Ethanol-water System

    Institute of Scientific and Technical Information of China (English)

    ZHANG Rong; LUO San-Lai; WU Wen-Juan

    2008-01-01

    All-atom molecular dynamics(MD)simulation combined with chemical shifts was performed to investigate the interactions over the entire concentration range of the ethanol(EtOH)-water system.The results of the simulation were adopted to explain the NMR experiments by hydrogen bonding analysis.The strong hydrogen bonds and weak C-H…O contacts coexist in the mixtures through the analysis of the radial distribution functions.And the liquid structures in the whole concentration of EtOH-water mixtures can be classified into three regions by the statistic analysis of the hydrogen-bonding network in the MD simulations.Moreover,the chemical shifts of the hydrogen atom are in agreement witb the statistical results of the average number hydrogen bonds in the MD simulations.Interestingly,the excess relative extent Eηrel calculated by the MD simulations and chemical shifts in the EtOH aqueous solutions shows the largest deviation at XEtOH≈0.18.The excess properties present good agreement with the excess enthalpy in the concentration dependence.

  5. 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…

  6. 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.

  7. 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.

  8. Investigation of Spark Ignition and Autoignition in Methane and Air Using Computational Fluid Dynamics and Chemical Reaction Kinetics. A numerical Study of Ignition Processes in Internal Combustion Engines

    Energy Technology Data Exchange (ETDEWEB)

    Nordrik, R.

    1993-12-01

    The processes in the combustion chamber of internal combustion engines have received increased attention in recent years because their efficiencies are important both economically and environmentally. This doctoral thesis studies the ignition phenomena by means of numerical simulation methods. The fundamental physical relations include flow field conservation equations, thermodynamics, chemical reaction kinetics, transport properties and spark modelling. Special attention is given to the inclusion of chemical kinetics in the flow field equations. Using his No Transport of Radicals Concept method, the author reduces the computational efforts by neglecting the transport of selected intermediate species. The method is validated by comparison with flame propagation data. A computational method is described and used to simulate spark ignition in laminar premixed methane-air mixtures and the autoignition process of a methane bubble surrounded by hot air. The spark ignition simulation agrees well with experimental results from the literature. The autoignition simulation identifies the importance of diffusive and chemical processes acting together. The ignition delay times exceed the experimental values found in the literature for premixed ignition delay, presumably because of the mixing process and lack of information on low temperature reactions in the skeletal kinetic mechanism. Transient turbulent methane jet autoignition is simulated by means of the KIVA-II code. Turbulent combustion is modelled by the Eddy Dissipation Concept. 90 refs., 81 figs., 3 tabs.

  9. 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,

  10. Molecular dynamics and quantum chemical calculation studies on 4,4-dimethyl-3-thiosemicarbazide as corrosion inhibitor in 2.5 M H{sub 2}SO{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Musa, Ahmed Y., E-mail: ahmed.musa@ymail.com [Department of Chemical and Process Engineering, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor (Malaysia); Kadhum, Abdul Amir H.; Mohamad, Abu Bakar; Takriff, Mohd Sobri [Department of Chemical and Process Engineering, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor (Malaysia)

    2011-09-15

    Highlights: {yields} This work deals with a study of chemical additives for corrosion inhibition of mild steel in acidic conditions. {yields} The effects of the additive 4,4-dimethyl-3-thiosemicarbazide (DTS) on mild steel were studied by means of electrochemical techniques. {yields} Quantum chemical calculations and molecular dynamic model were performed to characterize the inhibition mechanism. {yields} The calculations provided information that helps in the analysis/interpretation of the experimental work. - Abstract: The inhibition of mild steel corrosion in a 2.5 M H{sub 2}SO{sub 4} solution by 4,4-dimethyl-3-thiosemicarbazide (DTS) was studied at 30 deg. C using potentiodynamic polarization and electrochemical impedance spectroscopy (EIS). Quantum chemical parameters were calculated for DTS using PM3-SCF method. The molecular dynamic method was performed to simulate the adsorption of the DTS molecules on Fe surface. Results showed that DTS performed excellent as inhibitor for mild steel corrosion in a 2.5 M H{sub 2}SO{sub 4} solution and indicated that the inhibition efficiencies increase with the concentration of inhibitor. Theoretical results indicated that DTS could adsorb on the mild steel surface firmly through heteroatoms.

  11. 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.

  12. 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.

  13. 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.

  14. Classical and semiclassical aspects of chemical dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Gray, S.K.

    1982-08-01

    Tunneling in the unimolecular reactions H/sub 2/C/sub 2/ ..-->.. HC/sub 2/H, HNC ..-->.. HCN, and H/sub 2/CO ..-->.. H/sub 2/ + CO is studied with a classical Hamiltonian that allows the reaction coordinate and transverse vibrational modes to be considered directly. A combination of classical perturbation theory and the semiclassical WKB method allows tunneling probabilities to be obtained, and a statistical theory (RRKM) is used to construct rate constants for these reactions in the tunneling regime. In this fashion, it is found that tunneling may be important, particularly for low excitation energies. Nonadiabatic charge transfer in the reaction Na + I ..-->.. Na /sup +/ + I/sup -/ is treated with classical trajectories based on a classical Hamiltonian that is the analogue of a quantum matrix representation. The charge transfer cross section obtained is found to agree reasonably well with the exact quantum results. An approximate semiclassical formula, valid at high energies, is also obtained. The interaction of radiation and matter is treated from a classical viewpoint. The excitation of an HF molecule in a strong laser is described with classical trajectories. Quantum mechanical results are also obtained and compared to the classical results. Although the detailed structure of the pulse time averaged energy absorption cannot be reproduced classically, classical mechanics does predict the correct magnitude of energy absorption, as well as certain other qualitative features. The classical behavior of a nonrotating diatomic molecule in a strong laser field is considered further, by generating a period advance map that allows the solution over many periods of oscillation of the laser to be obtained with relative ease. Classical states are found to form beautiful spirals in phase space as time progresses. A simple pendulum model is found to describe the major qualitative features. (WHM)

  15. Chemical dynamics in time and energy space

    Energy Technology Data Exchange (ETDEWEB)

    Myers, J.D.

    1993-04-01

    The development of a versatile picosecond ultraviolet/vacuum ultraviolet temporal spectrometer and its potential use for measuring internal energy redistribution in isolated molecules are described in detail. A detailed description of the double-pass Nd:YAG amplifier and the dye amplifiers is given with the pulse energies achieved in the visible, ultraviolet, and vacuum ultraviolet. The amplified visible pulses are shown to be of sub-picosecond duration and near transform limited. The instrument`s temporal response ({le}10 ps) is derived from an instrument limited measurement of the dissociation lifetime of methyl iodide at 266 nm. The methyl iodide experiment is used to discuss the various sources of noise and background signals that are intrinsic to this type of experiment. Non-time-resolved experiments measuring the branching ratio and kinetic energy distributions of products from the 193 nm photodissociation of cyclopentadiene and thiophene are presented. These studies were done using the molecular beam Photofragment Translational Spectroscopy (PTS) technique. The results from the cyclopentadiene experiment confirm that H atom elimination to yield the cyclopentadienyl radical is the dominant dissociation channel. A barrier of {ge}5 kcal/mol can be understood in terms of the delocalization of the radical electron of the cyclopentadienyl fragment. A concerted elimination yielding cyclopropene and acetylene was also observed and is proposed to occur via a bicyclo-[2.1.0]pent-2-ene intermediate. Two other channels, yielding acetylene plus the CH{sub 2}CHCH triplet carbene, and CH{sub 2} plus 1-buten-3-yne, are postulated to occur via ring opening. The implications of the experimental results for bulk thermal oxidation and pyrolysis models are discussed. The thiophene experiment shows six competing dissociation channels. The postulated intermediates for the various thiophene dissociation channels include bicyclo, ring opened, and possibly ring contracted forms.

  16. Chemical dynamics in time and energy space

    Energy Technology Data Exchange (ETDEWEB)

    Myers, James Douglas [Univ. of California, Berkeley, CA (United States)

    1993-04-01

    The development of a versatile picosecond ultraviolet/vacuum ultraviolet temporal spectrometer and its potential use for measuring internal energy redistribution in isolated molecules are described in detail. A detailed description of the double-pass Nd:YAG amplifier and the dye amplifiers is given with the pulse energies achieved in the visible, ultraviolet, and vacuum ultraviolet. The amplified visible pulses are shown to be of sub-picosecond duration and near transform limited. The instrument`s temporal response (≤10 ps) is derived from an instrument limited measurement of the dissociation lifetime of methyl iodide at 266 nm. The methyl iodide experiment is used to discuss the various sources of noise and background signals that are intrinsic to this type of experiment. Non-time-resolved experiments measuring the branching ratio and kinetic energy distributions of products from the 193 nm photodissociation of cyclopentadiene and thiophene are presented. These studies were done using the molecular beam Photofragment Translational Spectroscopy (PTS) technique. The results from the cyclopentadiene experiment confirm that H atom elimination to yield the cyclopentadienyl radical is the dominant dissociation channel. A barrier of ≥5 kcal/mol can be understood in terms of the delocalization of the radical electron of the cyclopentadienyl fragment. A concerted elimination yielding cyclopropene and acetylene was also observed and is proposed to occur via a bicyclo-[2.1.0]pent-2-ene intermediate. Two other channels, yielding acetylene plus the CH2CHCH triplet carbene, and CH2 plus 1-buten-3-yne, are postulated to occur via ring opening. The implications of the experimental results for bulk thermal oxidation and pyrolysis models are discussed. The thiophene experiment shows six competing dissociation channels. The postulated intermediates for the various thiophene dissociation channels include bicyclo, ring opened, and possibly ring contracted

  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. 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

  19. 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.

  20. 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.

  1. Dynamic NMR and Quantum-Chemical Study of the Stereochemistry and Stability of the Chiral MoO2(acac)2 Complex in Solution.

    Science.gov (United States)

    Conte, Marco; Hippler, Michael

    2016-09-01

    The stereochemistry and dynamics of MoO2(acac)2 in benzene, chloroform, and toluene were investigated by variable temperature (1)H NMR, density functional theory (SOGGA11-X, B3LYP), and ab initio (MP2) methods. In solution, an equilibrium between two chiral enantiomers with C2 symmetry was identified, Λ-cis-MoO2(acac)2 and Δ-cis-MoO2(acac)2. The two enantiomers are connected via achiral cis transition states that switch the enantiomeric conformations via a Ray-Dutt, Bailar, and a newly described racemization twisting mechanism. All three mechanisms have similar calculated activation energies. Activation parameters Ea, ΔH(‡), and ΔS(‡) were experimentally determined for the exchange process, with a small, negative ΔS(‡), and a positive ΔH(‡) of 68.1 kJ mol(-1) in benzene, 54.9 kJ mol(-1) in chloroform, and 60.6 kJ mol(-1) in toluene, in reasonable general agreement with the calculations. Trans configurations of MoO2(acac)2 are very much higher in energy than cis and are not relevant in the temperature range experimentally studied, 243-340 K. The enantiomers interconvert within seconds near room temperature and much faster at elevated temperatures. Racemization will thus prevent the use of enantiomerically pure MoO2(acac)2 for chiral catalysis under practical conditions.

  2. 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.

  3. 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.

  4. A comparative study of the chemical and integrated treatments impact against the defoliating insects on the structure and dynamics of the edaphic mesofauna in two oak forests from North-Eastern Romania

    Directory of Open Access Journals (Sweden)

    Adina Cãlugãr

    2009-11-01

    Full Text Available The author presents in this paper some aspects about the edaphicmicroarthropods from the organic horizon of two forest soils belonging to the Ciurea Forest District, Iasi County: ªanta (mixed stands mainly with oak, chemically treated against defoliating insects and Poieni - Tomesti (Quercus robur and Quercuspetraea stands with integrated treatments. The study of edaphic microarthropods was performed both from qualitative and quantitative point of view. It considered the average of the total density of the microarthropod populations and by each taxonomic group, according to stations and subhorizons, as well as the ratio between thetaxonomical and trophic groups. The investigations concerning edaphic mesofauna consist in inventory and analysis of the mites belonging to Oribatida, Gamasida, Actinedida and Acaridida orders, of the Collembola, as well as other insects; other groups of microarthropods were taken into consideration too (pseudoscorpiones,myriapods etc. The consequences of the treatments against the defoliators on theedaphic mesofauna were performed at four different moments. Generally, lower densities were observed in the case of the chemically treated stands. The communities of the edaphic mesofauna from the integrated management treated stands are more stableduring the time. In the chemically treated stands, the densities of the microartropods vary between large limits; this instability could be assigned to this kind of treatment. The vertical distribution of the mesofauna depends on the textural characteristics of the soil, being at the same time a dynamic parameter that is modifyed according to the variation of the climatic factors.

  5. 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.

  6. 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.

  7. Studies in combustion dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Koszykowski, M.L. [Sandia National Laboratories, Livermore, CA (United States)

    1993-12-01

    The goal of this program is to develop a fundamental understanding and a quantitative predictive capability in combustion modeling. A large part of the understanding of the chemistry of combustion processes comes from {open_quotes}chemical kinetic modeling.{close_quotes} However, successful modeling is not an isolated activity. It necessarily involves the integration of methods and results from several diverse disciplines and activities including theoretical chemistry, elementary reaction kinetics, fluid mechanics and computational science. Recently the authors have developed and utilized new tools for parallel processing to implement the first numerical model of a turbulent diffusion flame including a {open_quotes}full{close_quotes} chemical mechanism.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. The RAVE-on catalog of stellar atmospheric parameters and chemical abundances for chemo-dynamic studies in the Gaia era

    CERN Document Server

    Casey, Andrew R; Hogg, David W; Ness, Melissa; Walter-Rix, Hans; Kordopatis, Georges; Kunder, Andrea; Steinmetz, Matthias; Koposov, Sergey; Enke, Harry; Sanders, Jason; Gilmore, Gerry; Zwitter, Tomaž; Freeman, Kenneth C; Casagrande, Luca; Matijevič, Gal; Seabroke, George; Bienaymé, Olivier; Bland-Hawthorn, Joss; Gibson, Brad K; Grebel, Eva K; Helmi, Amina; Munari, Ulisse; Navarro, Julio F; Reid, Warren; Siebert, Arnaud; Wyse, Rosemary

    2016-01-01

    The orbits, atmospheric parameters, chemical abundances, and ages of individual stars in the Milky Way provide the most comprehensive illustration of galaxy formation available. The Tycho-Gaia Astrometric Solution (TGAS) will deliver astrometric parameters for the largest ever sample of Milky Way stars, though its full potential cannot be realized without the addition of complementary spectroscopy. Among existing spectroscopic surveys, the RAdial Velocity Experiment (RAVE) has the largest overlap with TGAS ($\\gtrsim$200,000 stars). We present a data-driven re-analysis of 520,781 RAVE spectra using The Cannon. For red giants, we build our model using high-fidelity APOGEE stellar parameters and abundances for stars that overlap with RAVE. For main-sequence and sub-giant stars, our model uses stellar parameters from the K2/EPIC. We derive and validate effective temperature $T_{\\rm eff}$, surface gravity $\\log{g}$, and chemical abundances of up to seven elements (O, Mg, Al, Si, Ca, Fe, Ni). We report a total of 1...

  14. 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...

  15. 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

  16. Constraints on eruption dynamics of basaltic explosive activity derived from chemical and microtextural study: The example of the Fontana Lapilli Plinian eruption, Nicaragua

    Science.gov (United States)

    Costantini, L.; Houghton, B. F.; Bonadonna, C.

    2010-01-01

    The Fontana Lapilli deposit is one of very few examples of basaltic Plinian eruptions discovered so far. Juvenile clasts have uniform chemical composition and moderate ranges of density and bulk vesicularity. However, clast populations include two textural varieties which are microlite-poor and microlite-rich respectively. These two clast types have the same clast density range, making a distinction impossible on that base alone. The high bubble number density (˜ 10 7 cm - 3 ) and small bubble population of the Fontana clasts suggest that the magma underwent coupled degassing following rapid decompression and fast ascent rate, leading to non-equilibrium degassing with continuous nucleation as it is common for silicic analogues. The Fontana products have lower microlite contents (10-60 vol.%) with respect to the other documented basaltic Plinian eruptions suggesting that the brittle fragmentation, implied for the other basaltic Plinian deposits, does not apply to the Fontana products and another fragmentation mechanism led the basaltic magma to erupt in a Plinian fashion.

  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. Studying chemical reactions in biological systems with MBN Explorer

    DEFF Research Database (Denmark)

    Sushko, Gennady B.; Solov'yov, Ilia A.; Verkhovtsev, Alexey V.

    2016-01-01

    The concept of molecular mechanics force field has been widely accepted nowadays 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....... for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation- or collision-induced damage, and also in transformation and fragmentation processes involving biomolecular systems....

  19. 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.

  20. 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.

  1. 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

  2. Studying Dynamics in Business Networks

    DEFF Research Database (Denmark)

    Andersen, Poul Houman; Anderson, Helen; Havila, Virpi;

    1998-01-01

    This paper develops a theory on network dynamics using the concepts of role and position from sociological theory. Moreover, the theory is further tested using case studies from Denmark and Finland...

  3. Quantum chemical and direct dynamic study on homogeneous gas-phase formation of PBDD/Fs from 2,4,5-tribromophenol and 3,4-dibromophenol.

    Science.gov (United States)

    Yu, Wanni; Li, Pengfei; Xu, Fei; Hu, Jingtian; Zhang, Qingzhu; Wang, Wenxing

    2013-09-01

    2,4,5-Tribromophenol (2,4,5-TBP) and 3,4-dibromophenol (3,4-DBP) have the minimum number of Br atoms needed to form 2,3,7,8-PBDD/Fs, which are the most toxic among all 210 PBDD/F isomers. A mechanistic understanding of the formation of PBDD/Fs is a prerequisite for minimizing their emissions. In this paper, the homogeneous gas-phase formation of PBDD/Fs from 2,4,5-TBP and 3,4-DBP as precursors was investigated theoretically by using the density functional theory (DFT) method. The mathematical model to predict the formation of PBDD/Fs places a high demand on accurate kinetic parameters. So, the rate constants of key elementary steps involved in the formation of PBDD/Fs were calculated by using canonical variational transition-state (CVT) theory with small curvature tunneling (SCT) contribution over a wide temperature range of 600-1200K. The pre-exponential factors and the activation energies are also reported. This might be the first to investigate the formation of 2,3,7,8-PBDD/Fs. The present study shows that the formation of PBDDs dominates over the formation of PBDFs. The meta bromine facilitates the dimerization of bromophenoxy radicals (BPRs), whereas the para and ortho bromines suppress the dimerization of BPRs.

  4. Molecular beam studies of reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.

  5. 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.

  6. Herbert P. Broida Prize Lecture: Probing chemical dynamics with negative ion photodetachment

    Science.gov (United States)

    Neumark, Daniel

    2013-03-01

    Photoelectron spectroscopy and its variants have been used in our laboratory to study diverse phenomena in chemical dynamics, including transition state spectroscopy, the electronic and vibrational spectroscopy of clusters, the photodissociation of reactive free radicals, hydrated electron dynamics in clusters and liquid jets, and the ultrafast dynamics of helium nanodroplets. This talk will focus on two examples of this type of work: slow electron velocity map imaging (SEVI) of trapped and cooled negative ions, and time-resolved photoelectron spectroscopy (TRPES) of negative ions. SEVI of cold ions represents a powerful means of performing high resolution photoelectron spectroscopy on complex species. Time-resolved radiation chemistry in nucleobases will be carried out with TRPES. In this work, starting with iodide-nucleobase complexes, we inject electrons into low-lying unoccupied orbitals of the nucleobase and follow the ensuing dynamics.

  7. 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.

  8. Complexity of gold nanoparticle formation disclosed by dynamics study

    DEFF Research Database (Denmark)

    Engelbrekt, Christian; Jensen, Palle Skovhus; Sørensen, Karsten

    2013-01-01

    Although chemically synthesized gold nanoparticles (AuNPs) from gold salt (HAuCl4) are among the most studied nanomaterials, understanding the formation mechanisms is a challenge mainly due to limited dynamics information. A range of in situ methods with down to millisecond (ms) time resolution...... have been employed in the present report to monitor time-dependent physical and chemical properties in aqueous solution during the chemical synthesis. Chemical synthesis of AuNPs is a reduction process accompanied by release of ions and protons, and formation of solid particles. Dynamic information......]- to form Au atoms during the early stage of the synthesis process. pH- and conductivity-dynamics point further clearly to formation of coating layers on AuNPs and adsorbate exchange between MES and starch. © 2013 American Chemical Society....

  9. 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.

  10. 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

  11. 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.

  12. 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.

  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. Theoretical studies of combustion dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Bowman, J.M. [Emory Univ., Atlanta, GA (United States)

    1993-12-01

    The basic objectives of this research program are to develop and apply theoretical techniques to fundamental dynamical processes of importance in gas-phase combustion. There are two major areas currently supported by this grant. One is reactive scattering of diatom-diatom systems, and the other is the dynamics of complex formation and decay based on L{sup 2} methods. In all of these studies, the authors focus on systems that are of interest experimentally, and for which potential energy surfaces based, at least in part, on ab initio calculations are available.

  15. 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.

  16. Kinetic studies of elementary chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    Durant, J.L. Jr. [Sandia National Laboratories, Livermore, CA (United States)

    1993-12-01

    This program concerning kinetic studies of elementary chemical reactions is presently focussed on understanding reactions of NH{sub x} species. To reach this goal, the author is pursuing experimental studies of reaction rate coefficients and product branching fractions as well as using electronic structure calculations to calculate transition state properties and reaction rate calculations to relate these properties to predicted kinetic behavior. The synergy existing between the experimental and theoretical studies allow one to gain a deeper insight into more complex elementary reactions.

  17. 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

  18. 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

  19. 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].

  20. 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.

  1. 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.

  2. 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...

  3. 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.

  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.

    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.

  6. 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…

  7. Stability of Surface Nanobubbles: A Molecular Dynamics Study

    NARCIS (Netherlands)

    Maheshwari, Shantanu; Hoef, van der Martin; Zhang, Xuehua; Lohse, Detlef

    2016-01-01

    The stability and growth or dissolution of a single surface nanobubble on a chemically patterned surface are studied by molecular dynamics simulations of binary mixtures consisting of Lennard-Jones (LJ) particles. Our simulations reveal how pinning of the three-phase contact line on the surface can

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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...

  14. 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.

  15. 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.

  16. 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

  17. 40 CFR 792.135 - Physical and chemical characterization studies.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 31 2010-07-01 2010-07-01 true Physical and chemical characterization... A Study § 792.135 Physical and chemical characterization studies. (a) All provisions of the GLPs shall apply to physical and chemical characterization studies designed to determine...

  18. 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.

  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. Quantum chemical studies of estrogenic compounds

    Science.gov (United States)

    Quantum chemical methods are potent tools to provide information on the chemical structure and electronic properties of organic molecules. Modern computational chemistry methods have provided a great deal of insight into the binding of estrogenic compounds to estrogenic receptors (ER), an important ...

  2. 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.

  3. 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.

  4. 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.

  5. System chemical biology studies of endocrine disruptors

    DEFF Research Database (Denmark)

    Taboureau, Olivier; Oprea, Tudor I.

    Endocrine disrupting chemicals (EDCs) alter hormonal balance and other physiological systems through inappropriate developmental or adult exposure, perturbing the reproductive function of further generations. While disruption of key receptors (e.g., estrogen, androgen, and thyroid) at the ligand...

  6. 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.

  7. 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...

  8. 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.

  9. Roles of steady-state and dynamic models for regulation of hydrophobic chemicals in aquatic systems: A case study of decamethylcyclopentasiloxane (D5) and PCB-180 in three diverse ecosystems.

    Science.gov (United States)

    Kim, Jaeshin; Mackay, Donald; Powell, David E

    2017-02-12

    We seek to contribute to the improved regulatory use of mass balance models to complement environmental monitoring data by applying the steady-state Quantitative Water Air Sediment Interactive model (QWASI) and a novel unsteady-state QWASI model. A steady-state model can yield not only a useful simulation of chemical fate under near steady-state conditions, but it can provide insights into the likely influences of increasing or decreasing emission rates, temperature changes, and unexpectedly high sensitivities to model parameters that may require additional investigation. We compared the consistency of insights from both types of model, in the expectation that while the dynamic model provides a closer simulation of actual conditions, for many purposes a simple, less computationally demanding, more transparent and less expensive model may be adequate for many regulatory purposes. We investigated the response times of decamethylcyclopentasiloxane (D5) and PCB-180 concentrations in water and sediment under three emission scenarios in three different aquatic systems, namely Lake Ontario, Oslofjord, and Lake Pepin. D5 was predicted to be removed largely by hydrolysis and volatilization in Lake Ontario and Oslofjord whereas it is subject to removal by advective loss in Lake Pepin. The half-times of D5 water concentration to a stepwise reduction in emission were <60 days in all three water bodies. In contrast, the predicted half-times were 0.53, 1.4, and 2.9 years in Lake Pepin, Oslofjord, and Lake Ontario, respectively. We also explored how uncertainties in input parameters propagate into uncertainties of concentrations in water and sediments possibly necessitating more accurate values.

  10. A photometric study of chemically peculiar stars with the STEREO satellites. I. Magnetic chemically peculiar stars

    CERN Document Server

    Wraight, K T; Netopil, M; Paunzen, E; Rode-Paunzen, M; Bewsher, D; Norton, A J; White, G J

    2011-01-01

    About 10% of upper main sequence stars are characterised by the presence of chemical peculiarities, often found together with a structured magnetic field. The atmospheres of most of those chemically peculiar stars present surface spots, leading to photometric variability caused by rotational modulation. The study of the light curves of those stars therefore, permits a precise measurement of their rotational period, which is important to study stellar evolution and to plan further detailed observations. We analysed the light curves of 1028 chemically peculiar stars obtained with the STEREO spacecraft. We present here the results obtained for the 337 magnetic chemically peculiar stars in our sample. Thanks to the cadence and stability of the photometry, STEREO data are perfectly suitable to study variability signals with a periodicity typical of magnetic chemically peculiar stars. Using a matched filter algorithm and then two different period searching algorithms, we compiled a list of 82 magnetic chemically pe...

  11. 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.

  12. Electron transport studies of chemical nanostructures

    Science.gov (United States)

    Liang, Wenjie

    2005-11-01

    In this thesis, I present electron transport studies of chemical nanostructures: single-walled carbon nanotubes (SWNTs) and single molecules. In chemical nanostructures, coulomb blockade and electronic energy level quantization dominate electron transport properties. High order correlated transport processes also play an important role in those nanostructures that are strongly coupled to electrodes. The electron transport spectra of SWNTs are investigated as a function of coupling strength of nanotube-electrode contacts. Measurements of nanotube devices at different coupling regimes showed distinct transport phenomena, including coulomb charging and electron level quantization, the experimental determination of all Hartree-Fock parameters that govern the electronic structure of metallic nanotubes and the demonstration of Fabry-Perot resonators based on the interference of electron waves. The presence of defects is important in low dimensional materials, for instance 1D SWNTs. A scanned gate microscopy (SGM) is used to locate defect center on SWNTs and study electron resonant scattering by defects. The reflection coefficient at the peak of a scattering resonance is determined to be ˜0.5 at room temperature. An intra-tube quantum-dot device formed by two defects was demonstrated by low-temperature transport measurements. Transport investigation of semiconducting SWNTs transistors shows large hysteresis effect upon gate voltage sweeping, which came from local charge redistribution around semiconducting SWNTs. A nonvolatile charge storage memory operating at room temperature was realized. Single molecule transistors incorporating different molecule (divanadium molecule [(N,N',N ″-trimethyl-1,4,7-triazacyclononane)2V2(CN) 4(mu-C4N4)], ferrocene and nickelocene) molecule, were achieved utilizing electromigration-induced break junction technique. Transport spectrum of divanadium molecules showed strange Kondo resonance where individual divanadium molecule serves as

  13. 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.

  14. 40 CFR 160.135 - Physical and chemical characterization studies.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Physical and chemical characterization... and chemical characterization studies. (a) All provisions of the GLP standards shall apply to physical... physical and chemical characteristics of a test, control, or reference substance: § 160.31 (c), (d), and...

  15. Atomic dynamics of alumina melt: A molecular dynamics simulation study

    Directory of Open Access Journals (Sweden)

    S.Jahn

    2008-03-01

    Full Text Available The atomic dynamics of Al2O3 melt are studied by molecular dynamics simulation. The particle interactions are described by an advanced ionic interaction model that includes polarization effects and ionic shape deformations. The model has been shown to reproduce accurately the static structure factors S(Q from neutron and x-ray diffraction and the dynamic structure factor S(Q,ω from inelastic x-ray scattering. Analysis of the partial dynamic structure factors shows inelastic features in the spectra up to momentum transfers, Q, close to the principal peaks of partial static structure factors. The broadening of the Brillouin line widths is discussed in terms of a frequency dependent viscosity η(ω.

  16. Bioreactor Studies and Computational Fluid Dynamics

    Science.gov (United States)

    Singh, H.; Hutmacher, D. W.

    The hydrodynamic environment “created” by bioreactors for the culture of a tissue engineered construct (TEC) is known to influence cell migration, proliferation and extra cellular matrix production. However, tissue engineers have looked at bioreactors as black boxes within which TECs are cultured mainly by trial and error, as the complex relationship between the hydrodynamic environment and tissue properties remains elusive, yet is critical to the production of clinically useful tissues. It is well known in the chemical and biotechnology field that a more detailed description of fluid mechanics and nutrient transport within process equipment can be achieved via the use of computational fluid dynamics (CFD) technology. Hence, the coupling of experimental methods and computational simulations forms a synergistic relationship that can potentially yield greater and yet, more cohesive data sets for bioreactor studies. This review aims at discussing the rationale of using CFD in bioreactor studies related to tissue engineering, as fluid flow processes and phenomena have direct implications on cellular response such as migration and/or proliferation. We conclude that CFD should be seen by tissue engineers as an invaluable tool allowing us to analyze and visualize the impact of fluidic forces and stresses on cells and TECs.

  17. 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.

  18. 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.

  19. 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.

  20. Experimental study of chemical concentration variation of ASP flooding

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    A physical modeling system of long slim tube was established. Several pressure measuring and sampling points were laid out at different positions along the tube. Through real-time measurements of pressures and chemical concentrations at different points, the mass transfer and chemical concentration of ASP flooding in porous media are studied. The concentration of chemicals declines gradually during the fluid flow from the inlet to the outlet of the model. The concentration increases in the front edge of the slug faster than the concentration decreases in the rear edge of the slug. The concentration variation of the chemicals is an asymmetrical and offset process. The order of motion velocities of the chemicals from fast to slow is polymer, alkali and surfactant. The motion lag and comprehensive diffusion are strong in the vicinity of the inlet, the motion velocities of the chemicals are high, the difference of flow velocities among the three chemicals is significant and the chromatographic separation of the chemicals is obvious. In the area near the outlet, the comprehensive diffusion and motion lag become weak, the concentrations of the chemicals decrease, the motion velocities of the chemicals are slow, the difference among the motion velocities of the chemicals becomes small, the chromatographic separation is not obvious, the adsorption and retention of chemicals gradually increase as the chemical slug moves further along the tube, the adsorption and retention of polymer is the most serious.

  1. Study of Endocrine Disrupting Chemicals in Environment

    Directory of Open Access Journals (Sweden)

    Zoltán Juvancz

    2008-06-01

    Full Text Available Endocrine disrupting chemicals (EDC cause more and more seriousenvironmental pollutions. The EDCs show only ng-μg/l concentration level in theenvironment, therefore their determinations require multistep sample preparationprocesses and highly sophisticated instrumentation. This paper discuss the EDC effects,and show examples for determination of such compounds.

  2. 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

  3. 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.

  4. 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.

  5. Chemical approaches to studying stem cell biology

    Institute of Scientific and Technical Information of China (English)

    Wenlin Li; Kai Jiang; Wanguo Wei; Yan Shi; Sheng Ding

    2013-01-01

    Stem cells,including both pluripotent stem cells and multipotent somatic stem cells,hold great potential for interrogating the mechanisms of tissue development,homeostasis and pathology,and for treating numerous devastating diseases.Establishment of in vitro platforms to faithfully maintain and precisely manipulate stem cell fates is essential to understand the basic mechanisms of stem cell biology,and to translate stem cells into regenerative medicine.Chemical approaches have recently provided a number of small molecules that can be used to control cell selfrenewal,lineage differentiation,reprogramming and regeneration.These chemical modulators have been proven to be versatile tools for probing stem cell biology and manipulating cell fates toward desired outcomes.Ultimately,this strategy is promising to be a new frontier for drug development aimed at endogenous stem cell modulation.

  6. Physico-Chemical Dynamics of Nanoparticle Formation during Laser Decontamination

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, M.D.

    2005-06-01

    Laser-ablation based decontamination is a new and effective approach for simultaneous removal and characterization of contaminants from surfaces (e.g., building interior and exterior walls, ground floors, etc.). The scientific objectives of this research are to: (1) characterize particulate matter generated during the laser-ablation based decontamination, (2) develop a technique for simultaneous cleaning and spectroscopic verification, and (3) develop an empirical model for predicting particle generation for the size range from 10 nm to tens of micrometers. This research project provides fundamental data obtained through a systematic study on the particle generation mechanism, and also provides a working model for prediction of particle generation such that an effective operational strategy can be devised to facilitate worker protection.

  7. 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.

  8. Physical-chemical studies of transuranium elements

    Energy Technology Data Exchange (ETDEWEB)

    Peterson, J.R.

    1991-01-01

    Major advances in our continuing program to determine, interpret, and correlate the basic chemical and physical properties of the transuranium elements are summarized. Research topics include: Molar enthalpies of formation of BaCmO{sub 3} and BaCfO{sub 3}; luminescence of europium oxychloride at various pressures; and anti-stokes luminescence of selected actinide (III) compounds. 42 refs., 4 figs., 2 tabs.

  9. The Dynamical and Chemical Evolution of Dwarf Spheroidal Galaxies

    CERN Document Server

    Revaz, Y; Sawala, T; Hill, V; Letarte, B; Irwin, M; Battaglia, G; Helmi, A; Shetrone, M D; Tolstoy, E; Venn, K A

    2009-01-01

    We present a large sample of fully self-consistent hydrodynamical Nbody/Tree-SPH simulations of isolated dwarf spheroidal galaxies (dSphs). It has enabled us to identify the key physical parameters and mechanisms at the origin of the observed variety in the Local Group dSph properties. The initial total mass (gas + dark matter) of these galaxies is the main driver of their evolution. Star formation (SF) occurs in series of short bursts. In massive systems, the very short intervals between the SF peaks mimic a continuous star formation rate, while less massive systems exhibit well separated SF bursts, as identified observationally. The delay between the SF events is controlled by the gas cooling time dependence on galaxy mass. The observed global scaling relations, luminosity-mass and luminosity-metallicity, are reproduced with low scatter. We take advantage of the unprecedentedly large sample size and data homogeneity of the ESO Large Programme DART, and add to it a few independent studies, to constrain the s...

  10. Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins.

    Science.gov (United States)

    Das, A K; Meuwly, M

    2016-01-01

    Following chemical reactions in atomistic detail is one of the most challenging aspects of current computational approaches to chemistry. In this chapter the application of adiabatic reactive MD (ARMD) and its multistate version (MS-ARMD) are discussed. Both methods allow to study bond-breaking and bond-forming processes in chemical and biological processes. Particular emphasis is put on practical aspects for applying the methods to investigate the dynamics of chemical reactions. The chapter closes with an outlook of possible generalizations of the methods discussed.

  11. 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.

  12. 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.

  13. 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.

  14. Studies on Chemical Constituents From Artabotrys Hainanensis

    Institute of Scientific and Technical Information of China (English)

    CHEN Guangying; SONG Xiao-Ping; HAN Chang-ri

    2004-01-01

    Artabotrys Hainanensis R.E. Fries are plants of the Annonaccac family artabotrys genus,which includes an estimated 100 types of plants distributed mainly in the tropical zone and the subtropics areas. Four types of the plants are discovered in our country, two of which, A.Hongkongensis Hance and A. hexapetalus (Linn. F.) Bhandari, in Guangdong Province, and the other two, A. Pilosus and A. Hainanensis R.E. Fries, in Hainan Province. The latter are widely distributed in Hainan Island with very rich reserves. They have long been used among the ordinary people as medicinal plants with antipyretic, antidotal, antiphlogistic and analgesic effects and are often used for malaria. Scholars from home and abroad have paid much attention to the plants of the Annonaccac family for their containing anti-tumor activities, and after early or late research of the chemical constituents of the root, stem (derm), leaf and fruit of many types of plants of Artabotrys genus, more than 40 compounds including alkaloid, flavone and terpenoid have been isolated and obtained. Artabotrys Hainanensis R.E. Fries are Hainan endemic plants and there has been no report on the research of their chemical constituents and biological activities so far. In order to find new constituents of pharmacologic activity, we have researched the chemical constituents of the leaf and stem.The crude drugs were collected from Hainan Jianfeng Mountain and were identified as Artabotrys Hainanensis R.E. Fries of the Annonaccac family artabotrys genus. Its sample specimen is now kept in Chemistry Department of Hainan Normal University.After isolation and identification of constituent, six compounds were isolated from the leaf of Artabotrys Hainanensis R.E. Fries and elucidated as β -sitosterol (Ⅰ), catechin (Ⅱ), mangiferin (Ⅲ),(Ⅳ), (Ⅴ), (Ⅵ). All the compounds were obtained from this plant for the first time. Compounds Ⅱ, Ⅲ,Ⅳ, Ⅴ and Ⅵ were obtained from the genus of Artabotrys for the first time.

  15. Molecular dynamics studies of entangled polymer chains

    NARCIS (Netherlands)

    Bulacu, Monica Iulia

    2008-01-01

    The thesis presents three molecular dynamics studies of polymeric ensembles in which the chain entanglement plays the major role in the internal dynamics of the system. A coarse-grained model is used for representing the polymer chains as strings of beads connected by finite-extensible springs. In a

  16. Polyketide stereocontrol: a study in chemical biology

    Science.gov (United States)

    2017-01-01

    The biosynthesis of reduced polyketides in bacteria by modular polyketide synthases (PKSs) proceeds with exquisite stereocontrol. As the stereochemistry is intimately linked to the strong bioactivity of these molecules, the origins of stereochemical control are of significant interest in attempts to create derivatives of these compounds by genetic engineering. In this review, we discuss the current state of knowledge regarding this key aspect of the biosynthetic pathways. Given that much of this information has been obtained using chemical biology tools, work in this area serves as a showcase for the power of this approach to provide answers to fundamental biological questions.

  17. Can hydroxylamine be a more potent nucleophile for the reactivation of tabun-inhibited AChE than prototype oxime drugs? An answer derived from quantum chemical and steered molecular dynamics studies.

    Science.gov (United States)

    Lo, Rabindranath; Ganguly, Bishwajit

    2014-07-29

    Organophosphorus nerve agents are highly toxic compounds which strongly inhibit acetylcholinesterase (AChE) in the blood and in the central nervous system (CNS). Tabun is one of the highly toxic organophosphorus (OP) compounds and is resistant to many oxime drugs formulated for the reactivation of AChE. The reactivation mechanism of tabun-conjugated AChE with various drugs has been examined with density functional theory and ab initio quantum chemical calculations. The presence of a lone-pair located on the amidic group resists the nucleophilic attack at the phosphorus center of the tabun-conjugated AChE. We have shown that the newly designed drug candidate N-(pyridin-2-yl)hydroxylamine, at the MP2/6-31+G*//M05-2X/6-31G* level in the aqueous phase with the polarizable continuum solvation model (PCM), is more effective in reactivating the tabun-conjugated AChE than typical oxime drugs. The rate determining activation barrier with N-(pyridin-2-yl)hydroxylamine was found to be ∼1.7 kcal mol(-1), which is 7.2 kcal mol(-1) lower than the charged oxime trimedoxime (one of the most efficient reactivators in tabun poisonings). The greater nucleophilicity index (ω(-)) and higher CHelpG charge of pyridinylhydroxylamine compared to TMB4 support this observation. Furthermore, we have also examined the reactivation process of tabun-inhibited AChE with some other bis-quaternary oxime drug candidates such as methoxime (MMB4) and obidoxime. The docking analysis suggests that charged bis-quaternary pyridinium oximes have greater binding affinity inside the active-site gorge of AChE compared to the neutral pyridinylhydroxylamine. The peripheral ligand attached to the neutral pyridinylhydroxylamine enhanced the binding with the aromatic residues in the active-site gorge of AChE through effective π-π interactions. Steered molecular dynamics (SMD) simulations have also been performed with the charged oxime (TMB4) and the neutral hydroxylamine. From protein-drug interaction

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

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, Sean A.; Aprà, 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.

  19. 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.

  20. Studies of dynamical processes affecting global climate

    Energy Technology Data Exchange (ETDEWEB)

    Keller, C.; Cooper, D.; Eichinger, W. [and others

    1998-12-31

    This is the final report of a three-year, Laboratory Directed Research and Development project at the Los Alamos National Laboratory (LANL). The main objective was, by a combined theoretical and observational approach, to develop improved models of dynamic processes in the oceans and atmosphere and to incorporate them into large climate codes, chiefly in four main areas: numerical physics, chemistry, water vapor, and ocean-atmosphere interactions. Main areas of investigation included studies of: cloud parameterizations for global climate codes, Lidar and the planetary boundary layer, chemistry, climate variability using coupled ocean-atmospheric models, and numerical physical methods. This project employed a unique approach that included participation of a number of University of California faculty, postdoctoral fellows and graduate students who collaborated with Los Alamos research staff on specific tasks, thus greatly enhancing the research output. Overall accomplishments during the sensing of the atmospheric planetary were: (1) first two- and three-dimensional remote sensing of the atmospheric planetary boundary layer using Lidars, (2) modeling of 20-year cycle in both pressure and sea surface temperatures in North Pacific, (3) modeling of low frequency internal variability, (4) addition of aerosols to stratosphere to simulate Pinatubo effect on ozone, (5) development of fast, comprehensive chemistry in the troposphere for urban pollution studies, (6) new prognostic cloud parameterization in global atmospheric code remedied problems with North Pacific atmospheric circulation and excessive equatorial precipitation, (7) development of a unique aerosol analysis technique, the aerosol time-of-flight mass spectrometer (ATOFMS), which allows real-time analysis of the size and chemical composition of individual aerosol particles, and (8) numerical physics applying Approximate Inertial Manifolds to ocean circulation. 14 refs., 6 figs.

  1. THE STUDY OF CHEMICAL COMPOSITION FOR ANIMAL FATS DURING STORAGE

    OpenAIRE

    Flavia Pop; Cornel Laslo

    2009-01-01

    In this article the chemical composition for 3 types of animal fats (pork fat, beef tallow and buffalo tallow), following the variation of saturated and unsaturated fatty acids proportion during freezing storage was studied. Determination of chemical composition of animal fats is important in establishing organoleptic and physico-chemical parameters, the variation of them in time, nature and proportion of fatty acids conferring specific characteristics to them. For pork fat was determined the...

  2. [Studies on chemical compounds of Chlorella sorokiniana].

    Science.gov (United States)

    Zhang, Ling; Liu, Ping-huai; Wu, Jiao-na; Yang, Guo-fu; Suo, Yang-yang; Luo, Ning; Chen, Chen

    2015-04-01

    Chemical constituents of Chlorella sorokiniana were isolated and purified by repeated column chromatographies, over silicagel and Sephadex LH-20. Their structures were identified on the basis of physicochemical properties and spectroscopic data analysis. Five compounds were obtained from the petroleum ether extract of Chlorella sorokiniana, and their structures were identified as (22E, 24R)-5alpha, 3beta-epidioxiergosta-6, 22-dien-3beta-ol(1),(24S)-ergosta-7-en-3beta-ol(2), loliolide(3), stigmasta-7,22-dien-3beta,5alpha,6alpha-triol(4), and 3beta-hydroxy-5alpha,6alpha-epoxy-7-megastigmen-9-one(5). The main liposoluble fractions from Chlorella sorokiniana maiuly contain fatty acids, alkyl acids and olefine acids. Components 1-5 were isolated from the genus Chlorella for the first time.

  3. 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

  4. The Panel Study of Income Dynamics (PSID)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Panel Study of Income Dynamics (PSID) began in 1968 with a nationally representative sample of over 18,000 individuals living in 5,000 families in the United...

  5. 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...

  6. 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.

  7. 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)

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Chemical Physics: A Subject for Study at University?

    Science.gov (United States)

    Dunmur, D. A.

    1982-01-01

    Traces development of chemical physics as a distinct discipline and reviews its position as a subject for study in United Kingdom universities. Reports results of a survey of chemical physics courses and graduates (1975-1980), including employment data on these graduates. (Author/JN)

  14. 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.

  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. 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.

  17. 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.

  18. Dynamic study of milling low depth channels

    Directory of Open Access Journals (Sweden)

    Rosca Dorin Mircea

    2017-01-01

    Full Text Available This paper presents a study of dynamic aspects of the milling cutters used in particular case of low depth channels. A new calculation method was developed, taking into account the high variations of cutting forces during milling small depth channels with peripheral cutting tools. A new formula was established for the minimal value of channel depth that allows cutting process to be performed in conditions of dynamic stability.

  19. Chemical - Elwha River Dam Removal Study

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This study examines the ecosystem response of the Elwha River to the removal of the Elwha River dams. We will measure the following attributes of ecosystem response:...

  20. 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

  1. Feasibility and effectiveness of chemical bile duct embolization for chemical hepatectomy:a preliminary study

    Institute of Scientific and Technical Information of China (English)

    Fu-Yu Li; Ning Li; Li-Sheng Jiang; Jing-Qiu Cheng; Nan-Sheng Cheng; Xing-Wu Wu; Sheng He

    2006-01-01

    BACKGROUND: The high operative risk of hepatectomy for specially located intrahepatic stones is still a problem to be solved. This study was undertaken to investigate the feasibility and effectiveness of chemical bile duct embolization for chemical hepatectomy. METHODS: Oxybenzene or absolute ethanol plus N-butyl-cyanoacrylate was employed for embolization. The feasibility, effectiveness and mechanism of chemical hepatectomy were preliminarily analyzed histologically or by Fas, TIMP-1, TGF-β1, and collagenⅠ. RESULTS:Oxybenzene plus cyanonacrylate can preferably destroy and embolize the intrahepatic biliary duct, leading to the disappearance of hepatocytes in the periphery of embolized lobe and the achievement of effective chemical hepatectomy. The expressions of Fas, TIMP-1 and TGF-β1 in oxybenzene embolism group (88.90±38.10, 619.43± 183.42, 185.22±70.39) and ethanol embolism group (72.39± 29.51, 407.55±134.74, 163.56±51.75) were higher than those of biliary duct-ligated group (26.31±12.07, 195.31±107.67, 74.84±40.73) (P CONCLUSION: The effect of chemical hepatectomy may be achieved by chemical bile duct embolization.

  2. 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.

  3. 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

  4. Chemical Arsenal for the Study of O-GlcNAc

    Directory of Open Access Journals (Sweden)

    Eun J. Kim

    2011-02-01

    Full Text Available The concepts of both protein glycosylation and cellular signaling have been influenced by O-linked-β-N-acetylglucosamine (O-GlcNAc modification (O-GlcNAcylation on the hydroxyl group of serine or threonine residues. Unlike conventional protein glycosylation, O-GlcNAcylation is localized in the nucleocytoplasm and its cycling is a dynamic process that operates in a highly regulated manner in response to various cellular stimuli. These characteristics render O-GlcNAcylation similar to phosphorylation, which has long been considered a major regulatory mechanism in cellular processes. Various efficient chemical approaches and novel mass spectrometric (MS techniques have uncovered numerous O-GlcNAcylated proteins that are involved in the regulation of many important cellular events. These discoveries imply that O-GlcNAcylation is another major regulator of cellular signaling. However, in contrast to phosphorylation, which is regulated by hundreds of kinases and phosphatases, dynamic O-GlcNAc cycling is catalyzed by only two enzymes: uridine diphospho-N-acetyl-glucosamine:polypeptide β-N-acetylglucosaminyl transferase (OGT and β-D-N-acetylglucosaminidase (OGA. Many useful chemical tools have recently been used to greatly expand our understanding of the extensive crosstalk between O-GlcNAcylation and phosphorylation and hence of cellular signaling. This review article describes the various useful chemical tools that have been developed and discusses the considerable advances made in the O-GlcNAc field.

  5. An empirical study of dynamic graph algorithms

    Energy Technology Data Exchange (ETDEWEB)

    Alberts, D. [Freie Universitaet Berlin (Germany); Cattaneo, G. [Universita di Salerno (Italy); Italiano, G.F. [Universita Ca Forscari di Venezia (Italy)

    1996-12-31

    We conduct an empirical study on some dynamic graph algorithms which where developed recently. The following implementations were tested and compared with simple algorithms: dynamic connectivity, and dynamic minimum 1 spanning tree based on sparsification by Eppstein et al.; dynamic connectivity based on a very recent paper by Henzinger and King. In our experiments, we considered both random and non-random inputs. Moreover, we present a simplified variant of the algorithm by Henzinger and King, which for random inputs was always faster than the original implementation. Indeed, this variant was among the fastest implementations for random inputs. For non-random inputs, sparsification was the fastest algorithm for small sequences of updates; for medium and large sequences of updates, the original algorithm by Henzinger and King was faster. Perhaps one of the main practical results of this paper is that our implementations of the sophisticated dynamic graph algorithms were faster than simpler algorithms for most practical values of the graph parameters, and competitive with simpler algorithms even in case of very small graphs (say graphs with less than a dozen vertices and edges). From the theoretical point of view, we analyze the average case running time of sparsification and prove that the logarithmic overhead for simple sparsification vanishes for dynamic random graphs.

  6. 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.

  7. 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.

  8. SPECTROSCOPIC STUDIES OF STRUCTURE, DYNAMICS AND REACTIVITY IN IONIC LIQUIDS.

    Energy Technology Data Exchange (ETDEWEB)

    WISHART,J.F.

    2007-11-30

    Ionic liquids (ILs) are a rapidly expanding family of condensed-phase media with important applications in energy production, nuclear fuel and waste processing, improving the efficiency and safety of industrial chemical processes, and pollution prevention. ILs are generally nonvolatile, noncombustible, highly conductive, recyclable and capable of dissolving a wide variety of materials. They are finding new uses in chemical synthesis, catalysis, separations chemistry, electrochemistry and other areas. Ionic liquids have dramatically different properties compared to conventional molecular solvents, and they provide a new and unusual environment to test our theoretical understanding of charge transfer and other reactions. We are interested in how IL properties influence physical and dynamical processes that determine the stability and lifetimes of reactive intermediates and thereby affect the courses of chemical reactions and product distributions. Successful use of ionic liquids in radiation-filled environments, where their safety advantages could be significant, requires an understanding of ionic liquid radiation chemistry. For example, characterizing the primary steps of IL radiolysis will reveal radiolytic degradation pathways and suggest ways to prevent them or mitigate their effects on the properties of the material. An understanding of ionic liquid radiation chemistry will also facilitate pulse radiolysis studies of general chemical reactivity in ILs, which will aid in the development of applications listed above. Very early in our radiolysis studies it became evident that slow solvation dynamics of the excess electron in ILs (which vary over a wide viscosity range) increases the importance of pre-solvated electron reactivity and consequently alters product distributions. Parallel studies of IL solvation phenomena using coumarin-153 dynamic Stokes shifts and polarization anisotropy decay rates are done to compare with electron solvation studies and to evaluate

  9. Simulation study of water and sugar dynamics in supercooled mixtures

    Science.gov (United States)

    Molinero, Valeria; Cagin, Tahir; Goddard, William A.

    2003-03-01

    Water dynamics in concentrated carbohydrate solutions is of utmost importance in food and pharmaceutical technology, where low water mobility is desirable to slow down chemical degradation and preserve biomolecules. We have studied the microscopic mechanism of water diffusion in binary and polydisperse malto-oligosaccharides and water mixtures by means of molecular dynamics simulations. The computations were performed with a coarse grain model (M3B), derived from atomistic simulations of water and malto-oligosaccharides. The use of the M3B model permits simulations of the order of 0.1 microsecond, thus allowing us to explore water dynamics from the liquid to the deep supercooled regime. The dynamics of water confined in the sugar matrix is slowed down with respect to bulk water. We found that at low moisture content and low temperature, ranslational diffusion of water and glucose rotation proceed through a hopping-diffusion mechanism. Moreover, we found water mobility to be heterogeneous: there is a broad distribution of time scales for different water molecules in the mixtures. We discuss whether there is a relationship between the heterogeneous structure of these mixtures in the sub-nanometer scale and the heterogeneous dynamics of water molecules.

  10. Structural dynamics in complex liquids studied with multidimensional vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Tokmakoff, Andrei [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

    2013-08-31

    The development of new sustainable energy sources is linked to our understanding of the molecular properties of water and aqueous solutions. Energy conversion, storage, and transduction processes, particularly those that occur in biology, fuel cells, and batteries, make use of water for the purpose of moving energy in the form of charges and mediating the redox chemistry that allows this energy to be stored as and released from chemical bonds. To build our fundamental knowledge in this area, this project supports work in the Tokmakoff group to investigate the molecular dynamics of water’s hydrogen bond network, and how these dynamics influence its solutes and the mechanism of proton transport in water. To reach the goals of this grant, we developed experiments to observe molecular dynamics in water as directly as possible, using ultrafast multidimensional vibrational spectroscopy. We excite and probe broad vibrational resonances of water, molecular solutes, and protons in water. By correlating how molecules evolve from an initial excitation frequency to a final frequency, we can describe the underlying molecular dynamics. Theoretical modeling of the data with the help of computational spectroscopy coupled with molecular dynamics simulations provided the atomistic insight in these studies.

  11. VUV studies of molecular photofragmentation dynamics

    Energy Technology Data Exchange (ETDEWEB)

    White, M.G. [Brookhaven National Laboratory, Upton, NY (United States)

    1993-12-01

    State-resolved, photoion and photoelectron methods are used to study the neutral fragmentation and ionization dynamics of small molecules relevant to atmospheric and combustion chemistry. Photodissociation and ionization are initiated by coherent VUV radiation and the fragmentation dynamics are extracted from measurements of product rovibronic state distributions, kinetic energies and angular distributions. The general aim of these studies is to investigate the multichannel interactions between the electronic and nuclear motions which determine the evolution of the photoexcited {open_quotes}complex{close_quotes} into the observed asymptotic channels.

  12. In vivo Dynamic Studies of Brain Metabolism

    Institute of Scientific and Technical Information of China (English)

    LUO Xuechun; JIANG Yufeng; ZHANG Riqing

    2005-01-01

    Nuclear magnetic resonance (NMR) can noninvasively monitor intracellular concentrations and kinetic properties of numerous inorganic and organic compounds. A 31P NMR surface coil was used in vivo to dynamically measure phosphocreatine (PCr), adenosine triphosphate (ATP), and intracellular inorganic phosphate (Pi) levels in mouse brain during ischemia-reperfusion to study the damage of cerebral tissues caused by ischemia and effects of herbs on cerebral energy metabolism during ischemia-reperfusion. The study provides dynamic brain energy metabolism data during different periods. The data show that some herbs more rapidly increase the PCr level during the recovery phase than in the control group.

  13. 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.

  14. Study on scattering properties of tissues with hyperosmotic chemical agents

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Optical properties of biological tissue are variable due to the changes of micro-structures and scattering constituents after hyperosmotic chemical agents permeates into tissue. The changes of optical properties of biological tissue are due to the refractive indices matching between the scatterers with high refractive index and the ground substances, which reduce scattering of tissue. The main reasons are that permeated semipermeable chemical agents with higher refractive index than the ground substances of tissuemakes the refractive index of ground substances of tissue higher by the enhancement of the permeated concentration. We studied on the collimated transmittance changes of light penetrating biological tissue after the hyperosmotic chemical agents administrates with different concentration.

  15. 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

  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. 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...

  18. 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.

  19. 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.

  20. Weak Dynamic Non-Emptiability and Persistence of Chemical Kinetics Systems

    CERN Document Server

    Johnston, Matthew D

    2010-01-01

    A frequently desirable characteristic of chemical kinetics systems is that of persistence, the property that no initially present species may tend toward extinction. It is known that solutions of deterministically modelled mass-action systems may only approach portions of the boundary of the positive orthant which correspond to semi-locking sets (alternatively called siphons). Consequently, most recent work on persistence of these systems has been focused on these sets. In this paper, we focus on a result which states that, for a conservative mass-action system, persistence holds if every critical semi-locking set is dynamically non-emptiable and the system contains no nested locking sets. We will generalize this result by introducing the notion of a weakly dynamically non-emptiable semi-locking set and making novel use of the well-known Farkas' Lemma. We will also connect this result to known results regarding complex balanced systems and systems with facets.

  1. Cutaneous chemical burns in children - a comparative study.

    Science.gov (United States)

    Hardwicke, Joseph; Bechar, Janak; Bella, Husam; Moiemen, Naiem

    2013-12-01

    Exposure to chemicals is an unusual causation of cutaneous burns in children. The aim of this study is to look at childhood chemical burns and compare this to adult chemical burns from the same population. A total of 2054 patients were referred to the pediatric burns unit during the study period. This included 24 cutaneous chemical burns, equating to an incidence of 1.1%. Over half of the injuries occurred in the domestic setting. The mean total body surface area (TBSA) affected was 1.9%. When compared to a cohort of adult patients from the same population with cutaneous chemical burns, the TBSA affected was identical (1.9%) but distribution favored the buttock and perineum in children, rather than the distal lower limb in adults. Children presented earlier, had lower rates of surgical intervention and had a shorter length of stay in hospital (p Chemical burns in children are rare, but are becoming more common in our region. It is important to be aware of the characteristic distribution, etiology and need to identify children at risk of child protection issues.

  2. Molecular Dynamics Studies of Matrix Metalloproteases.

    Science.gov (United States)

    Díaz, Natalia; Suárez, Dimas

    2017-01-01

    Matrix metalloproteases are multidomain enzymes with a remarkable proteolytic activity located in the extracellular environment. Their catalytic activity and structural properties have been intensively studied during the last few decades using both experimental and theoretical approaches, but many open questions still remain. Extensive molecular dynamics simulations enable the sampling of the configurational space of a molecular system, thus contributing to the characterization of the structure, dynamics, and ligand binding properties of a particular MMP. Based on previous computational experience, we provide in this chapter technical and methodological guidelines that may be useful to and stimulate other researchers to perform molecular dynamics simulations to help address unresolved questions concerning the molecular mode of action of MMPs.

  3. CHEMICALS

    CERN Multimedia

    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

  4. A chemical EOR benchmark study of different reservoir simulators

    Science.gov (United States)

    Goudarzi, Ali; Delshad, Mojdeh; Sepehrnoori, Kamy

    2016-09-01

    chemical design for field-scale studies using commercial simulators. The benchmark tests illustrate the potential of commercial simulators for chemical flooding projects and provide a comprehensive table of strengths and limitations of each simulator for a given chemical EOR process. Mechanistic simulations of chemical EOR processes will provide predictive capability and can aid in optimization of the field injection projects. The objective of this paper is not to compare the computational efficiency and solution algorithms; it only focuses on the process modeling comparison.

  5. Dynamic Study of Bicycle Frame Structure

    Science.gov (United States)

    Sani, M. S. M.; Nazri, N. A.; Zahari, S. N.; Abdullah, N. A. Z.; Priyandoko, G.

    2016-11-01

    Bicycle frames have to bear variety of loads and it is needed to ensure the frame can withstand dynamic loads to move. This paper focusing on dynamic study for bicycle frame structure with a purpose to avoid the problem regarding loads on the structure and to ensure the structure is safe when multiple loads are applied on it. The main objectives of dynamic study are to find the modal properties using two method; finite element analysis (FEA) and experimental modal analysis (EMA). The correlation between two studies will be obtained using percentage error. Firstly, 3D model of mountain bike frame structure has been draw using computer-aided design (CAD) software and normal mode analysis using MSC Nastran Patran was executed for numerical method meanwhile modal testing using impact hammer was performed for experimental counterpart. From the correlation result, it show that percentage error between FEA and EMA were below 10% due to noise, imperfect experiment setup during perform EMA and imperfect modeling of mountain bike frame structure in CAD software. Small percentage error differences makes both of the method can be applied to obtain the dynamic characteristic of structure. It is essential to determine whether the structure is safe or not. In conclusion, model updating method is required to reduce more percentage error between two results.

  6. Population dynamics of earthworms in relation to soil physico-chemical parameters in agroforestry systems of Mizoram, India.

    Science.gov (United States)

    Lalthanzara, H; Ramanujam, S N; Jha, L K

    2011-09-01

    Earthworm population dynamics was studied in two agroforestry systems in the tropical hilly terrain of Mizoram, north-east India, over a period of 24 months, from July 2002 to June 2004. Two sites of agroforestry situated at Sakawrtuichhun (SKT) and Pachhunga University College (PUC) campus, Aizawl, having pineapple as the main crop, were selected for detail studies on population dynamics. Five of the total twelve species of earthworm reported from the state were recorded in the study sites. The density of earthworm ranged from 6 to 243 ind.m(-2) and biomass from 3.2 - 677.64 g.m(-2) in SKT. Comparatively the density and biomass in PUC, which is at relatively higher altitude were lowerwith a range of 0 to 176 ind.m(-2) and biomass from 0 - 391.36 g.m(-2) respectively. Population dynamics of earthworm was significantly correlated with rainfall and physical characters of the soil. Earthworm biomass was significantly affected by rainfall and moisture content of the soil. The influence of chemical factors was relatively less.

  7. Study of Nanowires Using Molecular Dynamics Simulations

    OpenAIRE

    Monk, Joshua D

    2007-01-01

    In this dissertation I present computational studies that focus on the unique characteristics of metallic nanowires. We generated virtual nanowires of nanocrystalline nickel (nc-Ni) and single crystalline silver (Ag) in order to investigate particular nanoscale effects. Three-dimensional atomistic molecular dynamics studies were performed for each sample using the super computer System X located at Virginia Tech. Thermal grain growth simulations were performed on 4 nm grain size nc-Ni by o...

  8. LOW-x Dynamics Through Jet Studies

    Science.gov (United States)

    Ferencei, Jozef; H1; ZEUS Collaborations

    One of the most challenging aspects of low x proton structure is the study of QCD dynamics - the evolution of partons between different kinematic regimes. In electron-proton deep-inelastic scattering, this can be investigated by studying processes in the target region of the proton - forward going jets. In this paper various measurements made at HERA by the H1 and ZEUS experiments are presented and compared to Monte Carlo models and fixed-order QCD calculations.

  9. The modelling of dynamic chemical state of paper machine unit operations; Dynaamisen kemiallisen tilan mallintaminen paperikoneen yksikkoeoperaatioissa - MPKT 04

    Energy Technology Data Exchange (ETDEWEB)

    Ylen, J.P.; Jutila, P. [Helsinki Univ. of Technology, Otaniemi (Finland)

    1998-12-31

    The chemical state of paper mass is considered to be a key factor to the smooth operation of the paper machine. There are simulators that have been developed either for dynamic energy and mass balances or for static chemical phenomena, but the combination of these is not a straight forward task. Control Engineering Laboratory of Helsinki University of Technology has studied the paper machine wet end phenomena with the emphasis on pH-modelling. VTT (Technical Research Centre of Finland) Process Physics has used thermodynamical modelling successfully in e.g. Bleaching processes. In this research the different approaches are combined in order to get reliable dynamical models and modelling procedures for various unit operations. A flexible pilot process will be constructed and different materials will be processed starting from simple inorganic substances (e.g. Calcium carbonate and distilled water) working towards more complex masses (thick pulp with process waters and various reagents). The pilot process is well instrumented with ion selective electrodes, total calcium analysator and all basic measurements. (orig.)

  10. 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...

  11. 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.

  12. 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.

  13. A Molecular Dynamics Study of the Structural and Dynamical Properties of Putative Arsenic Substituted Lipid Bilayers

    Directory of Open Access Journals (Sweden)

    Ratna Juwita

    2013-04-01

    Full Text Available Cell membranes are composed mainly of phospholipids which are in turn, composed of five major chemical elements: carbon, hydrogen, nitrogen, oxygen, and phosphorus. Recent studies have suggested the possibility of sustaining life if the phosphorus is substituted by arsenic. Although this issue is still controversial, it is of interest to investigate the properties of arsenated-lipid bilayers to evaluate this possibility. In this study, we simulated arsenated-lipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-arsenocholine (POAC, lipid bilayers using all-atom molecular dynamics to understand basic structural and dynamical properties, in particular, the differences from analogous 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, (POPC lipid bilayers. Our simulations showed that POAC lipid bilayers have distinct structural and dynamical properties from those of native POPC lipid bilayers. Relative to POPC lipid bilayers, POAC lipid bilayers have a more compact structure with smaller lateral areas and greater order. The compact structure of POAC lipid bilayers is due to the fact that more inter-lipid salt bridges are formed with arsenate-choline compared to the phosphate-choline of POPC lipid bilayers. These inter-lipid salt bridges bind POAC lipids together and also slow down the head group rotation and lateral diffusion of POAC lipids. Thus, it would be anticipated that POAC and POPC lipid bilayers would have different biological implications.

  14. Continuous game dynamics: an experimental study.

    Energy Technology Data Exchange (ETDEWEB)

    Patelli, P. (Palolo); Sato, Yuzuru

    2004-01-01

    In this paper we study an experiment with human agents strategically interacting in a game characterized by continuous time and continuous strategy space. The research is focused in studying the agents interaction dynamic under different experimental settings. The agents play a two person game that is an extension of the classic Cournot duopoly. Having agents making decision continuously allows us to track the temporal structure of strategy evolution very precisely. We can follow the agents continuous behavior evolution avoiding the data under-sampling. To our knowledge this is the first attempt to approach experimentally the continuous time decision making. We also emphasize that the focus of our work is not the Cournot model but rather the more general problem of studying the agents strategic interaction dynamic in continuous space time. Flaming the problem as the well studied Cournot Duopoly would be a good starting point. In economics dynamics studies the oligopoly model literature in both discrete and continuous time is one of the richest. There is also a vast literature in experimental economics about repeated games in general and more specifically in duopoly/oligopoly models. Cox and Walker studied whether subjects can learn to play the Cournot Duopoly strategies comparing the experimental results with the theoretical prediction of learning models. The Cox Walker experiment differs from our settings because it is in discrete time and is an evolutionary dynamics framework through a random matching mechanism of the experimental subjects. From the theoretical perspective many works have been focused in studying the Cournot model in a dynamical settings. Okuguchi and Szidarovsky formulated a continuous time version of the Cournot Oligopoly with multiproduct firms. They analyzed the stability of the equilibrium and proved that it is stable, under certain conditions, independently from the value of the adjustments. Chiarella and Khomin extended this analysis to

  15. Dynamic optimization case studies in DYNOPT tool

    Science.gov (United States)

    Ozana, Stepan; Pies, Martin; Docekal, Tomas

    2016-06-01

    Dynamic programming is typically applied to optimization problems. As the analytical solutions are generally very difficult, chosen software tools are used widely. These software packages are often third-party products bound for standard simulation software tools on the market. As typical examples of such tools, TOMLAB and DYNOPT could be effectively applied for solution of problems of dynamic programming. DYNOPT will be presented in this paper due to its licensing policy (free product under GPL) and simplicity of use. DYNOPT is a set of MATLAB functions for determination of optimal control trajectory by given description of the process, the cost to be minimized, subject to equality and inequality constraints, using orthogonal collocation on finite elements method. The actual optimal control problem is solved by complete parameterization both the control and the state profile vector. It is assumed, that the optimized dynamic model may be described by a set of ordinary differential equations (ODEs) or differential-algebraic equations (DAEs). This collection of functions extends the capability of the MATLAB Optimization Tool-box. The paper will introduce use of DYNOPT in the field of dynamic optimization problems by means of case studies regarding chosen laboratory physical educational models.

  16. Dynamic MRI study for breast tumors

    Energy Technology Data Exchange (ETDEWEB)

    Seki, Tsuneaki (Kyorin Univ., Mitaka, Tokyo (Japan). School of Medicine)

    1990-10-01

    Application of MRI for diagnosis of breast tumors was retrospectively examined in 103 consecutive cases. Contrast enhancement, mostly by dynamic study, was performed in 83 cases using Gd-DTPA and 0.5 T superconductive apparatus. Results were compared to those of mammography and sonography. On dynamic study, carcinoma showed abrupt rise of signal intensity with clear-cut peak formation in early phase, while benign fibroadenoma showed slow rise of signal intensity and prolonged enhancement without peak formation. In 12 of 33 carcinomas (33%), peripheral ring enhancement was noted reflecting vascular stroma of histologic sections. All fibroadenomas showed homogenous enhancement without peripheral ring. In MRI, sensitivity, specificity, and accuracy were 86%, 96%, 91%. In mammography 82%, 95%, 87% and in ultrasonography 91%, 95%, 93%. Although MRI should not be regarded as routine diagnostic procedure because of expense and limited availability, it may afford useful additional information when standard mammographic findings are not conclusive. (author).

  17. Chemical Reaction Rates from Ring Polymer Molecular Dynamics: Zero Point Energy Conservation in Mu + H2 → MuH + H.

    Science.gov (United States)

    Pérez de Tudela, Ricardo; Aoiz, F J; Suleimanov, Yury V; Manolopoulos, David E

    2012-02-16

    A fundamental issue in the field of reaction dynamics is the inclusion of the quantum mechanical (QM) effects such as zero point energy (ZPE) and tunneling in molecular dynamics simulations, and in particular in the calculation of chemical reaction rates. In this work we study the chemical reaction between a muonium atom and a hydrogen molecule. The recently developed ring polymer molecular dynamics (RPMD) technique is used, and the results are compared with those of other methods. For this reaction, the thermal rate coefficients calculated with RPMD are found to be in excellent agreement with the results of an accurate QM calculation. The very minor discrepancies are within the convergence error even at very low temperatures. This exceptionally good agreement can be attributed to the dominant role of ZPE in the reaction, which is accounted for extremely well by RPMD. Tunneling only plays a minor role in the reaction.

  18. Do High School Chemistry Examinations Inhibit Deeper Level Understanding of Dynamic Reversible Chemical Reactions?

    Science.gov (United States)

    Wheeldon, R.; Atkinson, R.; Dawes, A.; Levinson, R.

    2012-01-01

    Background and purpose: Chemistry examinations can favour the deployment of algorithmic procedures like Le Chatelier's Principle (LCP) rather than reasoning using chemical principles. This study investigated the explanatory resources which high school students use to answer equilibrium problems and whether the marks given for examination answers…

  19. Material Cycles and Chemicals: Dynamic Material Flow Analysis of Contaminants in Paper Recycling

    DEFF Research Database (Denmark)

    Pivnenko, Kostyantyn; Laner, David; Astrup, Thomas Fruergaard

    2016-01-01

    This study provides a systematic approach for assessment of contaminants in materials for recycling. Paper recycling is used as an illustrative example. Three selected chemicals, bisphenol A (BPA), diethylhexyl phthalate (DEHP) and mineral oil hydrocarbons (MOHs), are evaluated within the paper...

  20. [Scanning electron microscope study of chemically disinfected endodontic files].

    Science.gov (United States)

    Navarro, G; Mateos, M; Navarro, J L; Canalda, C

    1991-01-01

    Forty stainless steel endodontic files were observed at scanning electron microscopy after being subjected to ten disinfection cycles of 10 minutes each one, immersed in different chemical disinfectants. Corrosion was not observed on the surface of the files in circumstances that this study was made.

  1. Identity method-a new tool for studying chemical fluctuations

    Energy Technology Data Exchange (ETDEWEB)

    Mackowiak, M., E-mail: majam@if.pw.edu.pl [Warsaw University of Technology, Faculty of Physics (Poland)

    2012-06-15

    Event-by-event fluctuations of the chemical composition of the hadronic system produced in nuclear collisions are believed to be sensitive to properties of the transition between confined and deconfined strongly interacting matter. In this paper a new technique for the study of chemical fluctuation, the identity method, is introduced and its features are discussed. The method is tested using data on central PbPb collisions at 40 A GeV registered by the NA49 experiment at the CERN SPS.

  2. Osmosis : a molecular dynamics computer simulation study

    Science.gov (United States)

    Lion, Thomas

    Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..

  3. Preliminary study of chemical compositional data from Amazon ceramics

    Energy Technology Data Exchange (ETDEWEB)

    Toyota, Rosimeiri G.; Munita, Casimiro S.; Luz, Fabio A. [Instituto de Pesquisas Energeticas e Nucleares (IPEN), Sao Paulo, SP (Brazil)]. E-mail: rosimeiritoy@yahoo.com.br; Neves, Eduardo G. [Museu de Arqueologia e Etnolgia, Sao Paulo, SP (Brazil)]. E-mail: egneves@usp.br; Oliveira, Paulo M.S. [Sao Paulo Univ., SP (Brazil). Escola Politecnica. Inst. de Matematica e Estatistica]. E-mail: poliver@usp.br

    2005-07-01

    Eighty seven ceramic samples from Acutuba, Lago Grande and Osvaldo archaeological sites located in the confluence of the rivers Negro and Solimoes were submitted to chemical analysis using instrumental neutron activation analysis to determine As, Ba, Ce, Co, Cr, Cs, Eu, Fe, Hf, K, La, Lu, Rb, Na, Nd, Sb, Sc, Sm, Ta, Tb, Th, Yb, Zn, and U. The database were studied using the Mahalanobis distance, and discriminant analysis. The results showed that the ceramics of each site differ from each other in chemical composition and that they form three different groups. Chemical classification of the ceramics suggests that vessels were made locally, as only ceramics from the same area show homogeneity of data. (author)

  4. Solar dynamic power system definition study

    Science.gov (United States)

    Wallin, Wayne E.; Friefeld, Jerry M.

    1988-01-01

    The solar dynamic power system design and analysis study compared Brayton, alkali-metal Rankine, and free-piston Stirling cycles with silicon planar and GaAs concentrator photovoltaic power systems for application to missions beyond the Phase 2 Space Station level of technology for all power systems. Conceptual designs for Brayton and Stirling power systems were developed for 35 kWe and 7 kWe power levels. All power systems were designed for 7-year end-of-life conditions in low Earth orbit. LiF was selected for thermal energy storage for the solar dynamic systems. Results indicate that the Stirling cycle systems have the highest performance (lowest weight and area) followed by the Brayton cycle, with photovoltaic systems considerably lower in performance. For example, based on the performance assumptions used, the planar silicon power system weight was 55 to 75 percent higher than for the Stirling system. A technology program was developed to address areas wherein significant performance improvements could be realized relative to the current state-of-the-art as represented by Space Station. In addition, a preliminary evaluation of hardenability potential found that solar dynamic systems can be hardened beyond the hardness inherent in the conceptual designs of this study.

  5. 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.

  6. 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.

  7. Complex, dynamic combination of physical, chemical and nutritional variables controls spatio-temporal variation of sandy beach community structure.

    Science.gov (United States)

    Ortega Cisneros, Kelly; Smit, Albertus J; Laudien, Jürgen; Schoeman, David S

    2011-01-01

    Sandy beach ecological theory states that physical features of the beach control macrobenthic community structure on all but the most dissipative beaches. However, few studies have simultaneously evaluated the relative importance of physical, chemical and biological factors as potential explanatory variables for meso-scale spatio-temporal patterns of intertidal community structure in these systems. Here, we investigate macroinfaunal community structure of a micro-tidal sandy beach that is located on an oligotrophic subtropical coast and is influenced by seasonal estuarine input. We repeatedly sampled biological and environmental variables at a series of beach transects arranged at increasing distances from the estuary mouth. Sampling took place over a period of five months, corresponding with the transition between the dry and wet season. This allowed assessment of biological-physical relationships across chemical and nutritional gradients associated with a range of estuarine inputs. Physical, chemical, and biological response variables, as well as measures of community structure, showed significant spatio-temporal patterns. In general, bivariate relationships between biological and environmental variables were rare and weak. However, multivariate correlation approaches identified a variety of environmental variables (i.e., sampling session, the C∶N ratio of particulate organic matter, dissolved inorganic nutrient concentrations, various size fractions of photopigment concentrations, salinity and, to a lesser extent, beach width and sediment kurtosis) that either alone or combined provided significant explanatory power for spatio-temporal patterns of macroinfaunal community structure. Overall, these results showed that the macrobenthic community on Mtunzini Beach was not structured primarily by physical factors, but instead by a complex and dynamic blend of nutritional, chemical and physical drivers. This emphasises the need to recognise ocean-exposed sandy

  8. 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.

  9. Chemical reactivity of the compressed noble gas atoms and their reactivity dynamics during collisions with protons

    Indian Academy of Sciences (India)

    P K Chattaraj; B Maiti; U Sarkar

    2003-06-01

    Attempts are made to gain insights into the effect of confinement of noble gas atoms on their various reactivity indices. Systems become harder, less polarizable and difficult to excite as the compression increases. Ionization also causes similar effects. A quantum fluid density functional technique is adopted in order to study the dynamics of reactivity parameters during a collision between protons and He atoms in different electronic states for various projectile velocities and impact parameters. Dynamical variants of the principles of maximum hardness, minimum polarizability and maximum entropy are found to be operative.

  10. Studies on modelling of bubble driven flows in chemical reactors

    Energy Technology Data Exchange (ETDEWEB)

    Grevskott, Sverre

    1997-12-31

    Multiphase reactors are widely used in the process industry, especially in the petrochemical industry. They very often are characterized by very good thermal control and high heat transfer coefficients against heating and cooling surfaces. This thesis first reviews recent advances in bubble column modelling, focusing on the fundamental flow equations, drag forces, transversal forces and added mass forces. The mathematical equations for the bubble column reactor are developed, using an Eulerian description for the continuous and dispersed phase in tensor notation. Conservation equations for mass, momentum, energy and chemical species are given, and the k-{epsilon} and Rice-Geary models for turbulence are described. The different algebraic solvers used in the model are described, as are relaxation procedures. Simulation results are presented and compared with experimental values. Attention is focused on the modelling of void fractions and gas velocities in the column. The energy conservation equation has been included in the bubble column model in order to model temperature distributions in a heated reactor. The conservation equation of chemical species has been included to simulate absorption of CO{sub 2}. Simulated axial and radial mass fraction profiles for CO{sub 2} in the gas phase are compared with measured values. Simulations of the dynamic behaviour of the column are also presented. 189 refs., 124 figs., 1 tab.

  11. 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.

  12. Novel Control Vector Parameterization Method with Differential Evolution Algorithm and Its Application in Dynamic Optimization of Chemical Processes

    Institute of Scientific and Technical Information of China (English)

    SUN Fan; ZHONG Weimin; CHENG Hui; QIAN Feng

    2013-01-01

    Two general approaches are adopted in solving dynamic optimization problems in chemical processes,namely,the analytical and numerical methods.The numerical method,which is based on heuristic algorithms,has been widely used.An approach that combines differential evolution (DE) algorithm and control vector parameterization (CVP) is proposed in this paper.In the proposed CVP,control variables are approximated with polynomials based on state variables and time in the entire time interval.Region reduction strategy is used in DE to reduce the width of the search region,which improves the computing efficiency.The results of the case studies demonstrate the feasibility and efficiency of the proposed methods.

  13. 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

  14. Experimental studies of thermal and chemical interactions between molten aluminum and water

    Energy Technology Data Exchange (ETDEWEB)

    Farahani, A.A.; Corradini, M.L. [Univ. of Wisconsin, Madison, WI (United States)

    1995-09-01

    The possibility of rapid physical and chemical aluminum/water interactions during a core melt accident in a noncommercial reactor (e.g., HFIR, ATR) has resulted in extensive research to determine the mechanism by which these interactions occur and propagate on an explosive time scale. These events have been reported in nuclear testing facilities, i.e., during SPERT 1D experiment, and also in aluminum casting industries. Although rapid chemical reactions between molten aluminum and water have been subject of many studies, very few reliable measurements of the extent of the chemical reactions have thus far been made. We have modified an existing 1-D shock tube facility to perform experiments in order to determine the extent of the explosive thermal/chemical interactions between molton aluminum and water by measuring important physical quantities such as the maximum dynamic pressure and the amount of the generated hydrogen. Experimental results show that transient pressures greater than 69 MPa with a rise time of less than 125 {mu}sec can occur as the result of the chemical reaction of 4.2 grams of molton aluminum (approximately 15% of the total mass of the fuel of 28 grams) at 980 C with room temperature water.

  15. Communicating serum chemical concentrations to study participants: follow up survey

    Directory of Open Access Journals (Sweden)

    Louis Germaine M

    2010-05-01

    Full Text Available Abstract Background A considerable literature now supports the importance of effective communication with study participants, including how best to develop communication plans focusing on the uncertainty of health risks associated with particular environmental exposures. Strategies for communicating individual concentrations of environmental chemicals in human biological samples in the absence of clearly established safe or hazardous levels have been discussed from a conceptual basis and to a lesser extent from an empirical basis. We designed and evaluated an empirically based communication strategy for women of reproductive age who previously participated in a prospective study focusing on persistent environmental chemicals and reproductive outcomes. Methods A cohort of women followed from preconception through pregnancy or up to 12 menstrual cycles without pregnancy was given their individual serum concentrations for lead, dichloro-2,2-bisp-chlorophenyl ethylene, and select polychlorinated biphenyl congeners. Two versions of standardized letters were prepared depending upon women's exposure status, which was characterized as low or high. Letters included an introduction, individual concentrations, population reference values and guidance for minimizing future exposures. Participants were actively monitored for any questions or concerns following receipt of letters. Results Ninety-eight women were sent letters informing them of their individual concentrations to select study chemicals. None of the 89 (91% participating women irrespective of exposure status contacted the research team with questions or concerns about communicated exposures despite an invitation to do so. Conclusions Our findings suggest that study participants can be informed about their individual serum concentrations without generating unnecessary concern.

  16. Quantum-chemical studies of metal oxides for photoelectrochemical applications

    Science.gov (United States)

    Persson, P.; Bergström, R.; Ojamäe, L.; Lunell, S.

    A review of recent research, as well as new results, are presented on transition metal oxide clusters, surfaces, and crystals. Quantum-chemical calculations of clusters of first row transition metal oxides have been made to evaluate the accuracy of ab initio and density functional calculations. Adsorbates on metal oxide surfaces have been studied with both ab initio and semi-empirical methods, and results are presented for the bonding and electronic interactions of large organic adsorbates, e.g. aromatic molecules, on Ti02 and ZnO. Defects and intercalation, notably of H, Li, and Na in Ti02 have been investigated theoretically. Comparisons with experiments are made throughout to validate the calculations. Finally, the role of quantum-chemical calculations in the study of metal oxide based photoelectrochemical devices, such as dyesensitized solar cells and electrochromic displays. is discussed.

  17. Experimental study on dynamic gas adsorption

    Institute of Scientific and Technical Information of China (English)

    Qin Yueping; Wang Yaru; Yang Xiaobin; Liu Wei; Luo Wei

    2012-01-01

    In order to predict the actual adsorption amount as gas adsorption reaches the equilibrium,this research designed a dynamic gas adsorption experiment under constant temperature and pressure,and also studied the isopiestic adsorption characteristics of coal samples with same quality but different sizes.Through the experiment,the study found the adsorption-time changing relationships under different pressures of four different size samples.After regression analysis,we obtained the functional relationship between adsorption and time.According to this,the research resulted in the actual adsorption amount when gas adsorption reaches the equilibrium.In addition,the current study obtained the relationship between adsorption and pressure as well as the effect of the coal size to the adsorption rate.These results have great theoretical and practical significance for the prediction of gas amount in coal seam and gas adsorption process.

  18. Stability studies of Solar Optical Telescope dynamics

    Science.gov (United States)

    Gullapalli, Sarma N.; Pal, Parimal K.; Ruthven, Gregory P.

    1987-01-01

    The Solar Optical Telescope (SOT) is designed to operate as an attached payload mounted on the Instrument Pointing System (IPS) in the cargo bay of the Shuttle Orbiter. Pointing and control of SOT is accomplished by an active Articulated Primary Mirror (APM), an active Tertiary Mirror (TM), an elaborate set of optical sensors, electromechanical actuators and programmable controllers. The structural interactions of this complex control system are significant factors in the stability of the SOT. The preliminary stability study results of the SOT dynamical system are presented. Structural transfer functions obtained from the NASTRAN model of the structure were used. These studies apply to a single degree of freedom (elevation). Fully integrated model studies will be conducted in the future.

  19. NMR Dynamic Studies in Living Systems

    Institute of Scientific and Technical Information of China (English)

    闫永彬; 范明杰; 罗雪春; 张日清

    2002-01-01

    Nuclear magnetic resonance (NMR) can noninvasively monitor the intracellular concentrations and kinetic properties of numerous inorganic and organic compounds. These characteristics have made NMR a useful tool for dynamic studies of living systems. Applications of NMR to living systems have successfully extended to many areas, including studies of metabolic regulation, ion transport, and intracellular reaction rates in vivo. The major purpose of this review is to summarize the results that can be obtained by modern NMR techniques in living systems. With the advances of new techniques, NMR measurements of various nuclides have been performed for specific physiological purposes. Although some technical problems still remain and there are still discrepancies between NMR and traditional biochemical results, the abundant and unique information obtained from NMR spectra suggests that NMR will be more extensively applied in future studies of living systems. The fast development of these new techniques is providing many new NMR applications in living systems, as well as in structural biology.

  20. Molecular Dynamics Studies of Nanofluidic Devices

    DEFF Research Database (Denmark)

    Zambrano Rodriguez, Harvey Alexander

    in opposite direction to the imposed thermal gradient also we measure higher velocities as higher thermal gradients are imposed. Secondly, we present an atomistic analysis of a molecular linear motor fabricated of coaxial carbon nanotubes and powered by thermal gradients. The MD simulation results indicate...... in transport caused by the walls become more dominant and the fluid consists of fewer molecules. Carbon nanotubes are tubular graphite molecules which can be imagined to function as nanoscale pipes or conduits. Another important material for nanofluidics applications is silica. Nowadays, silica nanochannels...... of such devices. Computational nanofluidics complements experimental studies by providing detailed spatial and temporal information of the nanosystem. In this thesis, we conduct molecular dynamics simulations to study basic nanoscale devices. We focus our studies on the understanding of transport mechanism...

  1. Chemical Reactivity Dynamics and Quantum Chaos in Highly Excited Hydrogen Atoms in an External Field: A Quantum Potential Approach

    Directory of Open Access Journals (Sweden)

    B. Maiti

    2002-04-01

    Full Text Available Abstract: Dynamical behavior of chemical reactivity indices like electronegativity, hardness, polarizability, electrophilicity and nucleophilicity indices is studied within a quantum fluid density functional framework for the interactions of a hydrogen atom in its ground electronic state (n = 1 and an excited electronic state (n = 20 with monochromatic and bichromatic laser pulses. Time dependent analogues of various electronic structure principles like the principles of electronegativity equalization, maximum hardness, minimum polarizability and maximum entropy have been found to be operative. Insights into the variation of intensities of the generated higher order harmonics on the color of the external laser field are obtained. The quantum signature of chaos in hydrogen atom has been studied using a quantum theory of motion and quantum fluid dynamics. A hydrogen atom in the electronic ground state (n = 1 and in an excited electronic state ( n = 20 behaves differently when placed in external oscillating monochromatic and bichromatic electric fields. Temporal evolutions of Shannon entropy, quantum Lyapunov exponent and Kolmogorov – Sinai entropy defined in terms of the distance between two initially close Bohmian trajectories for these two cases show marked differences. It appears that a larger uncertainty product and a smaller hardness value signal a chaotic behavior.

  2. Study of interfacial phenomena for bio/chemical sensing applications

    Science.gov (United States)

    Min, Hwall

    This work presents the fundamental study of biological and chemical interfacial phenomena and (bio)chemical sensing applications using high frequency resonator arrays. To realize a versatile (bio)chemical sensing system for the fundamental study as well as their practical applications, the following three distinct components were studied and developed: i) detection platforms with high sensitivity, ii) novel innovative sensing materials with high selectivity, iii) analytical model for data interpretation. 8-pixel micromachined quartz crystal resonator (muQCR) arrays with a fundamental resonance frequency of 60 ¡V 90 MHz have been used to provide a reliable detection platform with high sensitivity. Room temperature ionic liquid (RTIL) has been explored and integrated into the sensing system as a smart chemical sensing material. The use of nanoporous gold (np-Au) enables the combination of the resonator and surface-enhanced Raman spectroscopy for both quantitative and qualitative measurement. A statistical model for the characterization of resonator behavior to study the protein adsorption kinetics is developed by random sequential adsorption (RSA) approach with the integration of an effective surface depletion theory. The investigation of the adsorption kinetics of blood proteins is reported as the fundamental study of biological phenomena using the proposed sensing system. The aim of this work is to study different aspects of protein adsorption and kinetics of adsorption process with blood proteins on different surfaces. We specifically focus on surface depletion effect in conjunction with the RSA model to explain the observed adsorption isotherm characteristics. A number of case studies on protein adsorption conducted using the proposed sensing system has been discussed. Effort is specifically made to understand adsorption kinetics, and the effect of surface on the adsorption process as well as the properties of the adsorbed protein layer. The second half of the

  3. Chemical elements in invertebrate orders for environmental quality studies

    Energy Technology Data Exchange (ETDEWEB)

    Magalhaes, Marcelo R.L.; Franca, Elvis J.; Paiva, Jose D.S.; Hazin, Clovis A., E-mail: marcelo_rlm@hotmail.com, E-mail: ejfranca@cnen.gov.br, E-mail: dan-paiva@hotmail.com, E-mail: chazin@cnen.gov.br [Centro Regional de Ciencias Nucleares do Nordeste (CRCN-NE/CNEN-PE), Recife, PE (Brazil); Fonseca, Felipe Y.; Fernandes, Elisabete A. de Nadai; Bacchi, Marcio A., E-mail: felipe-yamada@hotmail.com, E-mail: lis@cena.usp.br, E-mail: mabacchi@cena.usp.br [Centro de Energia Nuclear na Agricultura (CENA/USP), Piracicaba, SP (Brazil)

    2013-07-01

    Among the biomonitors of environmental quality, there is a lack of studies on using invertebrates to evaluate quantitatively chemical elements in ecosystems. This group of animals is quite numerous, widely distributed and adaptable to the most diverse environmental conditions. These features are very useful for the environmental quality assessment, as well as the several occurring insect-plant interactions performing essential functions in ecosystems. The objective of this work is to study the variability of chemical composition of invertebrate orders for using in environmental quality monitoring studies. Instrumental neutron activation analysis - INAA was applied to determine some nutrients and trace elements in invertebrate samples. Sampling by pitfall traps was carried out in riverine ecosystems from the urban area from the Piracicaba Municipality, State of Sao Paulo, Brazil. Invertebrate and reference material samples were irradiated in the nuclear research reactor IEA-R1, Instituto de Pesquisas Energeticas e Nucleares - IPEN/CNEN. Fragments of a Ni-Cr alloy were irradiated for monitoring the thermal neutron flux. Hymenoptera order was considered the most representative according to the total number of sampled species (about 60%). Significant amounts of Ba, Br, Fe and Sc were found in invertebrates of the order Opiliones. Potassium, rubidium and zinc were highly accumulated in species from Blattodea order, indicating a consistent pattern of accumulation for this invertebrate order. Taking into account the abundance of Hymenoptera order, the chemical composition of its species was significant different at the 95% confidence level for Br and Na in the sampled locals. (author)

  4. Earle K. Plyler Prize for Molecular Spectroscopy & Dynamics Lecture: Broadband Rotational Spectroscopy for Chemical Kinetics, Molecular Structure, and Analytical Chemistry

    Science.gov (United States)

    Pate, Brooks

    2013-03-01

    Advances in high-speed digital electronics have enabled a new generation of molecular rotational spectroscopy techniques that provide instantaneous broadband spectral coverage. These techniques use a chirped excitation pulse to coherently excite the molecular sample over a spectral bandwidth of 10 GHz or larger through rapid passage. The subsequent time-domain emission is recorded using high-speed digitizers (up to 100 Gigasample/s) and the frequency domain spectrum is produced by fast Fourier transformation. The chirped-pulse Fourier transform (CP-FT) method has been implemented in the microwave frequency range (2-40 GHz) for studies of cold samples in pulsed jet sources and in the mm-wave/terahertz (THz) frequency range for studies of samples at room-temperature. The method has opened new applications for molecular rotational spectroscopy in the area of chemical kinetics where dynamic rotational spectroscopy is used to measure the rates of unimolecular isomerization reactions in highly excited molecules prepared by pulsed infrared laser excitation. In these applications, the isomerization rate is obtained from an analysis of the overall line shapes which are modified by chemical exchange leading to coalescence behavior similar to the effect in NMR spectroscopy. The sensitivity of the method and the ability to extend it to low frequency (2-8 GHz) have significantly increased the size range of molecules and molecular clusters for structure determination using isotopic substitution to build up the 3D molecular structures atom-by-atom. Application to the structure of water clusters with up to 15 water molecules will be presented. When coupled with advances in solid-state mm-wave/THz devices, this method provides a direct digital technique for analytical chemistry of room-temperature gases based on molecular rotational spectroscopy. These high-throughput methods can analyze complex sample mixtures with unmatched chemical selectivity and short analysis times. Work

  5. 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.

  6. Dynamical Study of 3D Boson Stars

    Science.gov (United States)

    Choi, Dae-Il; Choptuik, M. W.

    1998-10-01

    We study the dynamical evolution of ``boson stars'' in 3D numerical relativity. Boson stars are equilibrium states of a self-gravitating, complex Klein-Gordon field: a resurgence of interest in scalar fields in the context of astroparticle physics and quantum cosmology has prompted investigation of their dynamics, particularly since they are possible dark matter candidates. In addition, even though any direct physical relevance has yet to be demonstrated, boson star systems provide excellent numerical laboratories in which to study strong gravitational fields. Specifically, the boson star model provides an ideal vehicle with which to implement and evaluate (1) various coordinate conditions in the context of the ADM formalism, and (2) multi-dimensional adaptive mesh refinement techniques which appear crucial for many problems in 3D numerical relativity. We first consider boson stars in the Newtonian regime, where the (numerical) stability of single stars is shown and the interaction of multiple-star-systems is simulated. We also discuss issues which hamper progress towards a stable evolution of general relativistic boson stars, and then show some preliminary results for the general relativistic case.

  7. Magnetoencephalography in the study of brain dynamics.

    Science.gov (United States)

    Pizzella, Vittorio; Marzetti, Laura; Della Penna, Stefania; de Pasquale, Francesco; Zappasodi, Filippo; Romani, Gian Luca

    2014-01-01

    To progress toward understanding of the mechanisms underlying the functional organization of the human brain, either a bottom-up or a top-down approach may be adopted. The former starts from the study of the detailed functioning of a small number of neuronal assemblies, while the latter tries to decode brain functioning by considering the brain as a whole. This review discusses the top-down approach and the use of magnetoencephalography (MEG) to describe global brain properties. The main idea behind this approach is that the concurrence of several areas is required for the brain to instantiate a specific behavior/functioning. A central issue is therefore the study of brain functional connectivity and the concept of brain networks as ensembles of distant brain areas that preferentially exchange information. Importantly, the human brain is a dynamic device, and MEG is ideally suited to investigate phenomena on behaviorally relevant timescales, also offering the possibility of capturing behaviorally-related brain connectivity dynamics.

  8. Allosteric dynamics of SAMHD1 studied by molecular dynamics simulations

    Science.gov (United States)

    Patra, K. K.; Bhattacharya, A.; Bhattacharya, S.

    2016-10-01

    SAMHD1 is a human cellular enzyme that blocks HIV-1 infection in myeloid cells and non-cycling CD4+T cells. The enzyme is an allosterically regulated triphosphohydrolase that modulates the level of cellular dNTP. The virus restriction is attributed to the lowering of the pool of dNTP in the cell to a point where reverse-transcription is impaired. Mutations in SAMHD1 are also implicated in Aicardi-Goutieres syndrome. A mechanistic understanding of the allosteric activation of the enzyme is still elusive. We have performed molecular dynamics simulations to examine the allosteric site dynamics of the protein and to examine the connection between the stability of the tetrameric complex and the Allosite occupancy.

  9. The chemical shock tube as a tool for studying high-temperature chemical kinetics

    Science.gov (United States)

    Brabbs, Theodore A.

    1986-01-01

    Although the combustion of hydrocarbons is our primary source of energy today, the chemical reactions, or pathway, by which even the simplest hydro-carbon reacts with atmospheric oxygen to form CO2 and water may not always be known. Furthermore, even when the reaction pathway is known, the reaction rates are always under discussion. The shock tube has been an important and unique tool for building a data base of reaction rates important in the combustion of hydrocarbon fuels. The ability of a shock wave to bring the gas sample to reaction conditions rapidly and homogeneously makes shock-tube studies of reaction kinetics extremely attractive. In addition to the control and uniformity of reaction conditions achieved with shock-wave methods, shock compression can produce gas temperatures far in excess of those in conventional reactors. Argon can be heated to well over 10 000 K, and temperatures around 5000 K are easily obtained with conventional shock-tube techniques. Experiments have proven the validity of shock-wave theory; thus, reaction temperatures and pressures can be calculated from a measurement of the incident shock velocity. A description is given of the chemical shock tube and auxiliary equipment and of two examples of kinetic experiments conducted in a shock tube.

  10. Chemically specific multiscale modeling of clay-polymer nanocomposites reveals intercalation dynamics, tactoid self-assembly and emergent materials properties.

    Science.gov (United States)

    Suter, James L; Groen, Derek; Coveney, Peter V

    2015-02-01

    A quantitative description is presented of the dynamical process of polymer intercalation into clay tactoids and the ensuing aggregation of polymer-entangled tactoids into larger structures, obtaining various characteristics of these nanocomposites, including clay-layer spacings, out-of-plane clay-sheet bending energies, X-ray diffractograms, and materials properties. This model of clay-polymer interactions is based on a three-level approach, which uses quantum mechanical and atomistic descriptions to derive a coarse-grained yet chemically specific representation that can resolve processes on hitherto inaccessible length and time scales. The approach is applied to study collections of clay mineral tactoids interacting with two synthetic polymers, poly(ethylene glycol) and poly(vinyl alcohol). The controlled behavior of layered materials in a polymer matrix is centrally important for many engineering and manufacturing applications. This approach opens up a route to computing the properties of complex soft materials based on knowledge of their chemical composition, molecular structure, and processing conditions.

  11. Dynamics of phytoplankton in relation to physico-chemical factors of Almatti reservoir of Bijapur District, Karnataka State.

    Science.gov (United States)

    Hulyal, S B; Kaliwal, B B

    2009-06-01

    The present investigation deals with limnobiotic status of the Almatti reservoir from February, 2003 to January, 2005. The study revealed that there exists a fluctuations of the physical factors viz., rainfall, humidity, air and water temperature, pH and electrical conductivity (EC), and chemical factors viz., dissolved oxygen (DO), free carbon dioxide, total alkalinity, total hardness, calcium, magnesium, chloride, nitrate, phosphate, sulphate, bicarbonate and total dissolved solids (TDS). From the data it was also apparent that correlations between the physico-chemical factors and dynamics of phytoplankton could be seen. The simple correlation coefficient test revealed that the cyanophytes number was positively correlated with DO, nitrate, phosphate and negatively significant with total hardness, total alkalinity, EC, calcium, magnesium, sulphate, bicarbonate and TDS. They are inversely correlated with pH, chloride, rainfall and humidity. Bacillariphyceae are correlated with total alkalinity, bicarbonates, magnesium and TDS, whereas inverse correlation was found with rainfall, humidity, pH and phosphate. Desmids showed positive correlation with nitrates, while it was inversely correlated with chloride, rainfall and humidity. Dinophytes density was positively correlated with total alkalinity, EC, total hardness, calcium, bicarbonate, while it showed inverse correlation with rainfall, humidity and phosphate. However, it is obvious that the absence of significant difference between sampling stations for all these parameters in the Almatti reservoir indicated fairly homogeneous conditions and the water quality is also found to be homogeneous.

  12. Molecular Mechanisms by Which Marine Phytoplankton Respond to Their Dynamic Chemical Environment

    Science.gov (United States)

    Palenik, Brian

    2015-01-01

    Marine scientists have long been interested in the interactions of marine phytoplankton with their chemical environments. Nutrient availability clearly controls carbon fixation on a global scale, but the interactions between phytoplankton and nutrients are complex and include both short-term responses (seconds to minutes) and longer-term evolutionary adaptations. This review outlines how genomics and functional genomics approaches are providing a better understanding of these complex interactions, especially for cyanobacteria and diatoms, for which the genome sequences of multiple model organisms are available. Transporters and related genes are emerging as the most likely candidates for biomarkers in stress-specific studies, but other genes are also possible candidates. One surprise has been the important role of horizontal gene transfer in mediating chemical-biological interactions.

  13. Chemical Approaches to Studying Labile Amino Acid Phosphorylation.

    Science.gov (United States)

    Marmelstein, Alan M; Moreno, Javier; Fiedler, Dorothea

    2017-04-01

    Phosphorylation of serine, threonine, and tyrosine residues is the archetypal posttranslational modification of proteins. While phosphorylation of these residues has become standard textbook knowledge, phosphorylation of other amino acid side chains is underappreciated and minimally characterized by comparison. This disparity is rooted in the relative instability of these chemically distinct amino acid side chain moieties, namely phosphoramidates, acyl phosphates, thiophosphates, and phosphoanhydrides. In the case of the O-phosphorylated amino acids, synthetic constructs were critical to assessing their stability and developing tools for their study. As the chemical biology community has become more aware of these alternative phosphorylation sites, methodology has been developed for the synthesis of well-characterized standards and close mimics of these phosphorylated amino acids as well. In this article, we review the synthetic chemistry that is a prerequisite to progress in this field.

  14. Tools for the study of dynamical spacetimes

    Science.gov (United States)

    Zhang, Fan

    This thesis covers a range of topics in numerical and analytical relativity, centered around introducing tools and methodologies for the study of dynamical spacetimes. The scope of the studies is limited to classical (as opposed to quantum) vacuum spacetimes described by Einstein's general theory of relativity. The numerical works presented here are carried out within the Spectral Einstein Code (SpEC) infrastructure, while analytical calculations extensively utilize Wolfram's Mathematica program. We begin by examining highly dynamical spacetimes such as binary black hole mergers, which can be investigated using numerical simulations. However, there are difficulties in interpreting the output of such simulations. One difficulty stems from the lack of a canonical coordinate system (henceforth referred to as gauge freedom) and tetrad, against which quantities such as Newman-Penrose Psi4 (usually interpreted as the gravitational wave part of curvature) should be measured. We tackle this problem in Chapter 2 by introducing a set of geometrically motivated coordinates that are independent of the simulation gauge choice, as well as a quasi-Kinnersley tetrad, also invariant under gauge changes in addition to being optimally suited to the task of gravitational wave extraction. Another difficulty arises from the need to condense the overwhelming amount of data generated by the numerical simulations. In order to extract physical information in a succinct and transparent manner, one may define a version of gravitational field lines and field strength using spatial projections of the Weyl curvature tensor. Introduction, investigation and utilization of these quantities will constitute the main content in Chapters 3 through 6. For the last two chapters, we turn to the analytical study of a simpler dynamical spacetime, namely a perturbed Kerr black hole. We will introduce in Chapter 7 a new analytical approximation to the quasi-normal mode (QNM) frequencies, and relate various

  15. Ultrasonic Study of Dislocation Dynamics in Lithium -

    Science.gov (United States)

    Han, Myeong-Deok

    1987-09-01

    Experimental studies of dislocation dynamics in LiF single crystals, using ultrasonic techniques combined with dynamic loading, were performed to investigate the time evolution of the plastic deformation process under a short stress pulse at room temperature, and the temperature dependence of the dislocation damping mechanism in the temperature range 25 - 300(DEGREES)K. From the former, the time dependence of the ultrasonic attenuation was understood as resulting from dislocation multiplication followed by the evolution of mobile dislocations to immobile ones under large stress. From the latter, the temperature dependence of the ultrasonic attenuation was interpreted as due to the motion of the dislocation loops overcoming the periodic Peierls potential barrier in a manner analogous to the motion of a thermalized sine-Gordon chain under a small stress. The Peierls stress obtained from the experimental results by application of Seeger's relaxation model with exponential dislocation length distribution was 4.26MPa, which is consistent with the lowest stress for the linear relation between the dislocation velocity and stress observed by Flinn and Tinder.

  16. Models of disk chemical evolution focusing the pure dynamical radial mixing

    Directory of Open Access Journals (Sweden)

    Re Fiorentin P.

    2012-02-01

    Full Text Available We performed N-body simulations to study the dynamical evolution of a stellar disk inside a Dark Matter (DM halo. Our results evidence how a standard -radially decreasing- metallicity gradient produces a negative vϕ vs. [Fe/H] correlation, similar to that shown by the thin disk stars, while an inverse radial gradient generates a positive rotation-metallicity correlation, as that observed in the old thick population.

  17. Quantum Chemical Study on Reaction of Acetaldehyde with Hydroxyl Radical

    Institute of Scientific and Technical Information of China (English)

    LI,Ming(李明); ZHANG,Jin-Sheng(张金生); SHEN,Wei(申伟); MENG,Qing-Xi(孟庆喜)

    2004-01-01

    The reaction of acetaldehyde with hydroxyl radical was studied by means of quantum chemical methods. The geometries for all the stationary points on the potential energy surfaces were optimized fully, respectively, at the G3MP2, G3, and MP2/6-311++G(d,p) levels. Single-point energies of all the species were calculated at the QCISD/6-311 + +G(d,p) level. The mechanism of the reaction studied was confirmed. The predicted product is acetyl radical that is in agreement with the experiment.

  18. 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.

  19. 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.

  20. 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

  1. Single-collision studies of energy transfer and chemical reaction

    Energy Technology Data Exchange (ETDEWEB)

    Valentini, J.J. [Columbia Univ., New York, NY (United States)

    1993-12-01

    The research focus in this group is state-to-state dynamics of reaction and energy transfer in collisions of free radicals such as H, OH, and CH{sub 3} with H{sub 2}, alkanes, alcohols and other hydrogen-containing molecules. The motivation for the work is the desire to provide a detailed understanding of the chemical dynamics of prototype reactions that are important in the production and utilization of energy sources, most importantly in combustion. The work is primarily experimental, but with an important and growing theoretical/computational component. The focus of this research program is now on reactions in which at least one of the reactants and one of the products is polyatomic. The objective is to determine how the high dimensionality of the reactants and products differentiates such reactions from atom + diatom reactions of the same kinematics and energetics. The experiments use highly time-resolved laser spectroscopic methods to prepare reactant states and analyze the states of the products on a single-collision time scale. The primary spectroscopic tool for product state analysis is coherent anti-Stokes Raman scattering (CARS) spectroscopy. CARS is used because of its generality and because the extraction of quantum state populations from CARS spectra is straightforward. The combination of the generality and easy analysis of CARS makes possible absolute cross section measurements (both state-to-state and total), a particularly valuable capability for characterizing reactive and inelastic collisions. Reactant free radicals are produced by laser photolysis of appropriate precursors. For reactant vibrational excitation stimulated Raman techniques are being developed and implemented.

  2. Chemical functionalization of graphene via aryne cycloaddition: a theoretical study.

    Science.gov (United States)

    Zhao, Jing-xiang; Wang, Hong-xia; Gao, Bo; Wang, Xiao-guang; Cai, Qing-hai; Wang, Xuan-zhang

    2012-06-01

    Chemical functionalization of graphene provides a promising route to improve its solubility in water and organic solvents as well as modify its electronic properties, thus significantly expanding its potential applications. In this article, by using density functional theory (DFT) methods, we have studied the effects of the chemical functionalization of graphenes via aryne cycloaddition on its properties. We found that the adsorption of an isolated aryne group on the graphene sheet is very weak with the adsorption energy of -0.204 eV, even though two new single C-C interactions are formed between the aryne group and the graphene. However, the interaction of graphene with the aryne group can be greatly strengthened by (i) substituting the H-atoms in aryne group with F-, Cl-, -NO(2) (electron-withdrawing capability), or CH(3)-group (electron-donating capability), and (ii) increasing the coverage of the adsorbed aryne groups on the graphene sheet. As expected, the strongest bonding is found on the graphene edges, in which the adsorbed aryne groups prefer to be far away from each other. Interestingly, chemical functionalization with aryne groups leads to an opening of the band gap of graphene, which is dependent on the coverage of the adsorbed aryne groups. The present work provides an insight into the modifications of graphene with aryne groups in experiment.

  3. Molecular dynamics study of ice structural evolution

    Institute of Scientific and Technical Information of China (English)

    Wang Yan; Dong Shun-Le

    2008-01-01

    Molecular dynamics simulation is employed to study the structural evolution of low density amorphous ice during its compression from one atmosphere to 2.5 GPa. Calculated results show that high density amorphous ice is formed at an intermediate pressure of~1.0GPa; the O-O-O bond angle ranges from 83° to 113°, and the O-H...O bond is bent from 112° to 160°. Very high density amorphous ice is obtained by quenching to 80K and decompressing the ice to ambient pressure from 160 K/1.3 GPa or 160 K/1.7 GPa; and the next-nearest O-O length is found to be 0.310 nm, just 0.035 nm beyond the nearest O-O distance of 0.275 nm.

  4. Monte Carlo study of real time dynamics

    CERN Document Server

    Alexandru, Andrei; Bedaque, Paulo F; Vartak, Sohan; Warrington, Neill C

    2016-01-01

    Monte Carlo studies involving real time dynamics are severely restricted by the sign problem that emerges from highly oscillatory phase of the path integral. In this letter, we present a new method to compute real time quantities on the lattice using the Schwinger-Keldysh formalism via Monte Carlo simulations. The key idea is to deform the path integration domain to a complex manifold where the phase oscillations are mild and the sign problem is manageable. We use the previously introduced "contraction algorithm" to create a Markov chain on this alternative manifold. We substantiate our approach by analyzing the quantum mechanical anharmonic oscillator. Our results are in agreement with the exact ones obtained by diagonalization of the Hamiltonian. The method we introduce is generic and in principle applicable to quantum field theory albeit very slow. We discuss some possible improvements that should speed up the algorithm.

  5. Dynamic speckle study of microbial growth

    Science.gov (United States)

    Vincitorio, F. M.; Mulone, C.; Marcuzzi, P. A.; Budini, N.; Freyre, C.; Lopez, A. J.; Ramil, A.

    2015-08-01

    In this work we present a characterization of yeast dynamic speckle activity during growth in an isolated agar culture medium. We found that it is possible to detect the growth of the microorganisms even before they turn out to be visible. By observing the time evolution of the speckle activity at different regions of the culture medium we could extract a map of the growth process, which served to analyze how the yeast develops and spreads over the agar's medium. An interesting point of this study concerns with the influence of the laser light on the yeast growth rate. We have found that yeast finds hard to develop at regions with higher laser light illumination, although we used a synchronous system to capture the speckle pattern. The results obtained in this work would serve us as a starting point to fabricate a detector of growing microorganism colonies, with obvious interesting applications in diverse areas.

  6. Relative influence of chemical and non-chemical stressors on invertebrate communities: a case study in the Danube River.

    Science.gov (United States)

    Rico, Andreu; Van den Brink, Paul J; Leitner, Patrick; Graf, Wolfram; Focks, Andreas

    2016-11-15

    A key challenge for the ecological risk assessment of chemicals has been to evaluate the relative contribution of chemical pollution to the variability observed in biological communities, as well as to identify multiple stressor groups. In this study we evaluated the toxic pressure exerted by >200 contaminants to benthic macroinvertebrates in the Danube River using the Toxic Unit approach. Furthermore, we evaluated correlations between several stressors (chemical and non-chemical) and biological indices commonly used for the ecological status assessment of aquatic ecosystems. We also performed several variation partitioning analyses to evaluate the relative contribution of contaminants and other abiotic parameters (i.e. habitat characteristics, hydromorphological alterations, water quality parameters) to the structural and biological trait variation of the invertebrate community. The results of this study show that most biological indices significantly correlate to parameters related to habitat and physico-chemical conditions, but showed limited correlation with the calculated toxic pressure. The calculated toxic pressure, however, showed little variation between sampling sites, which complicates the identification of pollution-induced effects. The results of this study show that the variation in the structure and trait composition of the invertebrate community are mainly explained by habitat and water quality parameters, whereas hydromorphological alterations play a less important role. Among the water quality parameters, physico-chemical parameters such as suspended solids, nutrients or dissolved oxygen explained a larger part of the variation in the invertebrate community as compared to metals or organic contaminants. Significant correlations exist between some physico-chemical measurements (e.g. nutrients) and some chemical classes (i.e. pharmaceuticals, chemicals related to human presence) which constitute important multiple stressor groups. This study

  7. Rotational coherence spectroscopy at FLASH. Toward dynamic studies in nanosuperfluids

    Energy Technology Data Exchange (ETDEWEB)

    Kickermann, Andreas

    2013-07-15

    The field of molecular physics, which is focusing on molecular motion in the transition states of physical, chemical, and biological changes, is a wide-spread research area. It strives to reveal the structural and functional properties of molecules, the chemical bonds between atoms and the time evolution. Many processes occurring in nature upon electronic excitation proceed on the ultrafast femtosecond timescale and can be triggered by modern ultrashort femtosecond-laser sources under laboratory conditions. In the present thesis pump-probe studies were performed to follow molecular motion using ultrashort light pulses in the nanometer wavelength range provided by an XUV freeelectron laser (FEL). In detail, alignment of molecular species in space under field-free conditions was investigated. In the specific case of rotational wave packets in molecules the rotational dynamics shows characteristic temporal features, which contain a wealth of information on molecular structure and give insight into molecular coupling mechanisms, i.e. rotational constants and transition frequencies. Within this thesis, Rotational Coherence Spectroscopy (RCS) reveals wave-packet motion observed by subsequent Coulomb explosion of Raman excited carbon monoxide, which results in a time-dependent asymmetry of spatial fragmentation patterns. With the method presented here, the time resolution to elucidate the fast dynamics of strong couplings can be pushed toward a single rotational period even for the fastest rotors. This is due to large pump-probe delays with small subpicosecond step size. This kind of spectroscopy can also be expanded to molecular species, which are not accessible by other powerful spectroscopic methods, such as Fourier-transform microwave spectroscopy (FTMW). Furthermore, it allows to measure weak molecular couplings on a long timescale (large pump-probe delays), e.g. couplings of molecules in a solution or molecules dissolved in quantum fluids. This is valuable to

  8. Molecular-dynamics study of detonation. II. The reaction mechanism

    Science.gov (United States)

    Rice, Betsy M.; Mattson, William; Grosh, John; Trevino, S. F.

    1996-01-01

    In this work, we investigate mechanisms of chemical reactions that sustain an unsupported detonation. The chemical model of an energetic crystal used in this study consists of heteronuclear diatomic molecules that, at ambient pressure, dissociate endothermically. Subsequent association of the products to form homonuclear diatomic molecules provides the energy release that sustains the detonation. A many-body interaction is used to simulate changes in the electronic bonding as a function of local atomic environment. The consequence of the many-body interaction in this model is that the intramolecular bond is weakened with increasing density. The mechanism of the reaction for this model was extracted by investigating the details of the molecular properties in the reaction zone with two-dimensional molecular dynamics. The mechanism for the initiation of the reaction in this model is pressure-induced atomization. There was no evidence of excitation of vibrational modes to dissociative states. This particular result is directly attributable to the functional form and choice of parameters for this model, but might also have more general applicability.

  9. 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.

  10. 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.

  11. Oxidation dynamics of nanophase aluminum clusters : a molecular dynamics study.

    Energy Technology Data Exchange (ETDEWEB)

    Ogata, S.

    1998-01-27

    Oxidation of an aluminum nanocluster (252,158 atoms) of radius 100{angstrom} placed in gaseous oxygen (530,727 atoms) is investigated by performing molecular-dynamics simulations on parallel computers. The simulation takes into account the effect of charge transfer between Al and O based on the electronegativity equalization principles. We find that the oxidation starts at the surface of the cluster and the oxide layer grows to a thickness of {approximately}28{angstrom}. Evolutions of local temperature and densities of Al and O are investigated. The surface oxide melts because of the high temperature resulting from the release of energy associated with Al-O bondings. Amorphous surface-oxides are obtained by quenching the cluster. Vibrational density-of-states for the surface oxide is analyzed through comparisons with those for crystalline Al, Al nanocluster, and {alpha}-Al{sub 2}O{sub 3}.

  12. Solid-State NMR Studies of Chemically Lithiated CFx

    Science.gov (United States)

    Leifer, N. D.; Johnson, V. S.; Ben-Ari, R.; Gan, H.; Lehnes, J. M.; Guo, R.; Lu, W.; Muffoletto, B. C.; Reddy, T.; Stallworth, P. E.; Greenbaum, S. G.

    2010-01-01

    Three types of fluorinated carbon, all in their original form and upon sequential chemical lithiations via n-butyllithium, were investigated by 13C and 19F solid-state NMR methods. The three starting CFx materials [where x = 1 (nominally)] were fiber based, graphite based, and petroleum coke based. The aim of the current study was to identify, at the atomic/molecular structural level, factors that might account for differences in electrochemical performance among the different kinds of CFx. Differences were noted in the covalent F character among the starting compounds and in the details of LiF production among the lithiated samples. PMID:20676233

  13. Studies on the Chemical Constituents and Bioactivities of Tripterygium Wilfordii

    Institute of Scientific and Technical Information of China (English)

    LI; YuanChao

    2001-01-01

    Tripterygium wilfordii Hook (TW) is a medicinal plant distributed widely in southern china. This plant was recently found to possess anti-inflammatory, antitumor and immunosuppressive activities. Some preparation of the plant root has been used for the treatment of rheumatoid arthritis, systemic acne rosacea, nephritis and some skin diseases. Chemical studies on this plant and its preparation have shown they contain a large number of sesquiterpenoid, diterpenoids, triterpenoids and alkaloids in which some diterpene triepoxy lactones such as triptolide and triptonide etc are considered as mainly active compounds.  ……

  14. Studies on the Chemical Constituents and Bioactivities of Tripterygium Wilfordii

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ Tripterygium wilfordii Hook (TW) is a medicinal plant distributed widely in southern china. This plant was recently found to possess anti-inflammatory, antitumor and immunosuppressive activities. Some preparation of the plant root has been used for the treatment of rheumatoid arthritis, systemic acne rosacea, nephritis and some skin diseases. Chemical studies on this plant and its preparation have shown they contain a large number of sesquiterpenoid, diterpenoids, triterpenoids and alkaloids in which some diterpene triepoxy lactones such as triptolide and triptonide etc are considered as mainly active compounds.

  15. Molecular Dynamics Study of Helicobacter pylori Urease.

    Science.gov (United States)

    Minkara, Mona S; Ucisik, Melek N; Weaver, Michael N; Merz, Kenneth M

    2014-05-13

    Helicobacter pylori have been implicated in an array of gastrointestinal disorders including, but not limited to, gastric and duodenal ulcers and adenocarcinoma. This bacterium utilizes an enzyme, urease, to produce copious amounts of ammonia through urea hydrolysis in order to survive the harsh acidic conditions of the stomach. Molecular dynamics (MD) studies on the H. pylori urease enzyme have been employed in order to study structural features of this enzyme that may shed light on the hydrolysis mechanism. A total of 400 ns of MD simulation time were collected and analyzed in this study. A wide-open flap state previously observed in MD simulations on Klebsiella aerogenes [Roberts et al. J. Am. Chem. Soc.2012, 134, 9934] urease has been identified in the H. pylori enzyme that has yet to be experimentally observed. Critical distances between residues on the flap, contact points in the closed state, and the separation between the active site Ni(2+) ions and the critical histidine α322 residue were used to characterize flap motion. An additional flap in the active site was elaborated upon that we postulate may serve as an exit conduit for hydrolysis products. Finally we discuss the internal hollow cavity and present analysis of the distribution of sodium ions over the course of the simulation.

  16. Matrix isolation as a tool for studying interstellar chemical reactions

    Science.gov (United States)

    Ball, David W.; Ortman, Bryan J.; Hauge, Robert H.; Margrave, John L.

    1989-01-01

    Since the identification of the OH radical as an interstellar species, over 50 molecular species were identified as interstellar denizens. While identification of new species appears straightforward, an explanation for their mechanisms of formation is not. Most astronomers concede that large bodies like interstellar dust grains are necessary for adsorption of molecules and their energies of reactions, but many of the mechanistic steps are unknown and speculative. It is proposed that data from matrix isolation experiments involving the reactions of refractory materials (especially C, Si, and Fe atoms and clusters) with small molecules (mainly H2, H2O, CO, CO2) are particularly applicable to explaining mechanistic details of likely interstellar chemical reactions. In many cases, matrix isolation techniques are the sole method of studying such reactions; also in many cases, complexations and bond rearrangements yield molecules never before observed. The study of these reactions thus provides a logical basis for the mechanisms of interstellar reactions. A list of reactions is presented that would simulate interstellar chemical reactions. These reactions were studied using FTIR-matrix isolation techniques.

  17. A Hybrid Improved Genetic Algorithm and Its Application in Dynamic Optimization Problems of Chemical Processes

    Institute of Scientific and Technical Information of China (English)

    SUN Fan; DU Wenli; QI Rongbin; QIAN Feng; ZHONG Weimin

    2013-01-01

    The solutions of dynamic optimization problems are usually very difficult due to their highly nonlinear and multidimensional nature.Genetic algorithm(GA)has been proved to be a feasible method when the gradient is difficult to calculate.Its advantage is that the control profiles at all time stages are optimized simultaneously,but its convergence is very slow in the later period of evolution and it is easily trapped in the local optimum.In this study,a hybrid improved genetic algorithm(HIGA)for solving dynamic optimization problems is proposed to overcome these defects.Simplex method(SM)is used to perform the local search in the neighborhood of the optimal solution.By using SM,the ideal searching direction of global optimal solution could be found as soon as possible and the convergence speed of the algorithm is improved.The hybrid algorithm presents some improvements,such as protecting the best individual,accepting immigrations,as well as employing adaptive crossover and Gaussian mutation operators.The efficiency of the proposed algorithm is demonstrated by solving several dynamic optimization problems.At last,HIGA is applied to the optimal production of secreted protein in a fed batch reactor and the optimal feed-rate found by HIGA is effective and relatively stable.

  18. Reaction dynamics. Extremely short-lived reaction resonances in Cl + HD (v = 1) → DCl + H due to chemical bond softening.

    Science.gov (United States)

    Yang, Tiangang; Chen, Jun; Huang, Long; Wang, Tao; Xiao, Chunlei; Sun, Zhigang; Dai, Dongxu; Yang, Xueming; Zhang, Dong H

    2015-01-02

    The Cl + H2 reaction is an important benchmark system in the study of chemical reaction dynamics that has always appeared to proceed via a direct abstraction mechanism, with no clear signature of reaction resonances. Here we report a high-resolution crossed-molecular beam study on the Cl + HD (v = 1, j = 0) → DCl + H reaction (where v is the vibrational quantum number and j is the rotational quantum number). Very few forward scattered products were observed. However, two distinctive peaks at collision energies of 2.4 and 4.3 kilocalories per mole for the DCl (v' = 1) product were detected in the backward scattering direction. Detailed quantum dynamics calculations on a highly accurate potential energy surface suggested that these features originate from two very short-lived dynamical resonances trapped in the peculiar H-DCl (v' = 2) vibrational adiabatic potential wells that result from chemical bond softening. We anticipate that dynamical resonances trapped in such wells exist in many reactions involving vibrationally excited molecules.

  19. Advances in chemical physics

    CERN Document Server

    Rice, Stuart A

    2012-01-01

    The Advances in Chemical Physics series-the cutting edge of research in chemical physics The Advances in Chemical Physics series provides the chemical physics field with a forum for critical, authoritative evaluations of advances in every area of the discipline. Filled with cutting-edge research reported in a cohesive manner not found elsewhere in the literature, each volume of the Advances in Chemical Physics series serves as the perfect supplement to any advanced graduate class devoted to the study of chemical physics. This volume explores: Quantum Dynamical Resonances in Ch

  20. STUDY REGARDING THE CORELATION BETWEEN SOMATIC CELLS COUNT AND MAJOR CHEMICAL COMPOUNDS IN RAW MILK

    Directory of Open Access Journals (Sweden)

    S. ACATINCĂI

    2013-12-01

    Full Text Available This study approaches the dynamic of somatic cells number and chemical composition of milk during 13 months of control. The study also investigates the correlations between the number of somatic cells and some chemical parameters in milk. Studies were carried out on Romanian Black and White cows between March 2005 and March 2006 at the Didactical farm of the Banat University of Agricultural Sciences Timisoara. As quality indicator, the number of somatic cells has different values among the controls. Average values for the 13 months of control, with the exception of three controls, were below maximum limit admitted from 1th of January 2007 (600000 SCC/ml milk. There weren’t any significant differences for SCC between the two seasons. Chemical parameters in milk varied in close limits and the differences were not significant, with one exception for fat percent. Fat percent is higher (p<0.05 in the cold season 3.87% compared with 3.55% during the warm season. Somatic cells number is weak correlated with lactose and strong correlated with proteins.

  1. Differential dynamic engagement within 24 SH3 domain: peptide complexes revealed by co-linear chemical shift perturbation analysis.

    Directory of Open Access Journals (Sweden)

    Elliott J Stollar

    Full Text Available There is increasing evidence for the functional importance of multiple dynamically populated states within single proteins. However, peptide binding by protein-protein interaction domains, such as the SH3 domain, has generally been considered to involve the full engagement of peptide to the binding surface with minimal dynamics and simple methods to determine dynamics at the binding surface for multiple related complexes have not been described. We have used NMR spectroscopy combined with isothermal titration calorimetry to comprehensively examine the extent of engagement to the yeast Abp1p SH3 domain for 24 different peptides. Over one quarter of the domain residues display co-linear chemical shift perturbation (CCSP behavior, in which the position of a given chemical shift in a complex is co-linear with the same chemical shift in the other complexes, providing evidence that each complex exists as a unique dynamic rapidly inter-converting ensemble. The extent the specificity determining sub-surface of AbpSH3 is engaged as judged by CCSP analysis correlates with structural and thermodynamic measurements as well as with functional data, revealing the basis for significant structural and functional diversity amongst the related complexes. Thus, CCSP analysis can distinguish peptide complexes that may appear identical in terms of general structure and percent peptide occupancy but have significant local binding differences across the interface, affecting their ability to transmit conformational change across the domain and resulting in functional differences.

  2. Vibrational spectroscopic studies of Isoleucine by quantum chemical calculations.

    Science.gov (United States)

    Moorthi, P P; Gunasekaran, S; Ramkumaar, G R

    2014-04-24

    In this work, we reported a combined experimental and theoretical study on molecular structure, vibrational spectra and NBO analysis of Isoleucine (2-Amino-3-methylpentanoic acid). The optimized molecular structure, vibrational frequencies, corresponding vibrational assignments, thermodynamics properties, NBO analyses, NMR chemical shifts and ultraviolet-visible spectral interpretation of Isoleucine have been studied by performing MP2 and DFT/cc-pVDZ level of theory. The FTIR, FT-Raman spectra were recorded in the region 4000-400 cm(-1) and 3500-50 cm(-1) respectively. The UV-visible absorption spectra of the compound were recorded in the range of 200-800 nm. Computational calculations at MP2 and B3LYP level with basis set of cc-pVDZ is employed in complete assignments of Isoleucine molecule on the basis of the potential energy distribution (PED) of the vibrational modes, calculated using VEDA-4 program. The calculated wavenumbers are compared with the experimental values. The difference between the observed and calculated wavenumber values of most of the fundamentals is very small. (13)C and (1)H nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method and compared with experimental results. The formation of hydrogen bond was investigated in terms of the charge density by the NBO calculations. Based on the UV spectra and TD-DFT calculations, the electronic structure and the assignments of the absorption bands were carried out. Besides, molecular electrostatic potential (MEP) were investigated using theoretical calculations.

  3. Chemical reaction and dust formation studies in laboratory hydrocarbon plasmas.

    Science.gov (United States)

    Hippler, Rainer; Majumdar, Abhijit; Thejaswini, H. C.

    Plasma chemical reaction studies with relevance to, e.g., Titan's atmosphere have been per-formed in various laboratory plasmas [1,2]. Chemical reactions in a dielectric barrier discharge at medium pressure of 250-300 mbar have been studied in CH4 /N2 and CH4 /Ar gas mixtures by means of mass spectrometry. The main reaction scheme is production of H2 by fragmenta-tion of CH4 , but also production of larger hydrocarbons like Cn Hm with n up to 10 including formation of different functional CN groups is observed. [1] A. Majumdar and R. Hippler, Development of dielectric barrier discharge plasma processing apparatus for mass spectrometry and thin film deposition, Rev. Sci. Instrum. 78, 075103 (2007) [2] H.T. Do, G. Thieme, M. Frühlich, H. Kersten, and R. Hippler, Ion Molecule and Dust Particle Formation in Ar/CH4 , Ar/C2 H2 and Ar/C3 H6 Radio-frequency Plasmas, Contrib. Plasma Phys. 45, No. 5-6, 378-384 (2005)

  4. Closed Loop Adaptive Refinement of Dynamical Models for Complex Chemical Reactions

    Science.gov (United States)

    2008-06-26

    CH3Br, Ar + H2O are given below. 3.1 Cl− + CH3Br Reaction A global RS-HDMR input/output map for the SN2 reaction Cl− +CH3Br→ ClCH3 +Br − (9) 3 was...2257-2266. [16] Wang H. B., Hase W. L. (1996). Reaction path Hamiltonian analysis of the dynamics for Cl− + CH3Br→ ClCH3 + Br − SN2 nucleophilic... reaction Cl − + CH3Br → ClCH3 + Br −, J. Chem. Phys., 111(24), 10887- 10894. [18] Sun, L., Hase, W. L., Song, K. (2001). Trajectory studies of SN2

  5. Combined spectroscopic and quantum chemical studies of ezetimibe

    Science.gov (United States)

    Prajapati, Preeti; Pandey, Jaya; Shimpi, Manishkumar R.; Srivastava, Anubha; Tandon, Poonam; Velaga, Sitaram P.; Sinha, Kirti

    2016-12-01

    Ezetimibe (EZT) is a hypocholesterolemic agent used for the treatment of elevated blood cholesterol levels as it lowers the blood cholesterol by blocking the absorption of cholesterol in intestine. Study aims to combine experimental and computational methods to provide insights into the structural and vibrational spectroscopic properties of EZT which is important for explaining drug substance physical and biological properties. Computational study on molecular properties of ezetimibe is presented using density functional theory (DFT) with B3LYP functional and 6-311++G(d,p) basis set. A detailed vibrational assignment has been done for the observed IR and Raman spectra of EZT. In addition to the conformational study, hydrogen bonding and molecular docking studies have been also performed. For conformational studies, the double well potential energy curves have been plotted for the rotation around the six flexible bonds of the molecule. UV absorption spectrum was examined in methanol solvent and compared with calculated one in solvent environment (IEF-PCM) using TD-DFT/6-31G basis set. HOMO-LUMO energy gap of both the conformers have also been calculated in order to predict its chemical reactivity and stability. The stability of the molecule was also examined by means of natural bond analysis (NBO) analysis. To account for the chemical reactivity and site selectivity of the molecules, molecular electrostatic potential (MEPS) map has been plotted. The combination of experimental and calculated results provide an insight into the structural and vibrational spectroscopic properties of EZT. In order to give an insight for the biological activity of EZT, molecular docking of EZT with protein NPC1L1 has been done.

  6. Corrosion study in the chemical air separation (MOLTOX trademark ) process

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Doohee; Wong, Kai P.; Archer, R.A.; Cassano, A.A.

    1988-12-01

    This report presents the results of studies aimed at solving the corrosion problems encountered during operation of the MOLTOX{trademark} pilot plant. These studies concentrated on the screening of commercial and developmental alloys under conditions simulating operation conditions in this high temperature molten salt process. Process economic studies were preformed in parallel with the laboratory testing to ensure that an economically feasible solution would be achieved. In addition to the above DOE co-funded studies, Air Products and Chemicals pursued proprietary studies aimed at developing a less corrosive salt mixture which would potentially allow the use of chemurgically available alloys such as stainless steels throughout the system. These studies will not be reported here; however, the results of corrosion tests in the new less corrosive salt mixtures are reported. Because our own studies on salt chemistry impacts heavily on the overall process and thereby has an influence on the experimental work conducted under this contract, some of the studies discussed here were impacted by our own proprietary data. Therefore, the reasons behind some of the experiments presented herein will not be explained because that information is proprietary to Air Products. 14 refs., 42 figs., 21 tabs.

  7. Fluorescence spectroscopic studies of DNA dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Scalettar, B.A.

    1987-04-01

    Random solvent induced motions of DNA are manifest as nanosecond torsional oscillations of the helix backbone, nanosecond through millisecond bending deformations and overall rotational and translational diffusion of the polymer. Fluorescence spectroscopy is used to study this spectrum of DNA motions while ethidium monoazide was covalently bounded. The steady state fluorescence depolarization data indicate that the covalent monoazide/DNA complex exhibits internal motions characterized by an average angular amplitude of 26 degrees confirming reports of fast torsional oscillations in noncovalent ethidium bromide/DNA systems. Data obtained by use of a new polarized photobleaching recovery technique (FPR) reflect both the rotational dynamics of the polymer and the reversible photochemistry of the dye. To isolate the reorientational motion of the DNA, the FPR experiments were ran in two modes that differ only in the polarization of the bleaching light. A quotient function constructed from the data obtained in these two modes monitors only the rotational component of the FPR recovery. In specific applications those bending deformations of long DNA molecules that have characteristic relaxation times on the order of 100 microseconds have been resolved. A fluorescence correlation technique that relates fluctuations in particle number to center-of-mass motion was used to measure translational diffusion on coefficients of the plasmid PBR322 and a short oligomeric DNA. A theory that describes angular correlation in systems exhibiting cyclic, biologically directed reorientation and random Brownian rotation is developed.

  8. Dynamics of crowd disasters: An empirical study

    Science.gov (United States)

    Helbing, Dirk; Johansson, Anders; Al-Abideen, Habib Zein

    2007-04-01

    Many observations of the dynamics of pedestrian crowds, including various self-organization phenomena, have been successfully described by simple many-particle models. For ethical reasons, however, there is a serious lack of experimental data regarding crowd panic. Therefore, we have analyzed video recordings of the crowd disaster in Mina/Makkah during the Hajj in 1426H on 12 January 2006. They reveal two subsequent, sudden transitions from laminar to stop-and-go and “turbulent” flows, which question many previous simulation models. While the transition from laminar to stop-and-go flows supports a recent model of bottleneck flows [D. Helbing , Phys. Rev. Lett. 97, 168001 (2006)], the subsequent transition to turbulent flow is not yet well understood. It is responsible for sudden eruptions of pressure release comparable to earthquakes, which cause sudden displacements and the falling and trampling of people. The insights of this study into the reasons for critical crowd conditions are important for the organization of safer mass events. In particular, they allow one to understand where and when crowd accidents tend to occur. They have also led to organizational changes, which have ensured a safe Hajj in 1427H.

  9. 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.

  10. Sensitivity study of SMILES-2 for chemical species

    Science.gov (United States)

    Suzuki, Makoto; Manago, Naohiro; Ozeki, Hiroyuki; Ochiai, Satoshi; Baron, Philippe

    2015-10-01

    Sensitivity studies of temperature and chemical species (Observed by ISS/JEM/SMILES: O3, HCl, ClO, HO2, BrO, HNO3, CH3CN, and Not observed by SMILES: Temperature, H2O, N2O, NO2, NO, CH3Cl, CO, H2CO, OH and O-atom) was carried out for the SMILES-2 proposal, a sub-mm and THz observation of limb emission from space over the spectral region from 400 GHz to 2.5 THz. Tentative but optimal candidate of frequency bands to cover these species was selected with 3 SIS (Superconductor-Insulator-Superconductor) mixers; SIS-1 (485-489 GHz + 523-527 GHz), SIS-2 (623-627 GHz + 648-652 GHz), SIS-3 (557 GHz + 576.3 GHz) and 2 HEB (Hot Electron Bolometer); HEB-1 (1.8 THz OH) and HEB-2 (2.06 THz O-atom). Temperature can be retrieved with 1 K precision and 1 km vertical resolution from 15 to 120 km. Other chemical species also showed very high single scan precision (random error) comparable to statistical standard error of previous satellite measurements.

  11. Studies on high chemical reactivity of nano-NaH

    Institute of Scientific and Technical Information of China (English)

    FAN Yinheng; ZOU Yunling; JIN Dan; WU Qiang; LIU Tong; XU Jie

    2007-01-01

    A comparison between the initial reaction rates of nanometric and commercial Nail has been studied in four test reactions: 1) hydrogenolysis of chlorobenzene; 2) selec-tive reduction of cinnamaldehyde to cinnamyl alcohol; 3)metallation of dimethyl sulfoxide; and 4) catalytic hydroge-nation ofolefins. The experimental results indicate that when Nail is used as a chemical reagent in the first three reactions,the initial reaction rates of nano-NaH is 230, 120 and 110 times higher than those of the commercial ones respectively,and it is in agreement with the difference in specific surface areas between these two forms of Nail. When Nail is used as a catalyst component together with Cp2TiCl2 in the fourth reaction, catalyst with nano-NaH gives extremely high activity in the hydrogenation of olefins, while the one with commercial Nail gives no activity at all even ifa large amount of the commercial Nail is used to make the total surface area equivalent to that of nano-NaH. Thus, it is evident that although large specific surface area is important for nano-Nail to be used as a catalyst component, high surface energy with surface defects seems to be more important. The largespecific surface and the activated surface of nano-NaH withhigh surface energy should be the main factors for thei rextremely high chemical reactivity, while whether the former or the latter one plays a leading role depends on the type of reactions involved.

  12. Study of the structure and dynamics of complex biological networks

    Science.gov (United States)

    Samal, Areejit

    2008-12-01

    In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large scale metabolic networks inside three organisms, Escherichia coli, Saccharomyces cerevisiae and Staphylococcus aureus. We also study the dynamics of the large scale genetic network controlling E. coli metabolism. We have tried to explain the observed system level dynamical properties of these networks in terms of their underlying structure. Our studies of the system level dynamics of these large scale biological networks provide a different perspective on their functioning compared to that obtained from purely structural studies. Our study also leads to some new insights on features such as robustness, fragility and modularity of these large scale biological networks. We also shed light on how different networks inside the cell such as metabolic networks and genetic networks are interrelated to each other.

  13. Some sensitivity studies of chemical transport simulated in models of the soil-plant-litter system

    Energy Technology Data Exchange (ETDEWEB)

    Begovich, C.L.; Luxmoore, R.J.

    1979-09-01

    Fifteen parameters in a set of five coupled models describing carbon, water, and chemical dynamics in the soil-plant-litter system were varied in a sensitivity analysis of model response. Results are presented for chemical distribution in the components of soil, plants, and litter along with selected responses of biomass, internal chemical transport (xylem and phloem pathways), and chemical uptake. Response and sensitivity coefficients are presented for up to 102 model outputs in an appendix. Two soil properties (chemical distribution coefficient and chemical solubility) and three plant properties (leaf chemical permeability, cuticle thickness, and root chemical conductivity) had the greatest influence on chemical transport in the soil-plant-litter system under the conditions examined. Pollutant gas uptake (SO/sub 2/) increased with change in plant properties that increased plant growth. Heavy metal dynamics in litter responded to plant properties (phloem resistance, respiration characteristics) which induced changes in the chemical cycling to the litter system. Some of the SO/sub 2/ and heavy metal responses were not expected but became apparent through the modeling analysis.

  14. Some Sensitivity Studies of Chemical Transport Simulated in Models of the Soil-Plant-Litter System

    Energy Technology Data Exchange (ETDEWEB)

    Begovich, C.L.

    2002-10-28

    Fifteen parameters in a set of five coupled models describing carbon, water, and chemical dynamics in the soil-plant-litter system were varied in a sensitivity analysis of model response. Results are presented for chemical distribution in the components of soil, plants, and litter along with selected responses of biomass, internal chemical transport (xylem and phloem pathways), and chemical uptake. Response and sensitivity coefficients are presented for up to 102 model outputs in an appendix. Two soil properties (chemical distribution coefficient and chemical solubility) and three plant properties (leaf chemical permeability, cuticle thickness, and root chemical conductivity) had the greatest influence on chemical transport in the soil-plant-litter system under the conditions examined. Pollutant gas uptake (SO{sub 2}) increased with change in plant properties that increased plant growth. Heavy metal dynamics in litter responded to plant properties (phloem resistance, respiration characteristics) which induced changes in the chemical cycling to the litter system. Some of the SO{sub 2} and heavy metal responses were not expected but became apparent through the modeling analysis.

  15. Quantum Chemical Study on the Corrosion Inhibition of Some Oxadiazoles

    Directory of Open Access Journals (Sweden)

    Hong Ju

    2015-01-01

    Full Text Available Quantum chemical calculations based on DFT method were performed on three nitrogen-bearing heterocyclic compounds used as corrosion inhibitors for the mild steel in acid media to determine the relationship between the molecular structure of inhibitors and inhibition efficiency. The structural parameters, such as energy and distribution of highest occupied molecular orbital (HOMO and lowest unoccupied molecular orbital (LUMO, the charge distribution of the studied inhibitors, the absolute electronegativity (χ values, and the fraction of electrons (ΔN transfer from inhibitors to mild steel were also calculated and correlated with inhibition efficiencies. The results showed that the inhibition efficiency of inhibitors increased with the increase in energy of HOMO and decrease in energy gap of frontier molecular orbital, and the areas containing N and O atoms are most possible sites for bonding the steel surface by donating electrons to the mild steel.

  16. Isotopic and chemical studies of early crustal metasedimentary rocks

    Science.gov (United States)

    Jacobsen, Stein B.

    1988-01-01

    The aim, within the bounds of the Early Crustal Genesis Project, was the isotopic and chemical study of selected early crustal meta-sedimentary rocks. Western Australia was chosen as the first field area to examine, as the Yilgarn and Pilbara Blocks comprise one of the largest and most varied Precambrian terranes. Furthermore, the Western Gneiss Terrane (on the western flank of the Yilgarn Block) and the Pilbara Block are both non-greenstone in character; these types of terrane were relatively neglected, but are of great significance in the understanding of early crustal meta-sediments. The meta-sediments of aluminous or peraluminous character, commonly also enriched in Mg and/or Fe relative to the more common pelitic meta-sediments, and at many locations, deficient in one or more of the elements Ca, N, and K, were initially chosen.

  17. Study of physical chemical characteristics of a shungite

    OpenAIRE

    Maira Kazankapova; A. Bekzhanova; Sergey Efremov; Mikhail Nauryzbayev

    2012-01-01

    The physico-chemical characteristics of shungite from the field of Kazakhstan ("Bakyrchik") and Russia ("Zazhegino") was studied by elemental analysis, IR- spectroscopy and electron microscopy. The content of carbon in the schungite field "Zazhegino" is 28,0-31,0 %,  in the field "Bakyrchik" - 15,0-19,0 %, in schungite concentrate  "Bakyrchik" is 40,0 ± 2,0 %.  IR-spectroscopic analysis have been shown that carboxyl groups appear in addition to the concentrate of polycyclic hydrocarbons conta...

  18. Chemical treatment of zinc surface and its corrosion inhibition studies

    Indian Academy of Sciences (India)

    S K Rajappa; T V Venkatesha; B M Praveen

    2008-02-01

    The surface treatment of zinc and its corrosion inhibition was studied using a product (BTSC) formed in the reaction between benzaldehyde and thiosemicarbozide. The corrosion behaviour of chemically treated zinc surface was investigated in aqueous chloride–sulphate medium using galvanostatic polarization technique. Zinc samples treated in BTSC solution exhibited good corrosion resistance. The measured electrochemical data indicated a basic modification of the cathode reaction during corrosion of treated zinc. The corrosion protection may be explained on the basis of adsorption and formation of BTSC film on zinc surface. The film was binding strongly to the metal surface through nitrogen and sulphur atoms of the product. The formation of film on the zinc surface was established by surface analysis techniques such as scanning electron microscopy (SEM–EDS) and Fourier transform infrared spectroscopy (FTIR).

  19. Quantum chemical study on asymmetric catalysis reduction of imine

    Institute of Scientific and Technical Information of China (English)

    LI; Ming; (李明); TIAN; Anmin; (田安民)

    2003-01-01

    The quantum chemical method is employed to study the enantioselective reduction of imine with borane catalyzed by chiral oxazaborolidine. All the structures are optimized completely at the B3LYP/6-31G(d) level. The catalysis property of oxazaborolidine is notable. The reduction goes mainly through the formations of the catalyst-borane adduct, the catalyst-borane-imine adduct, and the catalyst-amidoborane adduct and the dissociation of the catalyst-amidoborane adduct with the regeneration of the catalyst. The controlling step for the reduction is the dissociation of the catalyst-amidoborane adduct. The main reduced product predicted theoretically is (R )-sec- ondary amine, which is in agreement with the experiment.

  20. 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...

  1. 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...

  2. Flow study in channel with the use computational fluid dynamics (CFD)

    Science.gov (United States)

    Oliveira, W. D.; Pires, M. S. G.; Canno, L. M.; Ribeiro, L. C. L. J.

    2016-08-01

    The Computational Fluid Dynamics (CFD) is a tool used to numerically simulate fluid flow behavior, and all the laws that govern the study of fluids is the mass transfer and energy, chemical reactions, hydraulic behaviors, among others applications. This tool mathematical equation solves the problem in a specific manner over a region of interest, with predetermined boundary conditions on this region. This work is to study the flow channel through the CFD technique.

  3. ALTERNATIVE AND ENHANCED CHEMICAL CLEANING: CORROSION STUDIES RESULTS: FY2010

    Energy Technology Data Exchange (ETDEWEB)

    Wiersma, B.

    2010-09-29

    Due to the need to close High Level Waste storage tanks, chemical cleaning methods are needed for the removal of sludge heel materials remaining at the completion of mechanical tank cleaning efforts. Oxalic acid is considered the preferred cleaning reagent for heel dissolution of iron-based sludge. However, the large quantity of chemical reagents added to the tank farm from oxalic acid based cleaning has significant downstream impacts. Optimization of the oxalic acid cleaning process can potentially reduce the downstream impacts from chemical cleaning. To optimize oxalic acid usage, a detailed understanding of the chemistry of oxalic acid based sludge dissolution is required. Additionally, other acidic systems may be required for specific waste components that have low solubility in oxalic acid, and as a means to reduce oxalic acid usage in general. Electrochemical corrosion studies were conducted with 1 wt. % oxalic acid at mineral acid concentrations above and below the optimal conditions for this oxalic acid concentration. Testing environments included pure reagents, pure iron and aluminum phases, and sludge simulants. Mineral acid concentrations greater than 0.2 M and temperatures greater than 50 C result in unacceptably high corrosion rates. Results showed that manageable corrosion rates of carbon steel can be achieved at dilute mineral acid concentrations (i.e. less than 0.2 M) and low temperatures based on the contact times involved. Therefore, it is recommended that future dissolution and corrosion testing be performed with a dilute mineral acid and a less concentrated oxalic acid (e.g., 0.5 wt.%) that still promotes optimal dissolution. This recommendation requires the processing of greater water volumes than those for the baseline process during heel dissolution, but allows for minimization of oxalic acid additions. The following conclusions can be drawn from the test results: (1) In both nitric and sulfuric acid based reagents, the low temperature and

  4. [Study of quantum-pharmacological chemical characteristics of quercetin].

    Science.gov (United States)

    Zahorodnyĭ, M I

    2007-01-01

    It was established in the previous studies that quercetin prevented the development and caused faster regression of ulcers, petechia and anabroses in rats, which were induced by diclofenac taking. In the group of patients taking diclofenac together with quercetin, the ulcers and dyspeptic events were less found. The application of quercetin normalizes the function and metabolism of cartilage tissue of rabbits with an experimental osteoarthrosis and in patients with osteoartrosis. Quantum-chemical properties of molecule quercetin were studied using the methods of molecular mechanics MM+ and ab initio 6-31G*, and also semiempirical method. The following indices were investigated: distance between atoms (A), the distribution of electronic density of only external valency electrons, distribution of electrostatic potential; common energy of the exertion of molecule (kkal/mmol); binding energy (kkal/mmol); electron energy (kkal/mmol); energy of nucleus-nucleus interaction (kkal/mmol); formation heat (kkal/mmol); atomic charge (eB); value of the dipole moment of molecule (D); localization and energy of highest occupied orbital (HOMO) and the lowest unoccupied (LUMO) molecular orbital (eB) of quercetin miolecule; the value of absolute rigidity of chemical structure of bioflavonoid. It was shown, that bioflavonoid quercetin belongs to mild reagents, has nucleophilic properties, can react with alkaline, unsaturated and aromatic compounds,. Polar substitutes in the quercetine molecule influence on the distribution of superficial valency electrons and localization of HOMO and LUMO. The energy value of quercetin LUMO enables us to refer quercetine to the reducing agent and it is illustrated by antioxidant properties of this medicine.

  5. Final report for NIF chamber dynamics studies

    Energy Technology Data Exchange (ETDEWEB)

    Burnham, A; Peterson, P F; Scott, J M

    1998-09-01

    The National Ignition Facility (NIF), a 1.8 MJ, 192 laser beam facility, will have anticipated fusion yields of up to 20 MJ from D-T pellets encased in a gold hohlraum target. The energy emitted from the target in the form of x rays, neutrons, target debris kinetic energy, and target shrapnel will be contained in a 5 m. radius spherical target chamber. various diagnostics will be stationed around the target at varying distances from the target. During each shot, the target will emit x rays that will vaporize nearby target facing surfaces including those of the diagnostics, the target positioner, and other chamber structures. This ablated vapor will be transported throughout the chamber, and will eventually condense and deposit on surfaces in the chamber, including the final optics debris shields. The research at the University of California at Berkeley relates primarily to the NIF chamber dynamics. The key design issues are the ablation of the chamber structures, transport of the vapor through the chamber and the condensation or deposition processes of those vaporized materials. An understanding of these processes is essential in developing a concept for protecting the fina optics debris shields from an excessive coating (> 10 A) of target debris and ablated material, thereby prolonging their lifetime between change-outs. At Berkeley, we have studied the physical issues of the ablation process and the effects of varying materials, the condensation process of the vaporized material, and design schemes that can lower the threat posed to the debris shields by these processes. The work or portions of the work completed this year have been published in several papers and a dissertation [l-5].

  6. Decomposition Dynamics and Changes in Chemical Composition of Wheat Straw Residue under Anaerobic and Aerobic Conditions.

    Science.gov (United States)

    Gao, Hongjian; Chen, Xi; Wei, Junling; Zhang, Yajie; Zhang, Ligan; Chang, Jiang; Thompson, Michael L

    2016-01-01

    Soil aeration is a crucial factor that regulates crop residue decomposition, and the chemical composition of decomposing crop residues may change the forms and availability of soil nutrients, such as N and P. However, to date, differences in the chemical composition of crop straw residues after incorporation into soil and during its decomposition under anaerobic vs. aerobic conditions have not been well documented. The objective of the present study was to assess changes in the C-containing functional groups of wheat straw residue during its decomposition in anaerobic and aerobic environments. A 12-month incubation experiment was carried out to investigate the temporal variations of mass, carbon, and nitrogen loss, as well as changes in the chemical composition of wheat (Triticum aestivum L) straw residues under anaerobic and aerobic conditions by measuring C-containing functional groups using solid state nuclear magnetic resonance (NMR) spectroscopy. The residual mass, carbon content, and nitrogen content of the straw residue sharply declined during the initial 3 months, and then slowly decreased during the last incubation period from 3 to 12 months. The decomposition rate constant (k) for mass loss under aerobic conditions (0.022 d-1) was higher than that under anaerobic conditions (0.014 d-1). The residual mass percentage of cellulose and hemicellulose in the wheat straw gradually declined, whereas that of lignin gradually increased during the entire 12-month incubation period. The NMR spectra of C-containing functional groups in the decomposing straw under both aerobic and anaerobic conditions were similar at the beginning of the incubation as well as at 1 month, 6 months, and 12 months. The main alterations in C-containing functional groups during the decomposition of wheat straw were a decrease in the relative abundances of O-alkyl C and an increase in the relative abundances of alkyl C, aromatic C and COO/N-C = O functional groups. The NMR signals of alkyl C

  7. Radiation and quantum chemical studies of chalcone derivatives.

    Science.gov (United States)

    Gaikwad, P; Priyadarsini, K I; Naumov, S; Rao, B S M

    2010-08-05

    The reactions of oxidizing radicals ((*)OH, Br(2)(*-), and SO(4)(*-)) with -OH-, -CH(3)-, or -NH(2)-substituted indole chalcones and hydroxy benzenoid chalcones were studied by radiation and quantum chemical methods. The (*)OH radical was found to react by addition at diffusion-controlled rates (k = 1.1-1.7 x 10(10) dm(3) mol(-1) s(-1)), but Br(2)(*-) radical reacted by 2 orders of magnitude lower. Quantum chemical calculations at the B3LYP/6-31+G(d,p) level of theory have shown that the (C2-OH)(*), (C11-OH)(*), and (C10-OH)(*) adducts of the indole chalcones and the (C7-OH)(*) and (C8-OH)(*) adducts of the hydroxy benzenoid chalcones are more stable with DeltaH = -39 to -28 kcal mol(-1) and DeltaG = -32 to -19 kcal mol(-1). This suggests that (*)OH addition to the alpha,beta-unsaturated bond is a major reaction channel in both types of chalcones and is barrierless. The stability and lack of dehydration of the (*)OH adducts arise from two factors: strong frontier orbital interaction due to the low energy gap between interacting orbitals and the negligible Coulombic repulsion due to small absolute values of Mulliken charges. The transient absorption spectrum measured in the (*)OH radical reaction with all the indole chalcone derivatives exhibited a maximum at 390 nm, which is in excellent agreement with the computed value (394 nm). The formation of three phenolic products under steady-state radiolysis is in line with the three stable (*)OH adducts predicted by theory. Independent of the substituent, identical spectra (lambda(max) = 330-360 and approximately 580 nm) were obtained on one-electron oxidation of the three indole chalcones. MO calculations predict the deprotonation from the -NH group is more efficient than from the substituent due to the larger electron density on the N1 atom forming the chalcone indolyl radical. Its reduction potential was determined to be 0.56 V from the ABTS(*-)/ABTS(2-) couple. In benzenoid chalcones, the (*)OH adduct spectrum is

  8. Adsorption properties and degradation dynamics of endocrine-disrupting chemical levonorgestrel in soils.

    Science.gov (United States)

    Tang, Tao; Shi, Tianyu; Li, Deguang; Xia, Jinming; Hu, Qiongbo; Cao, Yongsong

    2012-04-25

    Levonorgestrel, a synthetic progesterone used as an oral contraceptive or emergency contraceptive pill, has been shown to be an endocrine-disrupting chemical. To assess the environmental risk of levonorgestrel, batch experiments and laboratory microcosm studies were conducted to investigate the adsorption and degradation of levonorgestrel in five contrasting soils of China. Freundlich and Langmuir models were applied to sorption data to examine the affinity of levonorgestrel for soils with varying physical and chemical properties. The K(f) of levonorgestrel in the tested soils ranged from 10.79 to 60.92 mg(1-n) L(n) kg(-1) with N between 0.69 and 1.23, and the Q(m) ranged from 18.18 to 196.08 mg/kg. The multiple regression analysis was conducted between K(f) and soil properties. Results indicate that total organic carbon plays a dominant role in the adsorption process. Gibbs free energy values less than 40 kJ/mol demonstrate that levonorgestrel sorption on soils could be considered as a physical adsorption. The degradation of levonorgestrel in five soils was fitted by the first-order reaction kinetics model. The half-lives of levonorgestrel were between 4.32 and 11.55 days. The initial concentration and sterilization experiments illustrated that the degradation rate of levonorgestrel in soil was concentration-dependent and microbially mediated. The low mobility potential of levonorgestrel in soils was predicted by the groundwater ubiquity score (GUS) and retardation factor (R(f)).

  9. A chemical study of the photodissociation region NGC 7023

    Science.gov (United States)

    Fuente, A.; Martin-Pintado, J.; Cernicharo, J.; Bachiller, R.

    1993-09-01

    To investigate the effects of the UV radiation on the chemistry of nitrogenated molecules in molecular clouds, we have carried out an observational study of the photodissociation region (PDR) associated with the reflection nebula NGC 7023. We mapped a region of 3' × 3' over the PDR in millimeter transitions of 12CO, 13CO, C18O, HCO+, HCN, HNC and N2H+. Spectra of CS, CN and C2H and of the rarer isotopic species H13CO+, H13CN, and HN13C, were also obtained at selected positions. We find evidences of selective photodissociation in the estimated 13CO/C15O ratio. Furthermore, all molecular abundances, except those of CN and perhaps C2H, decrease towards the star, and significant gradients in the values of some molecular abundance ratios (the HNC/HCN ratio decreases by a factor of 5, the N2H+/HCO+ ratio decreases by a factor of 12, the CN/HCN ratio increases by a factor of 8 and the (CN+HCN+HNC)/NH3 ratio increases by a factor of 30 towards the star position) reveal the existence of important chemical changes in this direction. Chemical equilibrium model calculations have been also carried out in order to interpret the observed behavior. Our results show that the variations found in molecular abundances cannot be explained by the kinetic temperature and/or the hydrogen density gradients measured in this region. The observed behavior is well explained by the influence of the stellar UV radiation on the chemistry of the molecular gas if the emission arises in a region at a visual extinction between 6 and 10 mag from the star. Molecular destruction in this region (Aυ ˜ 6 mag) is due mainly to reactions with H+, C, H, C+, O, and to electronic recombination. The CN/HCN ratio is suggested as a tracer of enhanced UV fields.

  10. Studies of Trace Gas Chemical Cycles Using Observations, Inverse Methods and Global Chemical Transport Models

    Science.gov (United States)

    Prinn, Ronald G.

    2001-01-01

    For interpreting observational data, and in particular for use in inverse methods, accurate and realistic chemical transport models are essential. Toward this end we have, in recent years, helped develop and utilize a number of three-dimensional models including the Model for Atmospheric Transport and Chemistry (MATCH).

  11. Beam Dynamics Studies for the SPARC Project

    Energy Technology Data Exchange (ETDEWEB)

    Ferrario, M.; Biagini, Maria E.; Boscolo, M.; Fusco, V.; Guiducci, S.; Migliorati, M.; Serafini, L.; Vaccarezza, C.; Bartolini, R.; Giannessi, L.; Quattromini, M.; Ronsivalle, C.; Limborg, C.G.; /Unlisted /Unlisted /ENEA, Frascati /SLAC

    2008-03-17

    The aim of the SPARC project, is to promote an R&D activity oriented to the development of a high brightness photoinjector to drive SASE-FEL experiments. We discuss in this paper the status of the beam dynamics simulation activities.

  12. 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)

  13. Material Development Study for a Hazardous Chemical Protective Clothing Outfit

    Science.gov (United States)

    1980-08-01

    chemicals was technical grade or better (>90%) and were used without further purification. Specialty chemicals including formuations such as agri- cultural...polycarbon- ate. Teflon yarn is available for sewing seams. Bonding patches over the seams would be required to cover holes left from sewing. Because

  14. Sustainability Indicators for Chemical Processes: III. Biodiesel Case Study

    Science.gov (United States)

    The chemical industry is one of the most important business sectors, not only economically, but also societally; as it allows humanity to attain higher standards and quality of life. Simultaneously, chemical products and processes can be the origin of potential human health and ...

  15. The Iron Blast Furnace: A Study in Chemical Thermodynamics.

    Science.gov (United States)

    Treptow, Richard S.; Jean, Luckner

    1998-01-01

    Discusses the furnace from a chemical thermodynamics perspective. Examines the enthalpy, entropy, and free energy change for each reaction of importance. These properties are interpreted on the molecular level then used to deduce the conditions necessary for each reaction to occur in its intended direction. Chemical kinetics is also discussed.…

  16. Quantum chemical studies on the reactivity of oxazole derivatives

    Science.gov (United States)

    Hosseinzadeh, Behzad; Eskandari, Khalil; Zarandi, Maryam; Asli, Reza

    2016-11-01

    The quantum chemical study of the reactivity of a series of oxazole derivatives substituted at 2, 4, and 5 positions was performed using B3LYP/6-311++G( d, p) and MP2/6-311++G( d, p) levels of theory. Different substituents have been applied to cover a wide range of electronic effects. On the basis of Fukui functions, oxazole derivatives in the gas phase are found to be suitable nucleophilic sites. For the most of studied substituents, it was observed that the calculated Fukui function f k - values at the N-position are small in case of electron-withdrawing substituents, resulting a preferred N-position for hard reactions. In contrast, large f k - values in case of electron-donating groups show a preferred N-position for soft reactions. These two local reactivity descriptors predicted the reactivity of the electron-rich oxazoles sequence to be 2-substituted oxazoles > 5-substituted oxazoles > 4-substituted oxazoles, where due to resonance effect, the reactivity toward electrophilic attack at the pyridine nitrogen atom is enhanced by electron donor substituents.

  17. Chemical studies of single-walled carbon nanotubes

    CERN Document Server

    Xu, C

    2001-01-01

    WCl sub 6 has also been introduced into arc-vapourised SWNTs. Chapter 6 gives the details for all the experimental work of the thesis. of H sub 2 have also been studied. Chapter four describes the various processes used to purify arc-vapourised SWNTs on a laboratory scale. Two potentially scalable processes have also been studied. Both acid and gas oxidants have been used to purify SWNTs grown in the CVD method. The chemical resistance of CVD SWNTs (48 h of conc. HNO sub 3 treatment) has been shown for the first time. Various assembly behaviours of purified SWNTs, including loop and spiral structures, straight long bundles or somewhat aligned structures, are also described. Chapter five presents the filling of arc-vapourised SWNTs with LnX sub n (X = Cl, Br and I, n = 2 or 3) using the capallarity method at high temperature (570-910 deg C). The first example of a polycrystalline structure within SWNTs filled with a single material (SmCl sub 3) has been provided. Fullerenes within SWNTs in the SWNT samples ext...

  18. NATO Advanced Study Institute on Chemical Transport in Melasomatic Processes

    CERN Document Server

    1987-01-01

    As indicated on the title page, this book is an outgrowth of the NATO Advanced Study Institute (ASI) on Chemical Transport in Metasomatic Processes, which was held in Greece, June 3-16, 1985. The ASI consisted of five days of invited lectures, poster sessions, and discussion at the Club Poseidon near Loutraki, Corinthia, followed by a two-day field trip in Corinthia and Attica. The second week of the ASI consisted of an excursion aboard M/S Zeus, M/Y Dimitrios II, and the M/S Irini to four of the Cycladic Islands to visit, study, and sample outstanding exposures of metasomatic activity on Syros, Siphnos, Seriphos, and Naxos. Nine­ teen invited lectures and 10 session chairmen/discussion leaders participated in the ASI, which was attended by a total of 92 professional scientists and graduate stu­ dents from 15 countries. Seventeen of the invited lectures and the Field Excursion Guide are included in this volume, together with 10 papers and six abstracts representing contributed poster sessions. Although more...

  19. Quantum chemical studies of photochromic properties of benzoxazine compound

    Energy Technology Data Exchange (ETDEWEB)

    Toliautas, Stepas, E-mail: stepas.toliautas@ff.stud.vu.lt [Department of Theoretical Physics, Vilnius University, Sauletekio 9-III, LT-10222 Vilnius (Lithuania); Sulskus, Juozas, E-mail: juozas.sulskus@ff.vu.lt [Department of Theoretical Physics, Vilnius University, Sauletekio 9-III, LT-10222 Vilnius (Lithuania); Valkunas, Leonas, E-mail: leonas.valkunas@ff.vu.lt [Department of Theoretical Physics, Vilnius University, Sauletekio 9-III, LT-10222 Vilnius (Lithuania); Institute of Physics, Center for Physical Sciences and Technology, Savanoriu 231, LT-02300 Vilnius (Lithuania); Vengris, Mikas, E-mail: mikas.vengris@ff.vu.lt [Department of Quantum Electronics, Vilnius University, Sauletekio 9-III, LT-10222 Vilnius (Lithuania)

    2012-08-24

    Highlights: Black-Right-Pointing-Pointer Photochromic indolo-benzoxazine compound is studied. Black-Right-Pointing-Pointer Advanced LC-TDDFT and GMC-QDPT methods are used for excited state calculations. Black-Right-Pointing-Pointer Oxazine ring opens upon UV light excitation. Black-Right-Pointing-Pointer Fragments of the compound assume structures similar to the ions of separate molecules. Black-Right-Pointing-Pointer Multiple pathways of the photo-induced reaction are expected. -- Abstract: Molecular electronic structure of ground and excited states of a photochromic indolo[2,1-b][1,3]benzoxazine compound incorporating closed-ring system, which opens upon UV light excitation, was studied using various quantum chemical methods. Three local minima of the ground electronic state potential energy surface and related transition states were identified along the path of rotation of 4-nitrophenol group. Additionally, three local minima of the excited electronic states were located. The evaluated transition energy barriers between local ground-state minima nearest to the initial structure of the investigated molecule are less than 2 k{sub B}T, making open structures likely to revert to the initial structure by thermalization. Results obtained using ab initio GMC-QDPT method were explored and compared to the widely used TD-DFT and semi-empiric ZINDO methods.

  20. Chemical and biological warfare: General studies. (Latest citations from the NTIS bibliographic database). Published Search

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-10-01

    The bibliography contains citations concerning federally sponsored and conducted studies into chemical and biological warfare operations and planning. These studies cover areas not addressed in other parts of this series. The topics include production and storage of agents, delivery techniques, training, military and civil defense, general planning studies, psychological reactions to chemical warfare, evaluations of materials exposed to chemical agents, and studies on banning or limiting chemical warfare. Other published searches in this series on chemical warfare cover detection and warning, defoliants, protection, and biological studies, including chemistry and toxicology. (Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  1. Chemical and biological warfare: General studies. (Latest citations from the NTIS bibliographic database). Published Search

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-11-01

    The bibliography contains citations concerning federally sponsored and conducted studies into chemical and biological warfare operations and planning. These studies cover areas not addressed in other parts of this series. The topics include production and storage of agents, delivery techniques, training, military and civil defense, general planning studies, psychological reactions to chemical warfare, evaluations of materials exposed to chemical agents, and studies on banning or limiting chemical warfare. Other published searches in this series on chemical warfare cover detection and warning, defoliants, protection, and biological studies, including chemistry and toxicology.(Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

  2. Alternative Enhanced Chemical Cleaning Basic Studies Results FY09

    Energy Technology Data Exchange (ETDEWEB)

    Hay, M.; King, W.

    2010-05-05

    Due to the need to close waste storage tanks, chemical cleaning methods are needed for the effective removal of the heels. Oxalic acid is the preferred cleaning reagent for sludge heel dissolution, particularly for iron-based sludge, due to the strong complexing strength of the oxalate. However, the large quantity of oxalate added to the tank farm from oxalic acid based chemical cleaning has significant downstream impacts. Optimization of the oxalic acid cleaning process can potentially reduce the downstream impacts from chemical cleaning. To optimize oxalic acid usage, a detailed understanding of the chemistry of oxalic acid based sludge dissolution is required. Additionally, other acid systems may be required for specific waste components with low solubility in oxalic acid and as a means to reduce oxalic acid usage in general. Solubility tests were conducted using non-radioactive, pure metal phases known to be the primary phases present in High Level Waste sludge. The metal phases studied included the aluminum phases gibbsite and boehmite and the iron phases magnetite and hematite. Hematite and boehmite are expected to be the most difficult iron and aluminum phases to dissolve. These mineral phases have been identified in both SRS and Hanford High Level Waste sludge. Acids evaluated for dissolution included oxalic, nitric, and sulfuric acids. The results of the solubility tests indicate that oxalic and sulfuric acids are more effective for the dissolution of the primary sludge phases. For boehmite, elevated temperature will be required to promote effective phase dissolution in the acids studied. Literature reviews, thermodynamic modeling, and experimental results have all confirmed that pH control using a supplemental proton source (additional acid) is critical for minimization of oxalic acid usage during the dissolution of hematite. These results emphasize the importance of pH control in optimizing hematite dissolution in oxalic acid and may explain the somewhat

  3. [Method for study of phase transitions in evaporating drop and its application for evaluation of physical-chemical properties of water and water solutions].

    Science.gov (United States)

    Iakhno, T A; Sanin, A G; Sanina, O A; Iakhno, V G

    2012-01-01

    Spatial-temporal crystallization features of inorganic chlorides in evaporating drops of water solutions, considering solid surface wettability, were studied using a microscopic technique and the acoustical impedansometry. Physical-chemical mechanisms responsible for the difference in "dynamical portraits" of distilled water and salt solutions, as well as relaxation effects in water were discussed. The study demonstrated the potential use of a drying drop method in registration of changes in water properties under the action of physical and chemical factors.

  4. Synthesis, XRD crystal structure, spectroscopic characterization (FT-IR, 1H and 13C NMR), DFT studies, chemical reactivity and bond dissociation energy studies using molecular dynamics simulations and evaluation of antimicrobial and antioxidant activities of a novel chalcone derivative, (E)-1-(4-bromophenyl)-3-(4-iodophenyl)prop-2-en-1-one

    Science.gov (United States)

    Zainuri, D. Alwani; Arshad, Suhana; Khalib, N. Che; Razak, I. Abdul; Pillai, Renjith Raveendran; Sulaiman, S. Fariza; Hashim, N. Shafiqah; Ooi, K. Leong; Armaković, Stevan; Armaković, Sanja J.; Panicker, C. Yohannan; Van Alsenoy, C.

    2017-01-01

    In the present study, the title compound named as (E)-1-(4-bromophenyl)-3-(4-iodophenyl)prop-2-en-1-one was synthesized and structurally characterized by single-crystal X-ray diffraction. The compound crystallizes in the monoclinic system with P21/c space group with the unit cell parameters of a = 16.147 (2) Å, b = 14.270 (2) Å, c = 5.9058 (9) Å, β = 92.577 (3)° and Z = 4. The molecular geometry obtained from X-Ray structure determination was optimized by Density Functional Theory (DFT) using B3LYP/6-31G+(d, p)/Lanl2dz(f) method in the ground state. The IR spectrum was recorded and interpreted in details with the aid of Density Functional Theory (DFT) calculations and Potential Energy Distribution (PED) analysis. In order to investigate local reactivity properties of the title molecule, we have conducted DFT calculations of average local ionization energy surface and Fukui functions which were mapped to the electron density surface. In order to predict the open air stability and possible degradation properties, within DFT approach, we have also calculated bond dissociation energies. 1H and 13C NMR spectra were recorded and chemical shifts were calculated theoretically and compared with the experimental values. In addition, in vitro antimicrobial results show that the title compound has great potential of antibacterial activity against Staphylococcus aureus, Staphylococcus epidermidis and Micrococcus luteus bacteria and antifungal activity against Candida albicans in comparison to some reported chalcone derivatives. Antioxidant studies revealed the highest metal chelating activity of this compound.

  5. STRUCTURE AND DYNAMICS OF ALKALI BORATE GLASSES - A MOLECULAR-DYNAMICS STUDY

    NARCIS (Netherlands)

    VERHOEF, AH; DENHARTOG, HW

    1995-01-01

    Structural and dynamical properties of lithium, cesium and mixed alkali (i.e., lithium and cesium) borate glasses have been studied by the molecular dynamics method. The calculations yield glass structures consisting of planar BO3 triangles and BO4 tetrahedrons with no sixfold ring structures at all

  6. Excess water dynamics in hydrotalcite: QENS study

    Indian Academy of Sciences (India)

    S Mitra; A Pramanik; D Chakrabarty; R Mukhopadhyay

    2004-08-01

    Results of the quasi-elastic neutron scattering (QENS) measurements on the dynamics of excess water in hydrotalcite sample with varied content of excess water are reported. Translational motion of excess water can be best described by random translational jump diffusion model. The observed increase in translational diffusivity with increase in the amount of excess water is attributed to the change in binding of the water molecules to the host layer.

  7. Aggregation of model asphaltenes: a molecular dynamics study

    Science.gov (United States)

    Costa, J. L. L. F. S.; Simionesie, D.; Zhang, Z. J.; Mulheran, P. A.

    2016-10-01

    Natural asphaltenes are defined as polyaromatic compounds whose chemical composition and structure are dependent on their geological origin and production history, hence are regarded as complex molecules with aromatic cores and aliphatic tails that occur in the heaviest fraction of crude oil. The aggregation of asphaltenes presents a range of technical challenges to the production and processing of oil. In this work we study the behaviour of the model asphaltene-like molecule hexa-tert-butylhexa-peri-hexabenzocoronene (HTBHBC) using molecular dynamics simulation. It was found that the regular arrangement of the tert-butyl side chains prevents the formation of strongly-bound dimers by severely restricting the configurational space of the aggregation pathway. In contrast, a modified molecule with only 3 side chains is readily able to form dimers. This work therefore confirms the influence of the molecular structure of polyaromatic compounds on their aggregation mechanism, and reveals the unexpected design rules required for model systems that can mimic the behavior of asphaltenes.

  8. Molecular Dynamics study on the Micellization of Rhamnolipids.

    Science.gov (United States)

    Munusamy, Elango; Schwartz, Steven D.

    2015-03-01

    Oil spills have become one of the most serious environmental and ecological problems owing to the growth of oil exploration, production and transportation. Millions of gallons of crude oil and refined products are spilled into marine waters worldwide each year. Large volumes of surfactants are applied to the ocean as a remediation strategy. Environmental and toxicity issues arise when such a voluminous amounts of chemical surfactants are applied. One prospective solution to this problem is to use greener surfactants that possess excellent biodegradation and toxicity characteristics relative to existing classes of commonly used surfactants. In this context, we are interested in designing and developing greener surfactants that are patterned after naturally occurring glycolipids. In the present work, we concentrate on one of the more commonly studied glycolipid, rhamnolipid (Rha1C10C10) . Despite the available experimental data, the molecular structure, shape and geometry of micelles formed by rhamnolipid is unknown. Molecular Dynamics (MD) simulations were performed to understand the aggregation behavior of rhamnolipids in aqueous solution and at air-water interface. All calculations were performed in NPT ensembles at 300 K using NAMD 2.8, a parallel code designed for high-performance simulation of large biological macromolecule using the CHARMM force field. The results obtained from MD simulations on the aggregation of rhamnolipids in water and at air-water interface will be presented.

  9. Low thermal conductivity of graphyne nanotubes from molecular dynamics study

    Science.gov (United States)

    Hu, Ming; Jing, Yuhang; Zhang, Xiaoliang

    2015-04-01

    It is well known that carbon nanotubes (CNTs) possess ultrahigh thermal conductivity that is comparable to bulk diamond. However, no research has studied the possible low thermal conductivity of different CNTs so far. By performing nonequilibrium molecular dynamic simulations, we reveal that the perfect graphyne nanotube (GNT) exhibits an unprecedentedly low thermal conductivity (below 10 W/mK at room temperature), which is generally two orders of magnitude lower than that of ordinary CNTs and even lower than the values reported for defected, doped, and chemically functionalized CNTs. By performing phonon polarization and spectral energy density analysis, we observe that the ultralow thermal conductivity stems from the unique atomic structure of the GNT, consisting of the weak acetylenic linkage (s p C-C bonds) and the strong hexagonal ring (s p2 C-C bonds), which results in a large vibrational mismatch between these two components, and thus induces significantly inefficient heat transfer. Moreover, the thermal transport in GNT with a large number of acetylenic linkages is dominated by the low frequency longitudinal modes in the linkage. Such strong confinement of the low frequency thermal energy results in the extremely low thermal conductivity due to the flattened phonon dispersion curves (low phonon group velocities). The exploration of the abnormal thermal transport of GNTs paves the way for design and application of the relevant devices that could benefit from the ultralow thermal conductivity, such as thermoelectrics for energy conversion.

  10. A stochastic chemical dynamic approach to correlate autoimmunity and optimal vitamin-D range.

    Directory of Open Access Journals (Sweden)

    Susmita Roy

    Full Text Available Motivated by several recent experimental observations that vitamin-D could interact with antigen presenting cells (APCs and T-lymphocyte cells (T-cells to promote and to regulate different stages of immune response, we developed a coarse grained but general kinetic model in an attempt to capture the role of vitamin-D in immunomodulatory responses. Our kinetic model, developed using the ideas of chemical network theory, leads to a system of nine coupled equations that we solve both by direct and by stochastic (Gillespie methods. Both the analyses consistently provide detail information on the dependence of immune response to the variation of critical rate parameters. We find that although vitamin-D plays a negligible role in the initial immune response, it exerts a profound influence in the long term, especially in helping the system to achieve a new, stable steady state. The study explores the role of vitamin-D in preserving an observed bistability in the phase diagram (spanned by system parameters of immune regulation, thus allowing the response to tolerate a wide range of pathogenic stimulation which could help in resisting autoimmune diseases. We also study how vitamin-D affects the time dependent population of dendritic cells that connect between innate and adaptive immune responses. Variations in dose dependent response of anti-inflammatory and pro-inflammatory T-cell populations to vitamin-D correlate well with recent experimental results. Our kinetic model allows for an estimation of the range of optimum level of vitamin-D required for smooth functioning of the immune system and for control of both hyper-regulation and inflammation. Most importantly, the present study reveals that an overdose or toxic level of vitamin-D or any steroid analogue could give rise to too large a tolerant response, leading to an inefficacy in adaptive immune function.

  11. Rodent-repellent studies. III. Advanced studies in the evaluation of chemical repellents

    Science.gov (United States)

    Bellack, E.; DeWitt, J.B.

    1949-01-01

    In order to bridge the gap between preliminary screening of chemicals for potential rodent repellency and the application ofthese compounds to paper cartons, more advanced studies in the evaluation ofpromising materials have been carried out. These studies have resulted in: (1) a modification of the food acceptance technique which eliminates doubtful compounds and also provides a closer analogy to the ultimate goal, and (2) a method for rapidly testing chemicals incorporated in paper. When the results of these latter tests are expressed as a function of time, it can be shown that a distinct correlation exists between the deterrency exhibited by treated paper and the repellency of treated food.

  12. Study of physical chemical characteristics of a shungite

    Directory of Open Access Journals (Sweden)

    Maira Kazankapova

    2012-05-01

    Full Text Available The physico-chemical characteristics of shungite from the field of Kazakhstan ("Bakyrchik" and Russia ("Zazhegino" was studied by elemental analysis, IR- spectroscopy and electron microscopy. The content of carbon in the schungite field "Zazhegino" is 28,0-31,0 %,  in the field "Bakyrchik" - 15,0-19,0 %, in schungite concentrate  "Bakyrchik" is 40,0 ± 2,0 %.  IR-spectroscopic analysis have been shown that carboxyl groups appear in addition to the concentrate of polycyclic hydrocarbons containing methylene groups. Analysis of electron microscopy have been shown that as a result of enrichment by carbon, shungite can get a more developed surface structure and porosity.

  13. Periodic quantum chemical studies on anhydrous and hydrated acid clinoptilolite.

    Science.gov (United States)

    Valdiviés Cruz, Karell; Lam, Anabel; Zicovich-Wilson, Claudio M

    2014-08-07

    Periodic quantum chemistry methods as implemented in the crystal09 code were considered to study acid clinoptilolite (HEU framework type), both anhydrous and hydrated. The most probable location of acid sites and water molecules together with other structural details has been the object of particular attention. Calculations were performed at hybrid and pristine DFT levels of theory with a VDZP quality basis set in order to compare performances. It arises that PBE0 provides the best agreement with experimental data as concerns structural features and the most stable Al distribution in the framework. The role of the water molecule distribution in the stability of the systems, the most probable structure that they induce in the material, and their eventual influence on further chemical modification processes, such as dealumination, are discussed in detail. Results show that, apart from the usually considered interactions of water molecules with the zeolite framework, that is, a H-bond with Brönsted acid sites and coordination with framework Al as Lewis ones, it is necessary to consider cooperation of other weaker effects so as to fully understand the hydration effect in this kind of materials.

  14. Studies on the Chemical Constituents from Marine Bryozoan Cryptosula pallasiana

    Directory of Open Access Journals (Sweden)

    Xiang-Rong Tian

    2015-06-01

    Full Text Available The aim of this study was to investigate the chemical constituents of marine bryozoan Cryptosula pallasiana inhabiting Huang Island of China. Three aromatic compounds, p-methylsulfonylmethyl-phenol (1, p-hydroxybenzaldehyde (4 and methylparaben (5, nine alkaloids, 7-bromoquinolin-4(1H-one (2, 7-bromo-2,4(1H,3H-quinazolinedione (3, benzamide (6, phenylacetamide (7, 4(3H-quinazolinone (8, thymine (9, uracil (10, hypoxanthine (11 and tryptophan (12, together with two glycerol derivatives, glycerol (13 and monoheneicosanoin (14, were isolated for the first time from this marine bryozoan. Among the isolates, compounds 1 and 2 were new natural products, and their spectral traits were reported for the first time. The structures of the two compounds were elucidated by extensive spectroscopic analyses, including HR-ESI-MS, EI-MS, 1D- and 2D-NMR techniques. The isolated compounds 1–3 were evaluated for their cytotoxicity against HL-60 human myeloid leukemia cell line. The results showed that bromated alkaloid (3 appeared strong cytotoxicity against HL-60 cells with IC 50 value of 11.87 µg/mL, while compounds 1 and 2 were inactivity.

  15. Forcing an entire bifurcation diagram: Case studies in chemical oscillators

    Science.gov (United States)

    Kevrekidis, I. G.; Aris, R.; Schmidt, L. D.

    1986-12-01

    We study the finite amplitude periodic forcing of chemical oscillators. In particular, we examine systems that, when autonomous, (i.e. for zero forcing amplitude) exhibit a single stable oscillation. Using one of the system parameters as a forcing variable by varying it periodically, we show through extensive numerical work how the bifurcation diagram of the autonomous system with respect to this parameter affects the qualitative response of the full forced system. As the forcing variable oscillates around its midpoint, its instantaneous values may cross points (such as Hopf bifurcation poiints) of the autonomous bifurcation diagram so that the characterization of the system as a simple forced oscillator is no longer valid. Such a neighboring Hopf bifurcation of the unforced system is found to set the scene for the interaction of resonance horns and the loss of tori in the full forced system as the amplitude of the forcing grows. Our test case presented here is the Continuous Stirred Tank Reactor (CSTR) with periodically forced coolant temperature.

  16. 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...

  17. USI/Chemplex/Quantum Chemical Co. Outfall Study, 1987

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Sediment samples collected in 1987 from the Quantum Chemical Corporation outfall on the Upper Mississippi River detected 14 polycyclic aromatic hydrocarbons (PAH's)....

  18. Study and interpretation of the chemical characteristics of natural water

    Science.gov (United States)

    Hem, John David

    1985-01-01

    The chemical composition of natural water is derived from many different sources of solutes, including gases and aerosols from the atmosphere, weathering and erosion of rocks and soil, solution or precipitation reactions occurring below the land surface, and cultural effects resulting from human activities. Broad interrelationships among these processes and their effects can be discerned by application of principles of chemical thermodynamics. Some of the processes of solution or precipitation of minerals can be closely evaluated by means of principles of chemical equilibrium, including the law of mass action and the Nernst equation. Other processes are irreversible and require consideration of reaction mechanisms and rates. The chemical composition of the crustal rocks of the Earth and the composition of the ocean and the atmosphere are significant in evaluating sources of solutes in natural freshwater.

  19. 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

  20. Lattice dynamical studies of HTSC materials

    Energy Technology Data Exchange (ETDEWEB)

    Pintschovius, L.; Pyka, N.; Reichardt, W. (Kernforschungszentrum Karlsruhe, INFP (Germany)); Rumiantsev, A.Yu.; Mitrofanov, N.L.; Ivanov, A.S. (I.V. Kurchatov-Inst. of Atomic Energy, Moscow (USSR)); Collin, G.; Bourges, P. (Lab. Leon Brillouin, CEA-CNRS, CEN Saclay, 91 - Gif-sur-Yvette (France))

    1991-12-01

    A survey is presented on recent progress in the understanding of the lattice dynamics in Nd{sub 2}CuO{sub 4}, (La,Sr){sub 2}CuO{sub 4} and YBa{sub 2}Cu{sub 3}O{sub 6/7}. Classical anharmonicity and twinning were found to be major complications for the interpretation of the data. The lattice vibrations of the cuprates can now largely be described within the framework of shell models for strongly ionic compounds. Phonon anomalies inferred from a comparison of doped and undoped compounds resemble those found in classical superconductors. (orig.).

  1. A Study on Physical Dispersion and Chemical Modification of Graphene

    Energy Technology Data Exchange (ETDEWEB)

    Yim, Eun-Chae; Kim, Seong-Jun [Chonnam National University, Gwangju (Korea, Republic of)

    2015-12-15

    Graphene has a wide spectrum on its application field due to various and excellent physical properties. However, it is very difficult to apply that graphene exists as lump or fold condition in general organic solvents. Besides, graphene was difficult to maintain as uniform condition due to chemical inert and distributions with various size and shapes. Therefore, this study was focused to study dispersion and modifying methods of aggregated graphene. The dispersion methods contain as follow: i) physical milling using glass bead, ii) co-treatment of glass bead and ultrasonic waves, iii) dispersion in organic solvents, iv) modifying with dry-ice. Milling using glass bead with size 2.5 mm was effective to be size decrease of 36.4% in comparison with control group. Mixed treatment of glass bead (size 2.5 mm) and ultrasonic waves (225W, 10 min) showed relative size decrease of 76%, suggesting that the size decrease depends on the size of glass bead, intensity of ultrasonic waves and treatment time. Solvents of Ethyl acetate (EA) and Isoprophyl alcohol (IPA) were used in order to improve dispersion by modifying surface of graphene. IPA of them showed a favorable dispersion with more -CO functional groups in the FT-IR analysis. On the other hand, the oxygen content of graphene surface modified by dry-ice was highly increased from 0.8 to 4.9%. From the results, it was decided that the favorable dispersion state for a long time was obtained under the condition of -CO functional group increase in IPA solvent.

  2. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity.

    Science.gov (United States)

    Papaleo, Elena

    2015-01-01

    In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.

  3. Molecular-dynamic study of liquid ethylenediamine

    Science.gov (United States)

    Balabaev, N. K.; Kraevskii, S. V.; Rodnikova, M. N.; Solonina, I. A.

    2016-10-01

    Models of liquid ethylenediamine (ED) are built using the molecular dynamics approach at temperatures of 293-363 K and a size of 1000 molecules in a basic cell as a cuboid. The structural and dynamic characteristics of liquid ED versus temperature are derived. The gauche conformation of the ED molecule that is characteristic of the gas phase is shown to transition easily into the trans conformation of the molecules in the liquid. NH···N hydrogen bonds are analyzed in liquid ED. The number of H-bonds per ED molecule is found to vary from 5.02 at 293 K to 3.86 at 363 K. The lifetimes in the range of the temperatures and dissociation activation energy for several H-bonds in liquid ED are found to range from 0.574 to 4.524 ps at 293 K; the activation energies are 8.8 kJ/mol for 50% of the H-bonds and 16.3 kJ/mol for 6.25% of them. A weaker and more mobile spatial grid of H-bonds in liquid ED is observed, compared to data calculated earlier for monoethanolamine.

  4. Photoexcited breathers in conjugated polyenes: an excited-state molecular dynamics study.

    Science.gov (United States)

    Tretiak, S; Saxena, A; Martin, R L; Bishop, A R

    2003-03-04

    pi-conjugated polymers have become an important class of materials for electronic devices. Design of these devices requires understanding such processes as photochemical reactions, spatial dynamics of photoexcitations, and energy and charge transport, which in turn involve complex coupled electron-vibrational dynamics. Here we study nonlinear photoexcitation dynamics in the polyene oligomers by using a quantum-chemical method suitable for the simulation of excited-state molecular dynamics in extended molecular systems with sizes up to hundreds of atoms. The method is based on the adiabatic propagation of the ground-state and transition single-electron density matrices along the trajectory. The simulations reveal formation of a self-localized vibronic excitation ("breather" or multiquanta bound state) with a typical period of 34 fs and allows us to identify specific slow and fast nuclear motions strongly coupled to the electronic degrees of freedom. The effect of chain imperfections and chemical defects on the dynamics is also investigated. A complementary two-dimensional analysis of corresponding transition density matrices provides an efficient way to monitor time-dependent real-space localization of the photoexcitation by identifying the underlying changes in charge densities and bond orders. Possible correlated electronic and vibrational spectroscopic signatures of photoexcited breathers are predicted, and generalizations to energy localization in complex macromolecules are discussed.

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

    Science.gov (United States)

    1984-11-30

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

  6. First-principles studies of atomic dynamics in tetrahedrite thermoelectrics

    Directory of Open Access Journals (Sweden)

    Junchao Li

    2016-10-01

    Full Text Available Cu12Sb4S13-based tetrahedrites are high-performance thermoelectrics that contain earth-abundant and environmentally friendly elements. At present, the mechanistic understanding of their low lattice thermal conductivity (<1 W m−1 K−1 at 300 K remains limited. This work applies first-principles molecular dynamics simulations, along with inelastic neutron scattering (INS experiments, to study the incoherent and coherent atomic dynamics in Cu10.5NiZn0.5Sb4S13, in order to deepen our insight into mechanisms of anomalous dynamic behavior and low lattice thermal conductivity in tetrahedrites. Our study of incoherent dynamics reveals the anomalous “phonon softening upon cooling” behavior commonly observed in inelastic neutron scattering data. By examining the dynamic Cu-Sb distances inside the Sb[CuS3]Sb cage, we ascribe softening to the decreased anharmonic “rattling” of Cu in the cage. On the other hand, our study of coherent dynamics reveals that acoustic modes are confined in a small region of dynamic scattering space, which we hypothesize leads to a minimum phonon mean free path. By assuming a Debye model, we obtain a lattice minimum thermal conductivity value consistent with experiments. We believe this study furthers our understanding of the atomic dynamics of tetrahedrite thermoelectrics and will more generally help shed light on the origin of intrinsically low lattice thermal conductivity in these and other structurally similar materials.

  7. Some case studies of random walks in dynamic random environments

    NARCIS (Netherlands)

    Soares dos Santos, Renato

    2012-01-01

    This thesis is dedicated to the study of random walks in dynamic random environments. These are models for the motion of a tracer particle in a disordered medium, which is called a static random environment if it stays constant in time, or dynamic otherwise. The evolution of the random walk is defi

  8. First-principles studies of atomic dynamics in tetrahedrite thermoelectrics

    Science.gov (United States)

    Li, Junchao; Zhu, Mengze; Abernathy, Douglas L.; Ke, Xianglin; Morelli, Donald T.; Lai, Wei

    2016-10-01

    Cu12Sb4S13-based tetrahedrites are high-performance thermoelectrics that contain earth-abundant and environmentally friendly elements. At present, the mechanistic understanding of their low lattice thermal conductivity (applies first-principles molecular dynamics simulations, along with inelastic neutron scattering (INS) experiments, to study the incoherent and coherent atomic dynamics in Cu10.5NiZn0.5Sb4S13, in order to deepen our insight into mechanisms of anomalous dynamic behavior and low lattice thermal conductivity in tetrahedrites. Our study of incoherent dynamics reveals the anomalous "phonon softening upon cooling" behavior commonly observed in inelastic neutron scattering data. By examining the dynamic Cu-Sb distances inside the Sb[CuS3]Sb cage, we ascribe softening to the decreased anharmonic "rattling" of Cu in the cage. On the other hand, our study of coherent dynamics reveals that acoustic modes are confined in a small region of dynamic scattering space, which we hypothesize leads to a minimum phonon mean free path. By assuming a Debye model, we obtain a lattice minimum thermal conductivity value consistent with experiments. We believe this study furthers our understanding of the atomic dynamics of tetrahedrite thermoelectrics and will more generally help shed light on the origin of intrinsically low lattice thermal conductivity in these and other structurally similar materials.

  9. A Case Study of Search Engine on World Wide Web for Chemical Fiber Engineering

    Institute of Scientific and Technical Information of China (English)

    张利; 邵世煌; 曾献辉; 尹美华

    2001-01-01

    Search engine is an effective approach to promote the service quality of the World Wide Web. On terms of the analysis of search engines at home and abroad, the developing principle of search engines is given according to the requirement of Web information for chemical fiber engineering. The implementation method for the communication and dynamic refreshment of information on home page of the search engines are elaborated by using programming technology of Active Server Page 3.0 (ASP3.0). The query of chemical fiber information and automatic linking of chemical fiber Web sites can be easily realized by the developed search engine under Internet environment according to users' requirement.

  10. On the chemical dynamics of extracellular polysaccharides in the high Arctic surface microlayer

    Directory of Open Access Journals (Sweden)

    Q. Gao

    2012-01-01

    Full Text Available The surface microlayer (SML represents a unique system of which the physicochemical characteristics may differ from those of the underlying subsurface seawater (SSW. Within the Arctic pack ice area, the SML has been characterized as enriched in small colloids of biological origin, resulting from extracellular polymeric secretions (EPS. During the Arctic Summer Cloud-Ocean Study (ASCOS in August 2008, particulate and dissolved organic matter (POM, DOM samples were collected and chemically characterized from the SML and the corresponding SSW at an open lead centered at 87.5° N and 5° E. Total organic carbon was persistently enriched in the SML with a mean enrichment factor (EF of 1.45 ± 0.41, whereas sporadic depletions of dissolved carbohydrates and amino acids were observed. Monosaccharide compositional analysis reveals that EPS in the Arctic lead was formed mainly of distinctive heteropolysaccharides, enriched in xylose, fucose and glucose. The mean concentrations of total hydrolysable neutral sugars in SSW were 94.9 ± 37.5 nM in high molecular weight (HMW DOM and 64.4 ± 14.5 nM in POM. The enrichment of polysaccharides in the SML appeared to be a common feature, with EFs ranging from 1.7 to 7.0 for particulate polysaccharides and 3.5 to 12.1 for polysaccharides in the HMW DOM fraction. A calculated monosaccharide yield suggests that polymers in the HMW DOM fraction were scavenged, without substantial degradation, into the SML. Bubble scavenging experiments showed that newly aggregated particles could be formed abiotically by coagulation of low molecular weight nanometer-sized gels. Experimentally-generated aerosol particles were enriched in polysaccharides by factors of 22–70, relative to the source seawater. We propose that bubble scavenging of surface-active polysaccharides was one of the possible mechanisms for the enrichment of polysaccharides in the SML.

  11. Predicting Fecundity of Fathead Minnows (Pimephales promelas) Exposed to Endocrine-Disrupting Chemicals Using a MATLAB®-Based Model of Oocyte Growth Dynamics.

    Science.gov (United States)

    Watanabe, Karen H; Mayo, Michael; Jensen, Kathleen M; Villeneuve, Daniel L; Ankley, Gerald T; Perkins, Edward J

    2016-01-01

    Fish spawning is often used as an integrated measure of reproductive toxicity, and an indicator of aquatic ecosystem health in the context of forecasting potential population-level effects considered important for ecological risk assessment. Consequently, there is a need for flexible, widely-applicable, biologically-based models that can predict changes in fecundity in response to chemical exposures, based on readily measured biochemical endpoints, such as plasma vitellogenin (VTG) concentrations, as input parameters. Herein we describe a MATLAB® version of an oocyte growth dynamics model for fathead minnows (Pimephales promelas) with a graphical user interface based upon a previously published model developed with MCSim software and evaluated with data from fathead minnows exposed to an androgenic chemical, 17β-trenbolone. We extended the evaluation of our new model to include six chemicals that inhibit enzymes involved in steroid biosynthesis: fadrozole, ketoconazole, propiconazole, prochloraz, fenarimol, and trilostane. In addition, for unexposed fathead minnows from group spawning design studies, and those exposed to the six chemicals, we evaluated whether the model is capable of predicting the average number of eggs per spawn and the average number of spawns per female, which was not evaluated previously. The new model is significantly improved in terms of ease of use, platform independence, and utility for providing output in a format that can be used as input into a population dynamics model. Model-predicted minimum and maximum cumulative fecundity over time encompassed the observed data for fadrozole and most propiconazole, prochloraz, fenarimol and trilostane treatments, but did not consistently replicate results from ketoconazole treatments. For average fecundity (eggs•female(-1)•day(-1)), eggs per spawn, and the number of spawns per female, the range of model-predicted values generally encompassed the experimentally observed values. Overall, we

  12. Predicting Fecundity of Fathead Minnows (Pimephales promelas Exposed to Endocrine-Disrupting Chemicals Using a MATLAB®-Based Model of Oocyte Growth Dynamics.

    Directory of Open Access Journals (Sweden)

    Karen H Watanabe

    Full Text Available Fish spawning is often used as an integrated measure of reproductive toxicity, and an indicator of aquatic ecosystem health in the context of forecasting potential population-level effects considered important for ecological risk assessment. Consequently, there is a need for flexible, widely-applicable, biologically-based models that can predict changes in fecundity in response to chemical exposures, based on readily measured biochemical endpoints, such as plasma vitellogenin (VTG concentrations, as input parameters. Herein we describe a MATLAB® version of an oocyte growth dynamics model for fathead minnows (Pimephales promelas with a graphical user interface based upon a previously published model developed with MCSim software and evaluated with data from fathead minnows exposed to an androgenic chemical, 17β-trenbolone. We extended the evaluation of our new model to include six chemicals that inhibit enzymes involved in steroid biosynthesis: fadrozole, ketoconazole, propiconazole, prochloraz, fenarimol, and trilostane. In addition, for unexposed fathead minnows from group spawning design studies, and those exposed to the six chemicals, we evaluated whether the model is capable of predicting the average number of eggs per spawn and the average number of spawns per female, which was not evaluated previously. The new model is significantly improved in terms of ease of use, platform independence, and utility for providing output in a format that can be used as input into a population dynamics model. Model-predicted minimum and maximum cumulative fecundity over time encompassed the observed data for fadrozole and most propiconazole, prochloraz, fenarimol and trilostane treatments, but did not consistently replicate results from ketoconazole treatments. For average fecundity (eggs•female(-1•day(-1, eggs per spawn, and the number of spawns per female, the range of model-predicted values generally encompassed the experimentally observed values

  13. 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

  14. 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.

  15. 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...

  16. Systems approaches to study root architecture dynamics

    Directory of Open Access Journals (Sweden)

    Candela eCuesta

    2013-12-01

    Full Text Available The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation.Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how lateral roots and thereby root system architecture is established and developed.

  17. Laser studies of chemical reaction and collision processes

    Energy Technology Data Exchange (ETDEWEB)

    Flynn, G. [Columbia Univ., New York, NY (United States)

    1993-12-01

    This work has concentrated on several interrelated projects in the area of laser photochemistry and photophysics which impinge on a variety of questions in combustion chemistry and general chemical kinetics. Infrared diode laser probes of the quenching of molecules with {open_quotes}chemically significant{close_quotes} amounts of energy in which the energy transferred to the quencher has, for the first time, been separated into its vibrational, rotational, and translational components. Probes of quantum state distributions and velocity profiles for atomic fragments produced in photodissociation reactions have been explored for iodine chloride.

  18. EXPERIMENTAL STUDY OF CHEMICAL CHOLECYSTECTOMY: OBSERVATION OF PATHOLOGICAL CHANGES

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Objective: TO verify through animal experiment the validity of chemical cholecystectomy . Methods: The experimental objects seven healthy juvenile pigs,hardener was infused into the gallbladder,after infusion the samples were collected by pathoiogical examination , according to the different duration under anesthestize. Reslts:The mucous destructive and digestive process remained with one week, the inflammatory reacton in two weeks,the chronic inflatoy reaction compained a a great deal of granu lation tissue and scar formation occurred in 4th-8th week,10 weeks latter,the inflmmatory reaction reduced ,and scar tissue formed. Conclusion: Chemical cholecystectomy is safe and reliable in clinical.

  19. EXPERIMENTAL STUDY OF CHEMICAL CHOLECYSTECTOMY OF PATHOLOGIC OBSERVATION

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Objective:To verify through animal experiment the validity of chemical cholecystectomy.Mothods:The expermental objects seven healthy juvenile pigs,hardener was infused into the gallbladder,after infusion the sapmles were collected by pathological examination,according to the different duration under anesthestize.Results:The mucous destructive and digestive process remained with one week,the inflammatory reaction in two weeks,the chronic inflammatory reaction compained a great deal of granulation tissue and scar formation occurred in 4th-8th week,10 weeks latter,the inflammatory reaction reduced,and scar tissue formed.Conlusion:Chemical cholecystecomy is safe and reliable in clinic.

  20. Dynamic range studies and improvements for multiplexed photonic Doppler velocimetry

    Science.gov (United States)

    Miller, Edward Kirk; Lee, Kevin; Larson, Eric; Daykin, Edward

    2017-01-01

    We present studies of the dynamic range achievable with multiplexed photonic Doppler velocimetry (MPDV) measurements, and we demonstrate some techniques to extend the dynamic range. Improved dynamic range for MPDV measurements is needed in order to track the velocity of the free surface behind a cloud of ejecta, so we have undertaken theoretical and experimental studies of factors affecting dynamic range, particularly in cases where the large number of MPDV probe points precludes high illumination power on each channel. To quantify the potential dynamic range of a given MPDV configuration, we introduce a metric called the frequency-domain number of bits, FNOB, which is less stringent than the formally defined equivalent number of bits (ENOB). This new metric is simple to compute in the lab, and it is well suited to conventional PDV analysis, which does not require digitizer phase coherence beyond tens of nanoseconds.

  1. Chemical bonding in TiSb(2) and VSb(2): a quantum chemical and experimental study.

    Science.gov (United States)

    Armbrüster, Marc; Schnelle, Walter; Schwarz, Ulrich; Grin, Yuri

    2007-08-06

    The chemical bonding in the isostructural intermetallic compounds TiSb2 and VSb2, crystallizing in the CuAl2 type, was investigated by means of quantum chemical calculations, particularly the electron localization function (ELF), as well as by Raman spectroscopy, Hall effect and conductivity measurements on oriented single crystals, and high-pressure X-ray powder diffraction. The homogeneity ranges of the compounds were determined by powder X-ray diffraction, WDXS, and DSC measurements. TiSb2 exhibits no significant homogeneity range, while VSb2 shows a small homogeneity range of approximately 0.3 at. %. According to the ELF calculations, the Sb atoms form dumbbells via a two-center two-electron bond, while the T atoms (T = Ti, V) build up chains along the crystallographic c-axis. Both building units are connected by covalent T-Sb-T three-center bonds, thus forming a three-dimensional network. The strength of the bonds involving Sb was determined by fitting a force constant model to the vibrational mode frequencies observed by polarized Raman measurements on oriented single crystals. The resulting bond order of the Sb2 dumbbells is 1, while the strength of the three-center bonds resembles a bond order of 1.5. The weak pressure dependence of the c/a ratio confirms the slightly different bonding picture in TiSb2 compared to that in CuAl2. Electrical transport measurements show the presence of free charge carriers, as well as a metal-like temperature dependence of the electrical resistivity.

  2. Hybrid density functional study on lattice vibration, thermodynamic properties, and chemical bonding of plutonium monocarbide

    Science.gov (United States)

    Rong, Yang; Bin, Tang; Tao, Gao; BingYun, Ao

    2016-06-01

    Hybrid density functional theory is employed to systematically investigate the structural, magnetic, vibrational, thermodynamic properties of plutonium monocarbide (PuC and PuC0.75). For comparison, the results obtained by DFT, DFT + U are also given. For PuC and PuC0.75, Fock-0.25 hybrid functional gives the best lattice constants and predicts the correct ground states of antiferromagnetic (AFM) structure. The calculated phonon spectra suggest that PuC and PuC0.75 are dynamically stable. Values of the Helmholtz free energy ΔF, internal energy ΔE, entropy S, and constant-volume specific heat C v of PuC and PuC0.75 are given. The results are in good agreement with available experimental or theoretical data. As for the chemical bonding nature, the difference charge densities, the partial densities of states and the Bader charge analysis suggest that the Pu-C bonds of PuC and PuC0.75 have a mixture of covalent character and ionic character. The effect of carbon vacancy on the chemical bonding is also discussed in detail. We expect that our study can provide some useful reference for further experimental research on the phonon density of states, thermodynamic properties of the plutonium monocarbide. Project supported by the National Natural Science Foundation of China (Grant Nos. 21371160 and 21401173).

  3. 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.

  4. Structural studies of chemical constituents of Thithonia Tagetiflora Desv (Asteraceae)

    DEFF Research Database (Denmark)

    Ngoc Huynh, Vinh; Nguyen Thi Hoai, Thu; Phi Phung Nguyen, Kim

    2013-01-01

    Tithonia tagetiflora Desv. (Asteraceae) is a widespread plant in Vietnam, and the species of Tithonia are known as plants containing many biologically active compounds. However, T. tagetiflora's chemical composition remains mostly unknown. Therefore, we now report the structural elucidation of two...

  5. The VENUS/NWChem Software Package. Tight Coupling Between Chemical Dynamics Simulations and Electronic Structure Theory

    Energy Technology Data Exchange (ETDEWEB)

    Lourderaj, Upakarasamy; Sun, Rui; De Jong, Wibe A.; Windus, Theresa L.; Hase, William L.

    2014-03-01

    The interface for VENUS and NWChem, and the resulting software package for direct dynamics simulations are described. The coupling of the two codes is considered to be a tight coupling. The two codes are compiled and linked together and act as one executable with data being passed between the two codes through routine calls. The advantages of this type of coupling are discussed. The interface has been designed to have as little interference as possible with the core codes of both VENUS and NWChem. VENUS is the code that propagates the direct dynamics trajectories and, therefore, is the program that drives the overall execution of VENUS/NWChem. VENUS has remained an essentially sequential code, which uses the highly parallel structure of NWChem. Subroutines of the interface which accomplish the data transmission and communication between the two computer programs are described. Recent examples of the use of VENUS/NWChem for direct dynamics simulations are summarized.

  6. Application of remote sensing technology for studying littoral sediment dynamics

    Digital Repository Service at National Institute of Oceanography (India)

    Kunte, P.D.; Wagle, B.G.

    Satellite remote sensing data pertaining to two areas, one each on east and west coasts of India has been utilized to study suspended sediment dynamics within the near-shore region. For this purpose, thematic mapper image and second principal...

  7. Study of cavitation bubble dynamics during Ho:YAG laser lithotripsy by high-speed camera

    Science.gov (United States)

    Zhang, Jian J.; Xuan, Jason R.; Yu, Honggang; Devincentis, Dennis

    2016-02-01

    Although laser lithotripsy is now the preferred treatment option for urolithiasis, the mechanism of laser pulse induced calculus damage is still not fully understood. This is because the process of laser pulse induced calculus damage involves quite a few physical and chemical processes and their time-scales are very short (down to sub micro second level). For laser lithotripsy, the laser pulse induced impact by energy flow can be summarized as: Photon energy in the laser pulse --> photon absorption generated heat in the water liquid and vapor (super heat water or plasma effect) --> shock wave (Bow shock, acoustic wave) --> cavitation bubble dynamics (oscillation, and center of bubble movement , super heat water at collapse, sonoluminscence) --> calculus damage and motion (calculus heat up, spallation/melt of stone, breaking of mechanical/chemical bond, debris ejection, and retropulsion of remaining calculus body). Cavitation bubble dynamics is the center piece of the physical processes that links the whole energy flow chain from laser pulse to calculus damage. In this study, cavitation bubble dynamics was investigated by a high-speed camera and a needle hydrophone. A commercialized, pulsed Ho:YAG laser at 2.1 mu;m, StoneLightTM 30, with pulse energy from 0.5J up to 3.0 J, and pulse width from 150 mu;s up to 800 μs, was used as laser pulse source. The fiber used in the investigation is SureFlexTM fiber, Model S-LLF365, a 365 um core diameter fiber. A high-speed camera with frame rate up to 1 million fps was used in this study. The results revealed the cavitation bubble dynamics (oscillation and center of bubble movement) by laser pulse at different energy level and pulse width. More detailed investigation on bubble dynamics by different type of laser, the relationship between cavitation bubble dynamics and calculus damage (fragmentation/dusting) will be conducted as a future study.

  8. Theoretical studies of lipid bilayer electroporation using molecular dynamics simulations

    Science.gov (United States)

    Levine, Zachary Alan

    Computer simulations of physical, chemical, and biological systems have improved tremendously over the past five decades. From simple studies of liquid argon in the 1960s to fully atomistic simulations of entire viruses in the past few years, recent advances in high-performance computing have continuously enabled simulations to bridge the gap between scientific theory and experiment. Molecular dynamics simulations in particular have allowed for the direct observation of spatial and temporal events which are at present inaccessible to experiments. For this dissertation I employ all-atom molecular dynamics simulations to study the transient, electric field-induced poration (or electroporation) of phospholipid bilayers at MV/m electric fields. Phospholipid bilayers are the dominant constituents of cell membranes and act as both a barrier and gatekeeper to the cell interior. This makes their structural integrity and susceptibility to external perturbations an important topic for study, especially as the density of electromagnetic radiation in our environment is increasing steadily. The primary goal of this dissertation is to understand the specific physical and biological mechanisms which facilitate electroporation, and to connect our simulated observations to experiments with live cells and to continuum models which seek to describe the underlying biological processes of electroporation. In Chapter 1 I begin with a brief introduction to phospholipids and phospholipid bilayers, followed by an extensive overview of electroporation and atomistic molecular dynamics simulations. The following chapters will then focus on peer-reviewed and published work we performed, or on existing projects which are currently being prepared for submission. Chapter 2 looks at how external electric fields affect both oxidized and unoxidized lipid bilayers as a function of oxidation concentration and oxidized lipid type. Oxidative damage to cell membranes represents a physiologically relevant

  9. On the chemical dynamics of extracellular polysaccharides in the high Arctic surface microlayer

    Directory of Open Access Journals (Sweden)

    Q. Gao

    2012-07-01

    Full Text Available The surface microlayer (SML represents a unique system of which the physicochemical characteristics may differ from those of the underlying subsurface seawater (SSW. Within the Arctic pack ice area, the SML has been characterized as enriched in small colloids of biological origin, resulting from extracellular polymeric secretions (EPS. During the Arctic Summer Cloud Ocean Study (ASCOS in August 2008, particulate organic matter (POM, with size range > 0.22 μm and dissolved organic matter (DOM, < 0.22 μm, obtained after filtration samples were collected and chemically characterized from the SML and the corresponding SSW at an open lead centered at 87.5° N and 5° E. Total organic carbon was persistently enriched in the SML with a mean enrichment factor (EF of 1.45 ± 0.41, whereas sporadic depletions of dissolved carbohydrates and amino acids were observed. Monosaccharide compositional analysis reveals that EPS in the Arctic lead was formed mainly of distinctive heteropolysaccharides, enriched in xylose, fucose and glucose. The mean concentrations of total hydrolysable neutral sugars in SSW were 94.9 ± 37.5 nM in high molecular weight (HMW DOM (> 5 kDa and 64.4 ± 14.5 nM in POM. The enrichment of polysaccharides in the SML appeared to be a common feature, with EFs ranging from 1.7 to 7.0 for particulate polysaccharides and 3.5 to 12.1 for polysaccharides in the HMW DOM fraction. A calculated monosaccharide yield suggests that polymers in the HMW DOM fraction were scavenged, without substantial degradation, into the SML. Bubble scavenging experiments showed that newly aggregated particles could be formed abiotically by coagulation of low molecular weight nanometer-sized gels. Aerosol particles, artificially generated by bubbling experiments, were enriched in polysaccharides by factors of 22–70, relative to the source seawater. We propose that bubble scavenging of surface-active polysaccharides could be one of the possible mechanisms for the

  10. Microbial population dynamics in an anaerobic CSTR treating a chemical synthesis-based pharmaceutical wastewater.

    Science.gov (United States)

    Oz, Nilgun Ayman; Ince, Orhan; Ince, Bahar Kasapgil; Akarsubasi, Alper Tunga; Eyice, Ozge

    2003-01-01

    Effects of a chemical synthesis based pharmaceutical wastewater on performance of an anaerobic completely stirred tank reactor (CSTR), activity of acetoclastic methanogens and microbial composition were evaluated under various influent compositions. Initially, the CSTR was fed with glucose up to an organic loading rate (OLR) of 6 kg COD/m3 x d corresponding to an F/M ratio of 0.43 with a hydraulic retention time (HRT) of 2.5 days. A COD removal efficiency of 92% and a methane yield of 0.32 m3 CH4/kg COD(removed) were achieved whilst specific methanogenic activity (SMA) was found to be 336mL CH4/gTVS x d. After the CSTR was fed with pre-aerated wastewater diluted by glucose in different dilution ratios of 10% (w/v), 30% (w/v), 70% (w/v), and 100% (w/v) pre-aerated wastewater, gradual decreases in COD removal efficiency to 71%, methane yield to 0.28 m3CH4/kg COD(removed) and SMA to 166 mL CH4/gTVS d occurred whilst volatile fatty acid concentration reached to 1474 mg/L. After the raw wastewater diluted with the pre-aerated wastewater was fed into the CSTR in increasing ratios of 10% (w/v), 30% (w/v), and 60% (w/v), there was a proportional deterioration in performance in terms of COD removal efficiency, methane yield and acetoclastic methanogenic activity. Epifluorescence microscopy of the seed sludge revealed that Methanococcus-like species, short, and medium rods were found to be equally dominant. The short and medium rod species remained equally dominant groups in the CSTR throughout the feeding regime whilst Methanococcus-like species and long rods were found to be in insignificant numbers at the end of the study. Changes in archael diversity were determined using molecular analyses such as polymerase chain reaction (PCR), and denaturent gradient gel electrophoresis (DGGE). Results showed that overall archeal diversity did not change much whereas changes in composition of eubacterial population occurred.

  11. Isotope effects in photodissociation: Chemical reaction dynamics and implications for atmospheres

    DEFF Research Database (Denmark)

    Jørgensen, Solvejg; Grage, Mette Marie-Louise; Nyman, Gunnar

    2008-01-01

    and implicitly involve the short time approximation. in the time-dependent methods the time-dependent Schrodinger equation is solved exactly and the method considers the effect of dynamics away from the Franck-Condon region. We illustrate the presented methods using small molecules (HCl, N2O, OCS and HCHO...

  12. Acceleration of the KINETICS Integrated Dynamical/Chemical Computational Model Using MPI

    Science.gov (United States)

    Grossman, Max; Willacy, Karen; Allen, Mark

    2011-01-01

    Understanding the evolution of a planet's atmosphere not only provides a better theoretical understanding of planetary physics and the formation of planets, but also grants useful insight into Earth's own atmosphere. One of the tools used at JPL for the modeling of planetary atmospheres and protostellar disks is KINETICS. KINETICS can simulate years of complex dynamics and chemistry.

  13. Theoretical study of charge exchange dynamics in He$^+$ + NO collisions

    CERN Document Server

    Bene, E

    2014-01-01

    We investigate the charge transfer mechanism in the collisions of helium ions on nitric oxide using a molecular description framework with consideration of the orientation of the projectile toward the target. The anisotropy of the collision process has been analysed in detail in connection with the non-adiabatic interactions around avoided crossings. Potential energy curves, radial and rotational coupling matrix elements have been determined by means of ab initio quantum chemical methods. The collision dynamics is performed in the [1.-25.] keV collision energy range using a semiclassical approach, and the total electron transfer cross sections are analysed with regard to available experimental data.

  14. Theoretical Studies of Chemical Reactions following Electronic Excitation

    Science.gov (United States)

    Chaban, Galina M.

    2003-01-01

    The use of multi-configurational wave functions is demonstrated for several processes: tautomerization reactions in the ground and excited states of the DNA base adenine, dissociation of glycine molecule after electronic excitation, and decomposition/deformation of novel rare gas molecules HRgF. These processes involve bond brealung/formation and require multi-configurational approaches that include dynamic correlation.

  15. Molecular Dynamic Studies of the Complex Polyethylenimine and Glucose Oxidase

    Directory of Open Access Journals (Sweden)

    Beata Szefler

    2016-10-01

    Full Text Available Glucose oxidase (GOx is an enzyme produced by Aspergillus, Penicillium and other fungi species. It catalyzes the oxidation of β-d-glucose (by the molecular oxygen or other molecules, like quinones, in a higher oxidation state to form d-glucono-1,5-lactone, which hydrolyses spontaneously to produce gluconic acid. A coproduct of this enzymatic reaction is hydrogen peroxide (H2O2. GOx has found several commercial applications in chemical and pharmaceutical industries including novel biosensors that use the immobilized enzyme on different nanomaterials and/or polymers such as polyethylenimine (PEI. The problem of GOx immobilization on PEI is retaining the enzyme native activity despite its immobilization onto the polymer surface. Therefore, the molecular dynamic (MD study of the PEI ligand (C14N8_07_B22 and the GOx enzyme (3QVR was performed to examine the final complex PEI-GOx stabilization and the affinity of the PEI ligand to the docking sites of the GOx enzyme. The docking procedure showed two places/regions of major interaction of the protein with the polymer PEI: (LIG1 of −5.8 kcal/mol and (LIG2 of −4.5 kcal/mol located inside the enzyme and on its surface, respectively. The values of enthalpy for the PEI-enzyme complex, located inside of the protein (LIG1 and on its surface (LIG2 were computed. Docking also discovered domains of the GOx protein that exhibit no interactions with the ligand or have even repulsive characteristics. The structural data clearly indicate some differences in the ligand PEI behavior bound at the two places/regions of glucose oxidase.

  16. Molecular Dynamic Studies of the Complex Polyethylenimine and Glucose Oxidase

    Science.gov (United States)

    Szefler, Beata; Diudea, Mircea V.; Putz, Mihai V.; Grudzinski, Ireneusz P.

    2016-01-01

    Glucose oxidase (GOx) is an enzyme produced by Aspergillus, Penicillium and other fungi species. It catalyzes the oxidation of β-d-glucose (by the molecular oxygen or other molecules, like quinones, in a higher oxidation state) to form d-glucono-1,5-lactone, which hydrolyses spontaneously to produce gluconic acid. A coproduct of this enzymatic reaction is hydrogen peroxide (H2O2). GOx has found several commercial applications in chemical and pharmaceutical industries including novel biosensors that use the immobilized enzyme on different nanomaterials and/or polymers such as polyethylenimine (PEI). The problem of GOx immobilization on PEI is retaining the enzyme native activity despite its immobilization onto the polymer surface. Therefore, the molecular dynamic (MD) study of the PEI ligand (C14N8_07_B22) and the GOx enzyme (3QVR) was performed to examine the final complex PEI-GOx stabilization and the affinity of the PEI ligand to the docking sites of the GOx enzyme. The docking procedure showed two places/regions of major interaction of the protein with the polymer PEI: (LIG1) of −5.8 kcal/mol and (LIG2) of −4.5 kcal/mol located inside the enzyme and on its surface, respectively. The values of enthalpy for the PEI-enzyme complex, located inside of the protein (LIG1) and on its surface (LIG2) were computed. Docking also discovered domains of the GOx protein that exhibit no interactions with the ligand or have even repulsive characteristics. The structural data clearly indicate some differences in the ligand PEI behavior bound at the two places/regions of glucose oxidase. PMID:27801788

  17. Physically and chemically stable ionic liquid-infused textured surfaces showing excellent dynamic omniphobicity

    Energy Technology Data Exchange (ETDEWEB)

    Miranda, Daniel F.; Urata, Chihiro; Masheder, Benjamin; Dunderdale, Gary J.; Hozumi, Atsushi, E-mail: a.hozumi@aist.go.jp [National Institute of Advanced Industrial Science and Technology (AIST), 2266-98, Anagahora, Shimo-Shidami, Moriyama-ku, Nagoya, Aichi 463-8560 (Japan); Yagihashi, Makoto [Nagoya Municipal Industrial Research Institute, Rokuban, Atsuta-ku, Nagoya 456-0058 (Japan)

    2014-05-01

    A fluorinated and hydrophobic ionic liquid (IL), 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide, effectively served as an advantageous lubricating liquid for the preparation of physically and chemically stable omniphobic surfaces based on slippery liquid-infused porous surfaces. Here, we used particulate microstructures as supports, prepared by the chemical vapor deposition of 1,3,5,7-tetramethylcyclotetrasiloxane and subsequent surface modification with (3-aminopropyl)triethoxysilane. Confirmed by SEM and contact angle measurements, the resulting IL-infused microtextured surfaces are smooth and not only water but also various low surface tension liquids can easily slide off at low substrate tilt angles of <5°, even after exposure to high temperature, vacuum, and UV irradiation.

  18. Physically and chemically stable ionic liquid-infused textured surfaces showing excellent dynamic omniphobicity

    Directory of Open Access Journals (Sweden)

    Daniel F. Miranda

    2014-05-01

    Full Text Available A fluorinated and hydrophobic ionic liquid (IL, 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl imide, effectively served as an advantageous lubricating liquid for the preparation of physically and chemically stable omniphobic surfaces based on slippery liquid-infused porous surfaces. Here, we used particulate microstructures as supports, prepared by the chemical vapor deposition of 1,3,5,7-tetramethylcyclotetrasiloxane and subsequent surface modification with (3-aminopropyltriethoxysilane. Confirmed by SEM and contact angle measurements, the resulting IL-infused microtextured surfaces are smooth and not only water but also various low surface tension liquids can easily slide off at low substrate tilt angles of <5°, even after exposure to high temperature, vacuum, and UV irradiation.

  19. Dynamics of the chemical composition and productivity of composts for the cultivation of Agaricus bisporus strains

    Directory of Open Access Journals (Sweden)

    Meire Cristina Nogueira de Andrade

    2013-12-01

    Full Text Available Two compost formulations based on oat straw (Avena sativa and brachiaria (Brachiaria sp. were tested for the cultivation of three Agaricus bisporus strains (ABI-07/06, ABI-05/03, and PB-1. The experimental design was a 2 x 3 factorial scheme (composts x strains with 6 treatments and 8 repetitions (boxes containing 12 kg of compost. The chemical characterization of the compost (humidity, organic matter, carbon, nitrogen, pH, raw protein, ethereal extract, fibers, ash, cellulose, hemicellulose, and lignin before and after the cultivation of A. bisporus and the production (basidiomata mass, productivity, and biological efficiency were evaluated. Data were submitted to variance analysis, and averages were compared by means of the Tukey's test. According to the results obtained, the chemical and production characteristics showed that the best performances for the cultivation of A. bisporus were presented by the compost based on oat and the strain ABI-07/06.

  20. Dynamics of the chemical composition and productivity of composts for the cultivation of Agaricus bisporus strains.

    Science.gov (United States)

    de Andrade, Meire Cristina Nogueira; de Jesus, João Paulo Furlan; Vieira, Fabrício Rocha; Viana, Sthefany Rodrigues Fernandes; Spoto, Marta Helena Fillet; de Almeida Minhoni, Marli Teixeira

    2013-12-01

    Two compost formulations based on oat straw (Avena sativa) and brachiaria (Brachiaria sp.) were tested for the cultivation of three Agaricus bisporus strains (ABI-07/06, ABI-05/03, and PB-1). The experimental design was a 2 × 3 factorial scheme (composts × strains) with 6 treatments and 8 repetitions (boxes containing 12 kg of compost). The chemical characterization of the compost (humidity, organic matter, carbon, nitrogen, pH, raw protein, ethereal extract, fibers, ash, cellulose, hemicellulose, and lignin) before and after the cultivation of A. bisporus and the production (basidiomata mass, productivity, and biological efficiency) were evaluated. Data were submitted to variance analysis, and averages were compared by means of the Tukey's test. According to the results obtained, the chemical and production characteristics showed that the best performances for the cultivation of A. bisporus were presented by the compost based on oat and the strain ABI-07/06.

  1. Accelerating Wave Function Convergence in Interactive Quantum Chemical Reactivity Studies

    CERN Document Server

    Mühlbach, Adrian H; Reiher, Markus

    2015-01-01

    The inherently high computational cost of iterative self-consistent-field (SCF) methods proves to be a critical issue delaying visual and haptic feedback in real-time quantum chemistry. In this work, we introduce two schemes for SCF acceleration. They provide a guess for the initial density matrix of the SCF procedure generated by extrapolation techniques. SCF optimizations then converge in fewer iterations, which decreases the execution time of the SCF optimization procedure. To benchmark the proposed propagation schemes, we developed a test bed for performing quantum chemical calculations on sequences of molecular structures mimicking real-time quantum chemical explorations. Explorations of a set of six model reactions employing the semi-empirical methods PM6 and DFTB3 in this testing environment showed that the proposed propagation schemes achieved speedups of up to thirty percent as a consequence of a reduced number of SCF iterations.

  2. Models of chemical biosignatures - a vibrational spectroscopic study

    Science.gov (United States)

    Bödeker, B.; Böttger, U.; Hübers, H.-W.; deVera, J.-P.; Fox, S.; Strasdeit, H.

    2013-09-01

    Investigating possible biosignatures is of central interest in the search for the oldest traces of terrestrial life. Possible biosignatures are: (i) physical structures, such as fossilized single-celled or colonyforming microorganisms; (ii) biomolecules and their altered residues (chemical biosignatures); (iii) altered element, isotope and mineral compositions in former microbial habitats and related effects caused by metabolic activity [1]. New insights in this field of research are also important in the search for life on other planets and moons, especially Mars. However, abiotically formed organic compounds are widely distributed in the universe. Therefore, in future Mars missions, it will be essential to know whether organic molecules are actually of biological origin. Here, we describe the syntheses and spectroscopic (Raman and infrared) properties of artificial chemical biosignatures that might help answering this question.

  3. Probing of Fast Chemical Dynamics at High Pressures and Temperatures using Pulsed Laser Techniques

    Science.gov (United States)

    2014-12-17

    and dissociation of ammonia at high pressure and high temperature, The Journal of Chemical Physics, (08 2012): 0. doi: 10.1063/1.4742340 Ross Howie...Alexander Goncharov, Mohammad F. Mahmood, Synthesis of Energetic Nitrogen and Hydrogen Compounds Using High Pressure and Multiphoton Absorption, Poster...27, 2014. Alexander Goncharov, High-pressure synthesis of novel materials with new bonding patterns and unusual stoichiometries, Invited talk

  4. Chemical and pharmacological studies of the plants from genus Celastrus.

    Science.gov (United States)

    Su, Xiao-Hui; Zhang, Man-Li; Zhan, Wen-Hong; Huo, Chang-Hong; Shi, Qing-Wen; Gu, Yu-Cheng; Kiyota, Hiromasa

    2009-02-01

    The plants of genus Celastrus, distributed in Asia, have been used as natural insecticides and folk medicines to treat fever, chill, joint pain, edema, rheumatoid arthritis, and bacterial infection in China for a long time. This contribution reviews the chemical constituents, isolated from the plants in genus Celastrus in the past few decades, and their biological activities. The compounds listed are sesquiterpenes (beta-agarofurans), diterpenes, triterpenes, alkaloids, and flavonoids.

  5. 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.

  6. Polynomial-time quantum algorithm for the simulation of chemical dynamics.

    Science.gov (United States)

    Kassal, Ivan; Jordan, Stephen P; Love, Peter J; Mohseni, Masoud; Aspuru-Guzik, Alán

    2008-12-02

    The computational cost of exact methods for quantum simulation using classical computers grows exponentially with system size. As a consequence, these techniques can be applied only to small systems. By contrast, we demonstrate that quantum computers could exactly simulate chemical reactions in polynomial time. Our algorithm uses the split-operator approach and explicitly simulates all electron-nuclear and interelectronic interactions in quadratic time. Surprisingly, this treatment is not only more accurate than the Born-Oppenheimer approximation but faster and more efficient as well, for all reactions with more than about four atoms. This is the case even though the entire electronic wave function is propagated on a grid with appropriately short time steps. Although the preparation and measurement of arbitrary states on a quantum computer is inefficient, here we demonstrate how to prepare states of chemical interest efficiently. We also show how to efficiently obtain chemically relevant observables, such as state-to-state transition probabilities and thermal reaction rates. Quantum computers using these techniques could outperform current classical computers with 100 qubits.

  7. Dynamic 3-D chemical agent cloud mapping using a sensor constellation deployed on mobile platforms

    Science.gov (United States)

    Cosofret, Bogdan R.; Konno, Daisei; Rossi, David; Marinelli, William J.; Seem, Pete

    2014-05-01

    The need for standoff detection technology to provide early Chem-Bio (CB) threat warning is well documented. Much of the information obtained by a single passive sensor is limited to bearing and angular extent of the threat cloud. In order to obtain absolute geo-location, range to threat, 3-D extent and detailed composition of the chemical threat, fusion of information from multiple passive sensors is needed. A capability that provides on-the-move chemical cloud characterization is key to the development of real-time Battlespace Awareness. We have developed, implemented and tested algorithms and hardware to perform the fusion of information obtained from two mobile LWIR passive hyperspectral sensors. The implementation of the capability is driven by current Nuclear, Biological and Chemical Reconnaissance Vehicle operational tactics and represents a mission focused alternative of the already demonstrated 5-sensor static Range Test Validation System (RTVS).1 The new capability consists of hardware for sensor pointing and attitude information which is made available for streaming and aggregation as part of the data fusion process for threat characterization. Cloud information is generated using 2-sensor data ingested into a suite of triangulation and tomographic reconstruction algorithms. The approaches are amenable to using a limited number of viewing projections and unfavorable sensor geometries resulting from mobile operation. In this paper we describe the system architecture and present an analysis of results obtained during the initial testing of the system at Dugway Proving Ground during BioWeek 2013.

  8. Quantifying the uncertainties of chemical evolution studies. II. Stellar yields

    CERN Document Server

    Romano, D; Tosi, M; Matteucci, F

    2010-01-01

    This is the second paper of a series which aims at quantifying the uncertainties in chemical evolution model predictions related to the underlying model assumptions. Specifically, it deals with the uncertainties due to the choice of the stellar yields. We adopt a widely used model for the chemical evolution of the Galaxy and test the effects of changing the stellar nucleosynthesis prescriptions on the predicted evolution of several chemical species. We find that, except for a handful of elements whose nucleosynthesis in stars is well understood by now, large uncertainties still affect the model predictions. This is especially true for the majority of the iron-peak elements, but also for much more abundant species such as carbon and nitrogen. The main causes of the mismatch we find among the outputs of different models assuming different stellar yields and among model predictions and observations are: (i) the adopted location of the mass cut in models of type II supernova explosions; (ii) the adopted strength ...

  9. Tracking chemicals in products around the world: introduction of a dynamic substance flow analysis model and application to PCBs.

    Science.gov (United States)

    Li, Li; Wania, Frank

    2016-09-01

    Dynamically tracking flows and stocks of problematic chemicals in products (CiPs) in the global anthroposphere is essential to understanding their environmental fates and risks. The complex behavior of CiPs during production, use and waste disposal makes this a challenging task. Here we introduce and describe a dynamic substance flow model, named Chemicals in Products - Comprehensive Anthropospheric Fate Estimation (CiP-CAFE), which facilitates the quantification of time-variant flows and stocks of CiPs within and between seven interconnected world regions and the generation of global scale emission estimates. We applied CiP-CAFE to polychlorinated biphenyls (PCBs), first to evaluate its ability to reproduce previously reported global-scale atmospheric emission inventories and second to illustrate its potential applications and merits. CiP-CAFE quantifies the pathways of PCBs during production, use and waste disposal stages, thereby deducing the temporal evolution of in-use and waste stocks and identifying their long-term final sinks. Time-variant estimates of PCB emissions into air, water and soil can be attributed to different processes and be fed directly into a global fate and transport model. By capturing the international movement of PCBs as technical chemicals, and in products and waste, CiP-CAFE reveals that the extent of global dispersal caused by humans is larger than that occurring in the natural environment. Sensitivity analysis indicates that the model output is most sensitive to the PCB production volume and the lifetime of PCB-containing products, suggesting that a shortening of that lifetime is key to reducing future PCB emissions.

  10. Factors associated with chemical burns in Zhejiang province, China: An epidemiological study

    Directory of Open Access Journals (Sweden)

    Jiang Rui M

    2011-09-01

    Full Text Available Abstract Background Work-related burns are common among occupational injuries. Zhejiang Province is an industrial area with a high incidence of chemical burns. We aimed to survey epidemiological features of chemical burns in Zhejiang province to determine associated factors and acquire data for developing a strategy to prevent and treat chemical burns. Methods Questionnaires were developed, reviewed and validated by experts, and sent to 25 hospitals in Zhejiang province to prospectively collect data of 492 chemical burn patients admitted during one year from Sept. 1, 2008 to Aug. 31, 2009. Questions included victims' characteristics and general condition, injury location, causes of accident, causative chemicals, total body surface area burn, concomitant injuries, employee safety training, and awareness level of protective measures. Surveys were completed for each of burn patients by burn department personnel who interviewed the hospitalized patients. Results In this study, 417 victims (87.61% got chemical burn at work, of which 355 victims (74.58% worked in private or individual enterprises. Most frequent chemicals involved were hydrofluoric acid and sulfuric acid. Main causes of chemical injury accidents were inappropriate operation of equipment or handling of chemicals and absence of or failure to use effective individual protection. Conclusions Most chemical burns are preventable occupational injuries that can be attributed to inappropriate operation of equipment or handling of chemicals, lack of employee awareness about appropriate action and lack of effective protective equipment and training. Emphasis on safety education and protection for workers may help protect workers and prevent chemical burns.

  11. Protonation states and catalysis: Molecular dynamics studies of intermediates in tryptophan synthase.

    Science.gov (United States)

    Huang, Yu-Ming M; You, Wanli; Caulkins, Bethany G; Dunn, Michael F; Mueller, Leonard J; Chang, Chia-En A

    2016-01-01

    The importance of protonation states and proton transfer in pyridoxal 5'-phosphate (PLP)-chemistry can hardly be overstated. Although experimental approaches to investigate pKa values can provide general guidance for assigning proton locations, only static pictures of the chemical species are available. To obtain the overall protein dynamics for the interpretation of detailed enzyme catalysis in this study, guided by information from solid-state NMR, we performed molecular dynamics (MD) simulations for the PLP-dependent enzyme tryptophan synthase (TRPS), whose catalytic mechanism features multiple quasi-stable intermediates. The primary objective of this work is to elucidate how the position of a single proton on the reacting substrate affects local and global protein dynamics during the catalytic cycle. In general, proteins create a chemical environment and an ensemble of conformational motions to recognize different substrates with different protonations. The study of these interactions in TRPS shows that functional groups on the reacting substrate, such as the phosphoryl group, pyridine nitrogen, phenolic oxygen and carboxyl group, of each PLP-bound intermediate play a crucial role in constructing an appropriate molecular interface with TRPS. In particular, the protonation states of the ionizable groups on the PLP cofactor may enhance or weaken the attractions between the enzyme and substrate. In addition, remodulation of the charge distribution for the intermediates may help generate a suitable environment for chemical reactions. The results of our study enhance knowledge of protonation states for several PLP intermediates and help to elucidate their effects on protein dynamics in the function of TRPS and other PLP-dependent enzymes.

  12. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics

    DEFF Research Database (Denmark)

    Papaleo, Elena

    2015-01-01

    In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the pos......In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us...... that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....

  13. Bandwidth Study on Energy Use and Potential Energy Saving Opportunities in U.S. Chemical Manufacturing

    Energy Technology Data Exchange (ETDEWEB)

    Sabine Brueske, Caroline Kramer, Aaron Fisher

    2015-06-01

    Energy bandwidth studies of U.S. manufacturing sectors can serve as foundational references in framing the range (or bandwidth) of potential energy savings opportunities. This bandwidth study examines energy consumption and potential energy savings opportunities in U.S. chemical manufacturing. The study relies on multiple sources to estimate the energy used in the production of 74 individual chemicals, representing 57% of sector-wide energy consumption. Energy savings opportunities for individual chemicals and for 15 subsectors of chemicals manufacturing are based on technologies currently in use or under development; these potential savings are then extrapolated to estimate sector-wide energy savings opportunity.

  14. Investigation of Dynamic Multivariate Chemical Process Monitoring%动态多变量过程监控研究

    Institute of Scientific and Technical Information of China (English)

    谢磊; 张建明; 王树青

    2006-01-01

    Chemical process variables are always driven by random noise and disturbances. The closed-loop control yields process measurements that are auto and cross correlated. The influence of auto and cross correlations on statistical process control (SPC) is investigated in detail by Monte Carlo experiments. It is revealed that in the sense of average performance, the false alarms rates (FAR) of principal component analysis (PCA), dynamic PCA are not affected by the time-series structures of process variables. Nevertheless, non-independent identical distribution will cause the actual FAR to deviate from its theoretic value apparently and result in unexpected consecutive false alarms for normal operating process. Dynamic PCA and ARMA-PCA are demonstrated to be inefficient to remove the influences of auto and cross correlations. Subspace identification-based PCA (SI-PCA) is proposed to improve the monitoring of dynamic processes. Through state space modeling, SI-PCA can remove the auto and cross correlations efficiently and avoid consecutive false alarms. Synthetic Monte Carlo experiments and the application in Tennessee Eastman challenge process illustrate the advantages of the proposed approach.

  15. Dynamic and Progressive Control of DNA Origami Conformation by Modulating DNA Helicity with Chemical Adducts.

    Science.gov (United States)

    Chen, Haorong; Zhang, Hanyu; Pan, Jing; Cha, Tae-Gon; Li, Shiming; Andréasson, Joakim; Choi, Jong Hyun

    2016-05-24

    DNA origami has received enormous attention for its ability to program complex nanostructures with a few nanometer precision. Dynamic origami structures that change conformation in response to environmental cues or external signals hold great promises in sensing and actuation at the nanoscale. The reconfiguration mechanism of existing dynamic origami structures is mostly limited to single-stranded hinges and relies almost exclusively on DNA hybridization or strand displacement. Here, we show an alternative approach by demonstrating on-demand conformation changes with DNA-binding molecules, which intercalate between base pairs and unwind DNA double helices. The unwinding effect modulates the helicity mismatch in DNA origami, which significantly influences the internal stress and the global conformation of the origami structure. We demonstrate the switching of a polymerized origami nanoribbon between different twisting states and a well-constrained torsional deformation in a monomeric origami shaft. The structural transformation is shown to be reversible, and binding isotherms confirm the reconfiguration mechanism. This approach provides a rapid and reversible means to change DNA origami conformation, which can be used for dynamic and progressive control at the nanoscale.

  16. ALTERNATIVE AND ENHANCED CHEMICAL CLEANING: BASIC STUDIES RESULTS FY2010

    Energy Technology Data Exchange (ETDEWEB)

    King, W.; Hay, M.

    2011-01-24

    In an effort to develop and optimize chemical cleaning methods for the removal of sludge heels from High Level Waste tanks, solubility tests have been conducted using nonradioactive, pure metal phases. The metal phases studied included the aluminum phase gibbsite and the iron phases hematite, maghemite, goethite, lepidocrocite, magnetite, and wustite. Many of these mineral phases have been identified in radioactive, High Level Waste sludge at the Savannah River and Hanford Sites. Acids evaluated for dissolution included oxalic, nitric, and sulfuric acids and a variety of other complexing organic acids. The results of the solubility tests indicate that mixtures of oxalic acid with either nitric or sulfuric acid are the most effective cleaning solutions for the dissolution of the primary metal phases in sludge waste. Based on the results, optimized conditions for hematite dissolution in oxalic acid were selected using nitric or sulfuric acid as a supplemental proton source. Electrochemical corrosion studies were also conducted (reported separately; Wiersma, 2010) with oxalic/mineral acid mixtures to evaluate the effects of these solutions on waste tank integrity. The following specific conclusions can be drawn from the test results: (1) Oxalic acid was shown to be superior to all of the other organic acids evaluated in promoting the dissolution of the primary sludge phases. (2) All iron phases showed similar solubility trends in oxalic acid versus pH, with hematite exhibiting the lowest solubility and the slowest dissolution. (3) Greater than 90% hematite dissolution occurred in oxalic/nitric acid mixtures within one week for two hematite sources and within three weeks for a third hematite sample with a larger average particle size. This dissolution rate appears acceptable for waste tank cleaning applications. (4) Stoichiometric dissolution of iron phases in oxalic acid (based on the oxalate concentration) and the formation of the preferred 1:1 Fe to oxalate complex

  17. ALTERNATIVE AND ENHANCED CHEMICAL CLEANING: BASIC STUDIES RESULTS FY2010

    Energy Technology Data Exchange (ETDEWEB)

    King, W.; Hay, M.

    2011-01-24

    In an effort to develop and optimize chemical cleaning methods for the removal of sludge heels from High Level Waste tanks, solubility tests have been conducted using nonradioactive, pure metal phases. The metal phases studied included the aluminum phase gibbsite and the iron phases hematite, maghemite, goethite, lepidocrocite, magnetite, and wustite. Many of these mineral phases have been identified in radioactive, High Level Waste sludge at the Savannah River and Hanford Sites. Acids evaluated for dissolution included oxalic, nitric, and sulfuric acids and a variety of other complexing organic acids. The results of the solubility tests indicate that mixtures of oxalic acid with either nitric or sulfuric acid are the most effective cleaning solutions for the dissolution of the primary metal phases in sludge waste. Based on the results, optimized conditions for hematite dissolution in oxalic acid were selected using nitric or sulfuric acid as a supplemental proton source. Electrochemical corrosion studies were also conducted (reported separately; Wiersma, 2010) with oxalic/mineral acid mixtures to evaluate the effects of these solutions on waste tank integrity. The following specific conclusions can be drawn from the test results: (1) Oxalic acid was shown to be superior to all of the other organic acids evaluated in promoting the dissolution of the primary sludge phases. (2) All iron phases showed similar solubility trends in oxalic acid versus pH, with hematite exhibiting the lowest solubility and the slowest dissolution. (3) Greater than 90% hematite dissolution occurred in oxalic/nitric acid mixtures within one week for two hematite sources and within three weeks for a third hematite sample with a larger average particle size. This dissolution rate appears acceptable for waste tank cleaning applications. (4) Stoichiometric dissolution of iron phases in oxalic acid (based on the oxalate concentration) and the formation of the preferred 1:1 Fe to oxalate complex

  18. REPRESENTING AEROSOL DYNAMICS AND PROPERTIES IN CHEMICAL TRANSPORT MODELS BY THE METHOD OF MOMENTS.

    Energy Technology Data Exchange (ETDEWEB)

    SCHWARTZ, S.E.; MCGRAW, R.; BENKOVITZ, C.M.; WRIGHT, D.L.

    2001-04-01

    Atmospheric aerosols, suspensions of solid or liquid particles, are an important multi-phase system. Aerosols scatter and absorb shortwave (solar) radiation, affecting climate (Charlson et al., 1992; Schwartz, 1996) and visibility; nucleate cloud droplet formation, modifying the reflectivity of clouds (Twomey et al., 1984; Schwartz and Slingo, 1996) as well as contributing to composition of cloudwater and to wet deposition (Seinfeld and Pandis, 1998); and affect human health through inhalation (NRC, 1998). Existing and prospective air quality regulations impose standards on concentrations of atmospheric aerosols to protect human health and welfare (EPA, 1998). Chemical transport and transformation models representing the loading and geographical distribution of aerosols and precursor gases are needed to permit development of effective and efficient strategies for meeting air quality standards, and for examining aerosol effects on climate retrospectively and prospectively for different emissions scenarios. Important aerosol properties and processes depend on their size distribution: light scattering, cloud nucleating properties, dry deposition, and penetration into airways of lungs. The evolution of the mass loading itself depends on particle size because of the size dependence of growth and removal processes. For these reasons it is increasingly recognized that chemical transport and transformation models must represent not just the mass loading of atmospheric particulate matter but also the aerosol microphysical properties and the evolution of these properties if aerosols are to be accurately represented in these models. If the size distribution of the aerosol is known, a given property can be evaluated as the integral of the appropriate kernel function over the size distribution. This has motivated the approach of determining aerosol size distribution, and of explicitly representing this distribution and its evolution in chemical transport models.

  19. A Rapid Compression Expansion Machine (RCEM) for studying chemical kinetics: Experimental principle and first applications

    CERN Document Server

    Werler, Marc; Maas, Ulrich

    2016-01-01

    A novel extension of a rapid compression machine (RCM), namely a Rapid Compression Expansion Machine (RCEM), is described and its use for studying chemical kinetics is demonstrated. Like conventional RCMs, the RCEM quickly compresses a fuel/air mixture by pushing a piston into a cylinder; the resulting high temperatures and pressures initiate chemical reactions. In addition, the machine can rapidly expand the compressed gas in a controlled way by pulling the piston outwards again. This freezes chemical activity after a pre-defined reaction duration, and therefore allows a convenient probe sampling and ex-situ gas analysis of stable species. The RCEM therefore is a promising instrument for studying chemical kinetics, including also partially reacted fuel/air mixtures. The setup of the RCEM, its experimental characteristics and its use for studying chemical reactions are outlined in detail. To allow comparisons of RCEM results with predictions of chemical reaction mechanisms, a simple numerical model of the RCE...

  20. Physico-Chemical Study of Barium (II) Dipivaloylmethanate Nature

    OpenAIRE

    Fedotova, N.; Igumenov, I.; Mamatyuk, V.; Sidorenko, G.

    1995-01-01

    A physico-chemical research of bis-(dipivaloylmethanato)baryum(II) (Ba(thd)2) has been carried out from the point of its use in CVD process as a precursor (thermal stability, immunity to external effects and etc.). The optimal conditions for synthesis, purification and storage have been found. It has been shown, that the sublimated product presents a mixture of several modifications with the main phase of a composition Ba4(th)8. At a lowered pressure the sublimated product is preserved withou...

  1. An Experimental Study on Electro Chemical Machining of Microelectrode

    Institute of Scientific and Technical Information of China (English)

    ZHANG Liao-yuan; LIU Yao

    2006-01-01

    Puts forward a new method in machining microelectrode by electro chemical machining (ECM) and plastic deformed theory. Theprocedure of this method is to machine the microelectrode according to the basic rule of ECM theory at first. Then, with the change of ECM machining parameters, one of the microelectrode ends is exerted by a load. As a result, the elastic and plastic deformation is produced at the machining section and the microelectrode diameter is reduced.It has been proved that the proposed method can determine the optimum machining parameters to machine the microelectrode of Cu.

  2. Collagen-curcumin interaction - A physico-chemical study

    Indian Academy of Sciences (India)

    N Nishad Fathima; R Saranya Devi; K B Rekha; Aruna Dhathathreyan

    2009-07-01

    Curcumin is a widely used therapeutic agent with a wide spectrum of biological and physiological applications like wound healing and interacts with the skin protein, collagen. This work reports the effect of curcumin on various physico-chemical properties of collagen. The results suggest that significant changes in viscosity and surface tension occur on collagen interacting with curcumin. Secondary structure analysis using circular dichroism shows that curcumin does not alter the triple helical structure of collagen. Increasing concentration of curcumin resulted in aggregation of the protein. Further, curcumin imparts high level of thermal stability to collagen with shrinkage temperature of collagen increasing from 60 to 90°C.

  3. Incorporating transgenerational testing and epigenetic mechanisms into chemical testing and risk assessment: A survey of transgenerational responses in environmental chemical studies

    Science.gov (United States)

    A number of environmental chemicals have been shown to alter markers of epigenetic change. Some published multi-generation rodent studies have identified effects on F2 and greater generations after chemical exposures solely to F0 dams, but were not focused on chemical safety. We ...

  4. Non-allergic cutaneous reactions in airborne chemical sensitivity--a population based study.

    Science.gov (United States)

    Berg, Nikolaj Drimer; Linneberg, Allan; Thyssen, Jacob Pontoppidan; Dirksen, Asger; Elberling, Jesper

    2011-06-01

    Multiple chemical sensitivity (MCS) is characterised by adverse effects due to exposure to low levels of chemical substances. The aetiology is unknown, but chemical related respiratory symptoms have been found associated with positive patch test. The purpose of this study was to investigate the relationship between cutaneous reactions from patch testing and self-reported severity of chemical sensitivity to common airborne chemicals. A total of 3460 individuals participating in a general health examination, Health 2006, were patch tested with allergens from the European standard series and screened for chemical sensitivity with a standardised questionnaire dividing the participants into four severity groups of chemical sensitivity. Both allergic and non-allergic cutaneous reactions--defined as irritative, follicular, or doubtful allergic reactions--were analysed in relationship with severity of chemical sensitivity. Associations were controlled for the possible confounding effects of sex, age, asthma, eczema, atopic dermatitis, psychological and social factors, and smoking habits. In unadjusted analyses we found associations between allergic and non-allergic cutaneous reactions on patch testing and the two most severe groups of self-reported sensitivity to airborne chemicals. When adjusting for confounding, associations were weakened, and only non-allergic cutaneous reactions were significantly associated with individuals most severely affected by inhalation of airborne chemicals (odds ratio = 2.5, p = 0.006). Our results suggest that individuals with self-reported chemical sensitivity show increased non-allergic cutaneous reactions based on day 2 readings of patch tests.

  5. Thermodynamic Study of Hydrolysis Reactions in Aqueous Solution from Ab Initio Potential and Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    S. Tolosa

    2013-01-01

    Full Text Available A procedure for the theoretical study of chemical reactions in solution by means of molecular dynamics simulations of aqueous solution at infinite dilution is described using ab initio solute-solvent potentials and TIP3P water model to describe the interactions. The procedure is applied to the study of neutral hydrolysis of various molecules (HCONH2, HNCO, HCNHNH2, and HCOOCH3 via concerted and water-assisted mechanisms. We used the solvent as a reaction coordinate and the free energy curves for the calculation of the properties related with the reaction mechanism, namely, reaction and activation energies.

  6. Temperature dependent dynamics of DegP-trimer: A molecular dynamics study.

    Science.gov (United States)

    Rai, Nivedita; Ramaswamy, Amutha

    2015-01-01

    DegP is a heat shock protein from high temperature requirement protease A family, which reacts to the environmental stress conditions in an ATP independent way. The objective of the present analysis emerged from the temperature dependent functional diversity of DegP between chaperonic and protease activities at temperatures below and above 28 °C, respectively. DegP is a multimeric protein and the minimal functional unit, DegP-trimer, is of great importance in understanding the DegP pathway. The structural aspects of DegP-trimer with respect to temperature variation have been studied using molecular dynamics simulations (for 100 ns) and principal component analysis to highlight the temperature dependent dynamics facilitating its functional diversity. The DegP-trimer revealed a pronounced dynamics at both 280 and 320 K, when compared to the dynamics observed at 300 K. The LA loop is identified as the highly flexible region during dynamics and at extreme temperatures, the residues 46-80 of LA loop express a flip towards right (at 280) and left ( at 320 K) with respect to the fixed β-sheet connecting the LA loop of protease for which Phe46 acts as one of the key residues. Such dynamics of LA loop facilitates inter-monomeric interaction with the PDZ1 domain of the neighbouring monomer and explains its active participation when DegP exists as trimer. Hence, the LA loop mediated dynamics of DegP-trimer is expected to provide further insight into the temperature dependent dynamics of DegP towards the understanding of its assembly and functional diversity in the presence of substrate.

  7. Temperature dependent dynamics of DegP-trimer: A molecular dynamics study

    Directory of Open Access Journals (Sweden)

    Nivedita Rai

    2015-01-01

    Full Text Available DegP is a heat shock protein from high temperature requirement protease A family, which reacts to the environmental stress conditions in an ATP independent way. The objective of the present analysis emerged from the temperature dependent functional diversity of DegP between chaperonic and protease activities at temperatures below and above 28 °C, respectively. DegP is a multimeric protein and the minimal functional unit, DegP-trimer, is of great importance in understanding the DegP pathway. The structural aspects of DegP-trimer with respect to temperature variation have been studied using molecular dynamics simulations (for 100 ns and principal component analysis to highlight the temperature dependent dynamics facilitating its functional diversity. The DegP-trimer revealed a pronounced dynamics at both 280 and 320 K, when compared to the dynamics observed at 300 K. The LA loop is identified as the highly flexible region during dynamics and at extreme temperatures, the residues 46–80 of LA loop express a flip towards right (at 280 and left ( at 320 K with respect to the fixed β-sheet connecting the LA loop of protease for which Phe46 acts as one of the key residues. Such dynamics of LA loop facilitates inter-monomeric interaction with the PDZ1 domain of the neighbouring monomer and explains its active participation when DegP exists as trimer. Hence, the LA loop mediated dynamics of DegP-trimer is expected to provide further insight into the temperature dependent dynamics of DegP towards the understanding of its assembly and functional diversity in the presence of substrate.

  8. Use of the LITEE Lorn Manufacturing Case Study in a Senior Chemical Engineering Unit Operations Laboratory

    Science.gov (United States)

    Abraham, Nithin Susan; Abulencia, James Patrick

    2011-01-01

    This study focuses on the effectiveness of incorporating the Laboratory for Innovative Technology and Engineering Education (LITEE) Lorn Manufacturing case into a senior level chemical engineering unit operations course at Manhattan College. The purpose of using the case study is to demonstrate the relevance of ethics to chemical engineering…

  9. CH 1 Introduction to Chemistry. Study Guide to Minicourse I - 13 Chemical Reaction Principles.

    Science.gov (United States)

    Schlenker, Richard

    Provided is a study guide for an introductory minicourse to the principles of chemical reactions. This written text is designed to accompany a series of audio tapes and 35mm slides which the student studies at his own pace. The course presents chemical kinetics, reaction mechanisms, reaction rates, and equilibrium. (SL)

  10. NMR Studies of Cartilage Dynamics, Diffusion, Degradation

    Science.gov (United States)

    Huster, Daniel; Schiller, Jurgen; Naji, Lama; Kaufmann Jorn; Arnold, Klaus

    An increasing number of people is suffering from rheumatic diseases, and, therefore, methods of early diagnosis of joint degeneration are urgently required. For their establishment, however, an improved knowledge about the molecular organisation of cartilage would be helpful. Cartilage consists of three main components: Water, collagen and chondroitin sulfate (CS) that is (together with further polysaccharides and proteins) a major constituent of the proteoglycans of cartilage. 1H and 13C MAS (magic-angle spinning) NMR (nuclear magnetic resonance) opened new perspectives for the study of the macromolecular components in cartilage. We have primarily studied the mobilities of CS and collagen in bovine nasal and pig articular cartilage (that differ significantly in their collagen/polysaccharide content) by measuring 13C NMR relaxation times as well as the corresponding 13C CP (cross polarisation) MAS NMR spectra. These data clearly indicate that the mobility of cartilage macromolecules is broadly distributed from almost completely rigid (collagen) to highly mobile (polysaccharides), which lends cartilage its mechanical strength and shock-absorbing properties.

  11. Synthesis of Formamide and Related Organic Species in the Interstellar Medium via Chemical Dynamics Simulations

    Science.gov (United States)

    Spezia, Riccardo; Jeanvoine, Yannick; Hase, William L.; Song, Kihyung; Largo, Antonio

    2016-08-01

    We show, by means of direct dynamics simulations, how it is possible to define possible reactants and mechanisms leading to the formation of formamide in the interstellar medium. In particular, different ion-molecule reactions in the gas phase were considered: NH3OH+, NH2OH{}2+, H2COH+, and NH4 + for the ions and NH2OH, H2CO, and NH3 for the partner neutrals. These calculations were combined with high level ab initio calculations to investigate possible further evolution of the products observed. In particular, for formamide, we propose that the NH2OH{}2+ + H2CO reaction can produce an isomer, NH2OCH{}2+, that, after dissociative recombination, can produce neutral formamide, which was observed in space. The direct dynamics do not pre-impose any reaction pathways and in other reactions, we did not observe the formation of formamide or any possible precursor. On the other hand, we obtained other interesting reactions, like the formation of NH2CH{}2+. Finally, some radiative association processes are proposed. All of the results obtained are discussed in light of the species observed in radioastronomy.

  12. Thermoelectric studies of charge density wave dynamics.

    Science.gov (United States)

    McDonald, Ross; Harrison, Neil; Singleton, John

    2008-03-01

    The conventional pyroelectric effect is intimately connected to the symmetry, or rather lack of center of symmetry, of the material. Although the experiments we discuss involve studies of low symmetry materials, the pyroelectric currents observed are of an entirely new origin. Systems with broken-translational-symmetry phases that incorporate orbital quantization can exhibit significant departures from thermodynamic equilibrium due to a change in magnetic induction. For charge density wave systems, this metastable state consists of a balance between the density-wave pinning force and the Lorentz force on the extended currents due to the drift of cyclotron orbits. In this way the density wave pinning potential plays a similar role to the edge potential in a two-dimensional electron gas, leading to a large Hall angle and quantization of the Hall resistance. A thermal perturbation that reduces the pinning potential returns the system towards thermal equilibrium, via a phason avalanche orthogonal to the sample surface. The observation of this new form of pyroelectric effect in the high magnetic field phase (B > 30 T) of the organic charge transfer salt α-(BEDT-TTF)2KHg(SCN)4, thus provides a measure of the phason thermopower.

  13. Studying Human Dynamics Through Web Analytics

    Science.gov (United States)

    Ramasco, Jose; Goncalves, Bruno

    2008-03-01

    When Tim Berners Lee, a physicist at the European Center for Nuclear Research (CERN) first conceived the World Wide Web (WWW) in 1990 as a way to facilitate the sharing of scientific information and results among the centers different researchers and groups, even the most ingenious of science fiction writers could not have imagined the role it would come to play in the following decades. The increasing ubiquitousness of Internet access and the frequency with which people interact with it raise the possibility of using it to better observe, understand, and even monitor several aspects of human social behavior. Websites with large numbers of frequently returning users, such as search engines, company or university websites, are ideal for this task. The properly anonymized logs detailing the access history to Emory University's website is studied. We find that a small number of users is responsible for a finite fraction of the total activity. A saturation phenomenon is observed where, certain connections age, becoming less attractive to new activity over time. Finally, by measuring the average activity as a function of the day of the week, we find that productivity seems to be higher on Tuesdays and Wednesdays, with Sundays being the least active day.

  14. TREATMENT TANK CORROSION STUDIES FOR THE ENHANCED CHEMICAL CLEANING PROCESS

    Energy Technology Data Exchange (ETDEWEB)

    Wiersma, B.

    2011-08-24

    Radioactive waste is stored in high level waste tanks on the Savannah River Site (SRS). Savannah River Remediation (SRR) is aggressively seeking to close the non-compliant Type I and II waste tanks. The removal of sludge (i.e., metal oxide) heels from the tank is the final stage in the waste removal process. The Enhanced Chemical Cleaning (ECC) process is being developed and investigated by SRR to aid in Savannah River Site (SRS) High-Level Waste (HLW) as an option for sludge heel removal. Corrosion rate data for carbon steel exposed to the ECC treatment tank environment was obtained to evaluate the degree of corrosion that occurs. These tests were also designed to determine the effect of various environmental variables such as temperature, agitation and sludge slurry type on the corrosion behavior of carbon steel. Coupon tests were performed to estimate the corrosion rate during the ECC process, as well as determine any susceptibility to localized corrosion. Electrochemical studies were performed to develop a better understanding of the corrosion mechanism. The tests were performed in 1 wt.% and 2.5 wt.% oxalic acid with HM and PUREX sludge simulants. The following results and conclusions were made based on this testing: (1) In 1 wt.% oxalic acid with a sludge simulant, carbon steel corroded at a rate of less than 25 mpy within the temperature and agitation levels of the test. No susceptibility to localized corrosion was observed. (2) In 2.5 wt.% oxalic acid with a sludge simulant, the carbon steel corrosion rates ranged between 15 and 88 mpy. The most severe corrosion was observed at 75 C in the HM/2.5 wt.% oxalic acid simulant. Pitting and general corrosion increased with the agitation level at this condition. No pitting and lower general corrosion rates were observed with the PUREX/2.5 wt.% oxalic acid simulant. The electrochemical and coupon tests both indicated that carbon steel is more susceptible to localized corrosion in the HM/oxalic acid environment than

  15. TREATMENT TANK CORROSION STUDIES FOR THE ENHANCED CHEMICAL CLEANING PROCESS

    Energy Technology Data Exchange (ETDEWEB)

    Wiersma, B.

    2011-08-24

    Radioactive waste is stored in high level waste tanks on the Savannah River Site (SRS). Savannah River Remediation (SRR) is aggressively seeking to close the non-compliant Type I and II waste tanks. The removal of sludge (i.e., metal oxide) heels from the tank is the final stage in the waste removal process. The Enhanced Chemical Cleaning (ECC) process is being developed and investigated by SRR to aid in Savannah River Site (SRS) High-Level Waste (HLW) as an option for sludge heel removal. Corrosion rate data for carbon steel exposed to the ECC treatment tank environment was obtained to evaluate the degree of corrosion that occurs. These tests were also designed to determine the effect of various environmental variables such as temperature, agitation and sludge slurry type on the corrosion behavior of carbon steel. Coupon tests were performed to estimate the corrosion rate during the ECC process, as well as determine any susceptibility to localized corrosion. Electrochemical studies were performed to develop a better understanding of the corrosion mechanism. The tests were performed in 1 wt.% and 2.5 wt.% oxalic acid with HM and PUREX sludge simulants. The following results and conclusions were made based on this testing: (1) In 1 wt.% oxalic acid with a sludge simulant, carbon steel corroded at a rate of less than 25 mpy within the temperature and agitation levels of the test. No susceptibility to localized corrosion was observed. (2) In 2.5 wt.% oxalic acid with a sludge simulant, the carbon steel corrosion rates ranged between 15 and 88 mpy. The most severe corrosion was observed at 75 C in the HM/2.5 wt.% oxalic acid simulant. Pitting and general corrosion increased with the agitation level at this condition. No pitting and lower general corrosion rates were observed with the PUREX/2.5 wt.% oxalic acid simulant. The electrochemical and coupon tests both indicated that carbon steel is more susceptible to localized corrosion in the HM/oxalic acid environment than

  16. Physico-chemical study of barium (II) dipivaloylmethanate nature

    Energy Technology Data Exchange (ETDEWEB)

    Fedotova, N.E. [Rossijskaya Akademiya Nauk, Novosibirsk (Russian Federation). Inst. of Inorganic Chemistry; Igumenov, I.K. [Rossijskaya Akademiya Nauk, Novosibirsk (Russian Federation). Inst. of Inorganic Chemistry; Mamatyuk, V.I. [Rossijskaya Akademiya Nauk, Novosibirsk (Russian Federation). Inst. of Inorganic Chemistry; Sidorenko, G.V. [Rossijskaya Akademiya Nauk, Novosibirsk (Russian Federation). Inst. of Inorganic Chemistry

    1995-06-01

    A physico-chemical research of bis-(dipivaloylmethanato)barium(II) (Ba(thd){sub 2}) has been carried out from the point of its use in CVD processes as a precursor (thermal stability, immunity to external effects and etc.). The optimal conditions for synthesis, purification and storage have been found. It has been shown, that the sublimated product presents a mixture of several modifications with the main phase of a composition Ba{sub 4}(thd){sub 8}. At a lowered pressure the sublimated product is preserved without decomposition for a long time. In the air it is a monomer of a composition Ba(thd){sub 2}*2H{sub 2}O, decomposing in the course of time with forming a free ligand or a diketone (C{sub 8}H{sub 21}O{sub 2}) depending on the way of purification of the initial compound. (orig.).

  17. Chemical characterization and dynamics of particulate combined amino acids in Pacific surface waters

    Science.gov (United States)

    Tsukasaki, Ayumi; Tanoue, Eiichiro

    2010-01-01

    Particulate organic matter (POM) in surface water plays an essential role in maintaining marine ecosystem and is a complex mixture of living POM (organisms) and non-living POM (detritus). Transformation of organic constituents of organisms to detritus may be the most active part in the decomposition processes of organic matter in marine biogeochemistry. Distribution and chemical fractionation of particulate combined amino acids (PCAAs) in surface waters from Southern Ocean to tropical waters along a transect of 170°W were examined to clarify the transfer processes of organic constituents of organisms to detritus. The observational facts may be summarized as follows. 1) Degradation Index (DI) based on principal component analysis of amino acid composition of bulk PCAAs agreed with the traditional degradation indicators of bulk POM, i.e., PCAAs-carbon (C)/particulate organic carbon (POC), PCAAs-nitrogen (N)/particulate nitrogen (PN) and C/N. 2) PCAAs were distinguished into 3 fractions, i.e., Urea-soluble, Sodium Dodecyl Sulfate (SDS)-soluble and SDS/Urea-insoluble fractions, by means of solubility against reagents frequently used for protein extraction from biological samples. Proportions of PCAAs of the 3 fractions to bulk PCAAs were almost constant, although concentrations of the PCAAs of 3 fractions as well as bulk in seawater varied two orders of magnitude over the transect. 3) There was no significant difference among DI values of the 3 fractions, although molecular mass distributions of the Urea-soluble and SDS-soluble fractions determined by SDS-polyacrylamide gel electrophoresis were different. The results indicated that no one fraction was particularly susceptible to degradation and that there is a common mechanism for transferring and maintaining the similar chemical quality of bulk POM over the transect.

  18. Chemical evolution of the Salton Sea, California: Nutrient and selenium dynamics

    Science.gov (United States)

    Schroeder, R.A.; Orem, W.H.; Kharaka, Y.K.

    2002-01-01

    The Salton Sea is a 1000-km2 terminal lake located in the desert area of southeastern California. This saline (???44 000 mg l-1 dissolved solids) lake started as fresh water in 1905-07 by accidental flooding of the Colorado River, and it is maintained by agricultural runoff of irrigation water diverted from the Colorado River. The Salton Sea and surrounding wetlands have recently acquired substantial ecological importance because of the death of large numbers of birds and fish, and the establishment of a program to restore the health of the Sea. In this report, we present new data on the salinity and concentration of selected chemicals in the Salton Sea water, porewater and sediments, emphasizing the constituents of concern: nutrients (N and P), Se and salinity. Chemical profiles from a Salton Sea core estimated to have a sedimentation rate of 2.3 mm yr-1 show increasing concentrations of OC, N, and P in younger sediment that are believed to reflect increasing eutrophication of the lake. Porewater profiles from two locations in the Sea show that diffusion from bottom sediment is only a minor source of nutrients to the overlying water as compared to irrigation water inputs. Although loss of N and Se by microbial-mediated volatilization is possible, comparison of selected element concentrations in river inputs and water and sediments from the Salton Sea indicates that most of the N (from fertilizer) and virtually all of the Se (delivered in irrigation water from the Colorado River) discharged to the Sea still reside within its bottom sediment. Laboratory simulation on mixtures of sediment and water from the Salton Sea suggest that sediment is a potential source of N and Se to the water column under aerobic conditions. Hence, it is important that any engineered changes made to the Salton Sea for remediation or for transfer of water out of the basin do not result in remobilization of nutrients and Se from the bottom sediment into the overlying water.

  19. Chemical Modification: an Effective Way of Avoiding the Collapse of SWNTs on Al Surface Revealed by Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Xie, J.; Xue, Q. Z.; Yan, K. Y.

    2009-01-01

    The rapid collapse of intrinsic single-walled carbon nanotube (SWNT) on the aluminum surface is observed using molecular dynamics simulation. The collapsing threshold is similar to 10 angstrom, and the length has no influence on its collapse. Furthermore, we report that the structural stability...... of cylindrical SWNTs oil the aluminum surface can be improved through the surface modification method. The stability of SWNTs call be enhanced by increasing the modification coverage. When the modification coverage exceeds 3.3% and 3.8% coverage, respectively, both amidogen- and carboxyl-modified SWNTs can...... basically maintain the cylindrical structure in our described systems. The results also show that, to avoid SWNTs collapse by chemical modification, the longer and larger SWNTs are, the more modification coverage SWNTs require. and vice versa. Our method allows potentially used modified SWNTs...

  20. Three studies of retail gasoline pricing dynamics

    Science.gov (United States)

    Atkinson, Benjamin James

    In many Canadian cities, retail gasoline prices appear to cycle, rising by large amounts in one or two days followed by several days of small consecutive price decreases. While many empirical studies examine such markets, certain questions cannot b e properly answered without high frequency, station-specific price data for an entire market. Thus, the first paper in this thesis uses bi-hourly price data collected for 27 stations in Guelph, Ontario, eight tunes per day for 103 days to examine several basic predictions of the Edgeworth cycle theory. The results are largely consistent with this theory. However, most independent firms do not tend to undercut their rivals' prices, contrary to previous findings. Furthermore, the tuning, sizes and leaders of price increases appear to be very predictable, and a specific pattern of price movements has been detected on days when prices increase. These findings suggest that leading a price increase might not be as risky as one may expect. The second paper uses these same data to examine the implications o f an informal theory of competitive gasoline pricing, as advanced by industry and government. Consistent with this theory, stations do tend to set prices to match (or set a small positive or negative differential with) a small number of other stations, which are not necessarily the closest stations. Also, while retailers frequently respond to price changes within two hours, many take considerably longer to respond than is predicted by the theory. Finally, while price decreases do ripple across the market like falling dominos, increases appear to propagate based more on geographic location and source of price control than proximity to the leaders. The third paper uses both these data and Guelph price data collected every 12 hours during the same 103 days from OntarioGasPrices.com to examine the sample selection biases that might exist in such Internet price data, as well as their implications for empirical research. It is

  1. COOEE bitumen: chemical aging

    CERN Document Server

    Lemarchand, Claire A; Dyre, Jeppe C; Hansen, Jesper S

    2013-01-01

    We study chemical aging in "COOEE bitumen" using molecular dynamic simulations. The model bitumen is composed of four realistic molecule types: saturated hydrocarbon, resinous oil, resin, and asphaltene. The aging reaction is modelled by the chemical reaction: "2 resins $\\rightarrow$ 1 asphaltene". Molecular dynamic simulations of four bitumen compositions, obtained by a repeated application of the aging reaction, are performed. The stress autocorrelation function, the fluid structure, the rotational dynamics of the plane aromatic molecules, and the diffusivity of each molecule, are determined for the four different compositions. The aging reaction causes a significant dynamics slowdown, which is correlated to the aggregation of asphaltene molecules in larger and dynamically slower nanoaggregates. Finally, a detailed description of the role of each molecule types in the aggregation and aging processes is given.

  2. Study Abroad: The Reality of Building Dynamic Group Learning.

    Science.gov (United States)

    Ransbury, Molly K.; Harris, Sandra A.

    1994-01-01

    The collaborative effort of a professor of human development with expertise in group process and a general education professor with expertise in Greek mythology and culture uses a case study format to apply theoretical models of group dynamics to the travel and learning experience of study abroad. Implications for course design and group process…

  3. Proton Exchange in a Paramagnetic Chemical Exchange Saturation Transfer Agent from Experimental Studies and ab Initio Metadynamics Simulation.

    Science.gov (United States)

    Pollet, Rodolphe; Bonnet, Célia S; Retailleau, Pascal; Durand, Philippe; Tóth, Éva

    2017-03-27

    The proton-exchange process between water and a carbamate has been studied experimentally and theoretically in a lanthanide-based paramagnetic chemical exchange saturation transfer agent endowed with potential multimodality detection capabilities (optical imaging, or T1 MRI for the Gd(III) analogue). In addition to an in-depth structural analysis by a combined approach (using X-ray crystallography, NMR, and molecular dynamics), our ab initio simulation in aqueous solution sheds light on the reaction mechanism for this proton exchange, which involves structural Grotthuss diffusion.

  4. Chemical imaging of molecular changes in a hydrated single cell by dynamic secondary ion mass spectrometry and super-resolution microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Hua, Xin; Szymanski, Craig J.; Wang, Zhaoying; Zhou, Yufan; Ma, Xiang; Yu, Jiachao; Evans, James E.; Orr, Galya; Liu, Songqin; Zhu, Zihua; Yu, Xiao-Ying

    2016-05-15

    Chemical imaging of single cells is important in capturing biological dynamics. Single cell correlative imaging is realized between structured illumination microscopy (SIM) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) using System for Analysis at the Liquid Vacuum Interface (SALVI), a multimodal microreactor. SIM characterized cells and guided subsequent ToF-SIMS analysis. Dynamic ToF-SIMS provided time- and space-resolved cell molecular mapping. Lipid fragments were identified in the hydrated cell membrane. Principal component analysis was used to elucidate chemical component differences among mouse lung cells that uptake zinc oxide nanoparticles. Our results provided submicron chemical spatial mapping for investigations of cell dynamics at the molecular level.

  5. Structure-function studies of DNA damage using AB INITIO quantum mechanics and molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Miller, J.; Miaskiewicz, K. [Pacific Northwest Lab., Richland, WA (United States); Osman, R. [Mount Sinai School of Medicine, New York, NY (United States). Dept. of Physiology and Biophysics

    1993-12-01

    Studies of ring-saturated pyrimidine base lesions are used to illustrate an integrated modeling approach that combines quantum-chemical calculations with molecular dynamics simulation. Electronic-structure calculations on the lesions in Isolation reveal strong conformational preferences due to interactions between equatorial substituents to the pyrimidine ring. Large distortions of DNA should result when these interactions force the methyl group of thymine to assume an axial orientation, as is the case for thymine glycol but not for dihydrothymine. Molecular dynamics simulations of the dodecamer d(CGCGAATTCGCG){sub 2} with and without a ring-saturated thymine lesion at position T7 support this conclusion. Implications of these studies for recognition of thymine lesions by endonuclease III are also discussed.

  6. Dynamics of IGBT based PWM Converter A Case Study

    Directory of Open Access Journals (Sweden)

    Vijay Shukla

    2012-04-01

    Full Text Available Optimizing the efficiency and dynamics of power converters is a critical tradeoff in power electronics. The increase of switching frequency can improve the dynamics of power converters, but theefficiency may be degraded as well as the switching losses. As power semiconductor devices like diodes, MOSFETS, IGBTs, Thyristors, BJTs have their own characterstics and dynamic responses. It is desired toanalyze and observe the dynamics of different semiconductor devices before they actually employed in the model. Inclusion of different PWM techniques help in the removal of power line interferences like harmonic losses, unwanted ripples, chopped frequencies, spikes. In this paper, we have studied and analyzed the dynamics of IGBT based PWM converter with subjected to different conditions like transient state, steady state feeding the RLC load. Snubber circuits are used to reduce the switching losses. The IGBT based PWM converter reflects the better dynamics with improved efficiency and reduced harmonics as compared to some other power semiconductor devices when FFT is performed and subjected to standard parameterized RLC load understeady state and transient analysis.

  7. Study of dynamics of level of physical preparedness of students.

    Directory of Open Access Journals (Sweden)

    Коvalenko Y.A.

    2010-12-01

    Full Text Available The dynamics of level of physical preparedness of students is studied in the article. A tendency is marked to the decline of level of physical preparedness of students of 1-3 courses. Methodical recommendations are presented on the improvement of the system of organization of physical education of students of the Zaporizhzhya national university. The dynamics of indexes of physical preparedness of students 1, 2, 3 courses of different years of teaching is studied. Principal reasons of decline of level of physical preparedness of students are certain. There are recommendations the department of physical education in relation to physical preparedness of students.

  8. Influence of solid-liquid interactions on dynamic wetting: a molecular dynamics study

    Science.gov (United States)

    Bertrand, Emilie; Blake, Terence D.; De Coninck, Joël

    2009-11-01

    Large-scale molecular dynamics (MD) simulations of liquid drops spreading on a solid substrate have been carried out for a very wide range of solid-liquid interactions and equilibrium contact angles. The results for these systems are shown to be consistent with the molecular-kinetic theory (MKT) of dynamic wetting, which emphasizes the role of contact-line friction as the principal channel of energy dissipation. Several predictions have been confirmed. These include a quantitative link between the dynamics of wetting and the work of adhesion and the existence of an optimum equilibrium contact angle that maximizes the speed of wetting. A feature of the new work is that key parameters (κ0 and λ), normally accessible only by fitting the MKT to dynamic contact angle data, are also obtained directly from the simulations, with good agreement between the two sources. This validates the MKT at some fundamental level. Further verification is provided by contact angle relaxation studies, which also lend support to the interfacial tension relaxation process invoked in Shikhmurzaev's hydrodynamic model of dynamic wetting.

  9. Identifying Enclosed Chemical Reaction and Dynamics at the Molecular Level Using Shell-Isolated Miniaturized Plasmonic Liquid Marble.

    Science.gov (United States)

    Han, Xuemei; Lee, Hiang Kwee; Lee, Yih Hong; Hao, Wei; Liu, Yejing; Phang, In Yee; Li, Shuzhou; Ling, Xing Yi

    2016-04-21

    Current microscale tracking of chemical kinetics is limited to destructive ex situ methods. Here we utilize Ag nanocube-based plasmonic liquid marble (PLM) microreactor for in situ molecular-level identification of reaction dynamics. We exploit the ultrasensitive surface-enhanced Raman scattering (SERS) capability imparted by the plasmonic shell to unravel the mechanism and kinetics of aryl-diazonium surface grafting reaction in situ, using just a 2-μL reaction droplet. This reaction is a robust approach to generate covalently functionalized metallic surfaces, yet its kinetics remain unknown to date. Experiments and simulations jointly uncover a two-step sequential grafting process. An initial Langmuir chemisorption of sulfonicbenzene diazonium (dSB) salt onto Ag surfaces forms an intermediate sulfonicbenzene monolayer (Ag-SB), followed by subsequent autocatalytic multilayer growth of Ag-SB3. Kinetic rate constants reveal 19-fold faster chemisorption than multilayer growth. Our ability to precisely decipher molecular-level reaction dynamics creates opportunities to develop more efficient processes in synthetic chemistry and nanotechnology.

  10. Prediction of the Chapman-Jouguet chemical equilibrium state in a detonation wave from first principles based reactive molecular dynamics.

    Science.gov (United States)

    Guo, Dezhou; Zybin, Sergey V; An, Qi; Goddard, William A; Huang, Fenglei

    2016-01-21

    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 state parameters, providing the means to predict the performance of new materials prior to synthesis and characterization, allowing the simulation based design to be done in silico. Our Rx2CJ method is based on atomistic reactive molecular dynamics (RMD) using the QM-derived ReaxFF force field. We validate this method here by predicting the CJ point and detonation products for three typical energetic materials. We find good agreement between the predicted and experimental detonation velocities, indicating that this method can reliably predict the CJ state using modest levels of computation.

  11. 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 ...

  12. Estimating evolution of δ13CH4 during methanization of cellulosic waste based on stoichiometric chemical reactions, microbial dynamics and stable carbon isotope fractionation.

    Science.gov (United States)

    Vavilin, V A

    2012-04-01

    A change in δ(13)CH(4) during mesophilic methanization of cellulosic waste (paper and cardboard) was described using a mathematical model based on stoichiometric chemical reactions, microbial dynamics and the equation for the (13)C isotope accumulation in products including isotope fractionation. In this study, experimental data, previously obtained by Qu et al. (2009), was used to model metabolic pathways of cellulose transformation. A significant change in δ(13)CH(4) occurred in time during cellulosic waste methanization which was in accordance with the model. It was explained by the change in input of acetoclastic and hydrogenotrophic methanogenesis as well as by fractionation of stable carbon isotopes (13)C and (12)C which was much higher for hydrogenotrophic methanogenesis when compared to acetoclastic methanogenesis.

  13. Interfacial studies of chemical-vapor-infiltrated ceramic matrix composites

    Energy Technology Data Exchange (ETDEWEB)

    Brennan, J.J. (United Technologies Research Center, East Hartford, CT (USA))

    1990-06-15

    The objective of this program was to investigate the fiber-matrix interfacial chemistry in chemical-vapor-infiltrated SiC matrix composites utilizing NICALON SiC and Nextel 400 mullite fibers and how this interface influences composite properties such as strength, toughness and environmental stability. The SiC matrix was deposited using three different reactants: methyldichlorosilane, methyltrichlorosilane and dimethyldichlorosilane. It was found that by varying the reactant gas flow rates, the ratio of carrier gas to reactant gas, the type of carrier gas (hydrogen or argon), the flushing gas used in the reactor prior to deposition (hydrogen or argon) or the type of silane reactant gas used, the composition of the deposited SiC could be varied from very silicon rich (75 at.%) to carbon rich (60%) to almost pure carbon. Stoichiometric SiC was found to bond very strongly to both NICALON and Nextel fibers, resulting in a weak and brittle composite. A thin carbon interfacial layer deposited either deliberately by the decomposition of methane or inadvertently by the introduction of argon into the reactor prior to silane flow resulted in a weakly bonded fiber-matrix interface and strong and tough composites. However, composites with this type of interface were not oxidatively stable. Preliminary results point ot the use of a carbon-rich SiC (mixture of carbon plus SiC) interfacial zone to achieve a relatively weak, crack-deflecting fiber-matrix bond but also exhibiting oxidative stability. (orig.).

  14. Study of Aerosol Chemical Composition Based on Aerosol Optical Properties

    Science.gov (United States)

    Berry, Austin; Aryal, Rudra

    2015-03-01

    We investigated the variation of aerosol absorption optical properties obtained from the CIMEL Sun-Photometer measurements over three years (2012-2014) at three AERONET sites GSFC; MD Science_Center and Tudor Hill, Bermuda. These sites were chosen based on the availability of data and locations that can receive different types of aerosols from land and ocean. These absorption properties, mainly the aerosol absorption angstrom exponent, were analyzed to examine the corresponding aerosol chemical composition. We observed that the retrieved absorption angstrom exponents over the two sites, GSFC and MD Science Center, are near 1 (the theoretical value for black carbon) and with low single scattering albedo values during summer seasons indicating presence of black carbon. Strong variability of aerosol absorption properties were observed over Tudor Hill and will be analyzed based on the air mass embedded from ocean side and land side. We will also present the seasonal variability of these properties based on long-range air mass sources at these three sites. Brent Holben, NASA GSFC, AERONET, Jon Rodriguez.

  15. [Advances in studies on chemical constituents and biological activities of Desmodium species].

    Science.gov (United States)

    Liu, Chao; Wu, Ying; Zhang, Qian-Jun; Kang, Wen-Yi; Zhang, Long; Zhou, Qing-Di

    2013-12-01

    The chemical constituents isolated from Desmodium species (Leguminosae) included terpenoids, flavonoids, steroids, alkaloids compounds. Modem pharmacological studies have showed that the Desmodium species have antioxidant, antibacterial, anti-inflammatory, hepatoprotective, diuretic, antipyretic, analgesic and choleretic activity. This article mainly has reviewed the research advances of chemical constituents and biological activities of Desmodium species since 2003.

  16. Use of terrestrial field studies in the derivation of bioaccumulation potential of chemicals

    NARCIS (Netherlands)

    Brink, van den N.W.; Arblaster, J.A.; Bowman, S.R.; Conder, J.M.; Elliott, J.E.; Johnson, M.S.; Muir, D.C.G.; Natal-da-Luz, Tiago; Rattner, B.A.; Sample, B.E.; Shore, R.F.

    2016-01-01

    Field-based studies are an essential component of research addressing the behavior of organic chemicals, and a unique line of evidence that can be used to assess bioaccumulation potential in chemical registration programs and aid in development of associated laboratory and modeling efforts. To ai

  17. Immunotoxic effects of chemicals: A matrix for occupational and environmental epidemiological studies.

    NARCIS (Netherlands)

    Veraldi, Angela; Costantini, Adele Seniori; Bolejack, Vanessa; Miligi, Lucia; Vineis, Paolo; Loveren, Henk van

    2006-01-01

    BACKGROUND: Many biological and chemical agents have the capacity to alter the way the immune system functions in human and animals. This study evaluates the immunotoxicity of 20 substances used widely in work environments. METHODS: A systematic literature search on the immunotoxicity of 20 chemical

  18. Dynamic Modeling and Plantwide Control of a Hybrid Power and Chemical Plant: An Integrated Gasification Combined Cycle Coupled with a Methanol Plant

    Science.gov (United States)

    Robinson, Patrick J.

    simulators Aspen Plus and Aspen Dynamics. This dissertation first presents a simple approximate method for achieving the objective of having a gasifier model that can be exported into Aspen Dynamics. Limitations in the software dealing with solids make this a necessary task. The basic idea is to use a high molecular weight hydrocarbon that is present in the Aspen library as a pseudo fuel. For many plantwide dynamic studies, a rigorous high-fidelity dynamic model of the gasifier is not needed because its dynamics are very fast and the gasifier gas volume is a relatively small fraction of the total volume of the entire plant. The proposed approximate model captures the essential macro-scale thermal, flow, composition and pressure dynamics. This paper does not attempt to optimize the design or control of gasifiers, but merely presents an idea of how to dynamically simulate coal gasification in an approximate way. This dissertation also presents models of the downstream units of a typical IGCC. Dynamic simulations of the H2S absorption/stripping unit, Water-gas Shift (WGS) reactors, and CO2 absorption/stripping unit are essential for the development of stable and agile plantwide control structures of this hybrid power/chemical plant. Due to the high pressure of the system, hydrogen sulfide is removed by means of physical absorption. SELEXOLRTM (a mixture of the dimethyl ethers of polyethylene glycol) is used to achieve a gas purity of less than 5 ppm H2S. This desulfurized synthesis gas is sent to two water gas shift reactors that convert a total of 99% of carbon monoxide to hydrogen. Physical absorption of carbon dioxide with Selexol produces a hydrogen rich stream (90 mol% H2) to be fed into combustion turbines or to a methanol plant. Steady-state economic designs and plantwide control structures are developed in this dissertation. A steady-state economic design, control structure, and successful turndown of the methanol plant are shown in this dissertation. The Plantwide

  19. Inelastic neutron scattering and lattice dynamics studies in complex solids

    Indian Academy of Sciences (India)

    Mala N Rao; R Mittal; Narayani Choudhury; S L Chaplot

    2004-07-01

    At Trombay, lattice dynamics studies employing coherent inelastic neutron scattering (INS) experiments have been carried out at the two research reactors, CIRUS and Dhruva. While the early work at CIRUS involved many elemental solids and ionic molecular solids, recent experiments at Dhruva have focussed on certain superconductors (cuprates and intermetallics), geophysically important minerals (Al2SiO5, ZrSiO4, MnCO3) and layered halides (BaFCl, ZnCl2). In most of the studies, theoretical modelling of lattice dynamics has played a significant role in the interpretation and analysis of the results from experiments. This talk summarises the developments and current activities in the field of inelastic neutron scattering and lattice dynamics at Trombay.

  20. Chemical equilibria model of strontium-90 adsorption and transport in soil in response to dynamic alkaline conditions.

    Science.gov (United States)

    Spalding, B P; Spalding, I R

    2001-01-15

    Strontium-90 is a major hazardous contaminant of radioactive wastewater and its processing sludges at many Department of Energy (DOE) facilities. In the past, such contaminated wastewater and sludge have been disposed in soil seepage pits, lagoons, or cribs often under highly perturbed alkaline conditions (pH > 12) where 90Sr solubility is low and its adsorption to surrounding soil is high. As natural weathering returns these soils to near-neutral or slightly acidic conditions, the adsorbed and precipitated calcium and magnesium phases, in which 90Sr is carried, change significantly in both nature and amounts. No comprehensive computational method has been formulated previously to quantitatively simulate the dynamics of 90Sr in the soil-groundwater environment under such dynamic and wide-ranging conditions. A computational code, the Hydrologic Utility Model for Demonstrating Integrated Nuclear Geochemical Environmental Responses (HUMDINGER), was composed to describe the changing equilibria of 90Sr in soil based on its causative chemical reactions including soil buffering, pH-dependent cation-exchange capacity, cation selectivity, and the precipitation/dissolution of calcium carbonate, calcium hydroxide, and magnesium hydroxide in response to leaching groundwater characteristics including pH, acid-neutralizing capacity, dissolved cations, and inorganic carbonate species. The code includes a simulation of one-dimensional transport of 90Sr through a soil column as a series of soil mixing cells where the equilibrium soluble output from one cell is applied to the next cell. Unamended soil leaching and highly alkaline soil treatments, including potassium hydroxide, sodium silicate, and sodium aluminate, were simulated and compared with experimental findings using large (10 kg) soil columns that were leached with 90Sr-contaminated groundwater after treatment. HUMDINGER's simulations were in good agreement with dynamic experimental observations of soil exchange capacity

  1. Chemically-specific time-resolved surface photovoltage spectroscopy: Carrier dynamics at the interface of quantum dots attached to a metal oxide

    Science.gov (United States)

    Spencer, Ben F.; Cliffe, Matthew J.; Graham, Darren M.; Hardman, Samantha J. O.; Seddon, Elaine A.; Syres, Karen L.; Thomas, Andrew G.; Sirotti, Fausto; Silly, Mathieu G.; Akhtar, Javeed; O'Brien, Paul; Fairclough, Simon M.; Smith, Jason M.; Chattopadhyay, Swapan; Flavell, Wendy R.

    2015-11-01

    We describe a new experimental pump-probe methodology where a 2D delay-line detector enables fast (ns) monitoring of a narrow XPS spectrum in combination with a continuous pump laser. This has been developed at the TEMPO beamline at Synchrotron SOLEIL to enable the study of systems with intrinsically slow electron dynamics, and to complement faster measurements that use a fs laser as the pump. We demonstrate its use in a time-resolved study of the surface photovoltage of the m-plane ZnO (10 1 bar 0) surface which shows persistent photoconductivity, requiring monitoring periods on ms timescales and longer. We make measurements from this surface in the presence and absence of chemically-linked quantum dots (QDs), using type I PbS and type II CdSe/ZnSe (core/shell) QDs as examples. We monitor signals from both the ZnO substrate and the bound QDs during photoexcitation, yielding evidence for charge injection from the QDs into the ZnO. The chemical specificity of the technique allows us to observe differences in the extent to which the QD systems are influenced by the field of the surface depletion layer at the ZnO surface, which we attribute to differences in the band structure at the interface.

  2. Studying Chemical Reactions, One Bond at a Time, with Single Molecule AFM Techniques

    Science.gov (United States)

    Fernandez, Julio M.

    2008-03-01

    The mechanisms by which mechanical forces regulate the kinetics of a chemical reaction are unknown. In my lecture I will demonstrate how we use single molecule force-clamp spectroscopy and protein engineering to study the effect of force on the kinetics of thiol/disulfide exchange. Reduction of disulfide bond via the thiol/disulfide exchange chemical reaction is crucial in regulating protein function and is of common occurrence in mechanically stressed proteins. While reduction is thought to proceed through a substitution nucleophilic bimolecular (SN2) reaction, the role of a mechanical force in modulating this chemical reaction is unknown. We apply a constant stretching force to single engineered disulfide bonds and measure their rate of reduction by dithiothreitol (DTT). We find that while the reduction rate is linearly dependent on the concentration of DTT, it is exponentially dependent on the applied force, increasing 10-fold over a 300 pN range. This result predicts that the disulfide bond lengthens by 0.34 å at the transition state of the thiol/disulfide exchange reaction. In addition to DTT, we also study the reduction of the engineered disulfide bond by the E. coli enzyme thioredoxin (Trx). Thioredoxins are enzymes that catalyze disulfide bond reduction in all organisms. As before, we apply a mechanical force in the range of 25-450 pN to the engineered disulfide bond substrate and monitor the reduction of these bonds by individual enzymes. In sharp contrast with the data obtained with DTT, we now observe two alternative forms of the catalytic reaction, the first requiring a reorientation of the substrate disulfide bond, causing a shortening of the substrate polypeptide by 0.76±0.07 å, and the second elongating the substrate disulfide bond by 0.21±0.01 å. These results support the view that the Trx active site regulates the geometry of the participating sulfur atoms, with sub-ångström precision, in order to achieve efficient catalysis. Single molecule

  3. Electrical and magnetoresistivity studies in chemical solution deposited La

    Energy Technology Data Exchange (ETDEWEB)

    Angappane, S.; Murugaraj, P.; Sethupathi, K.; Rangarajan, G.; Sastry, V. S.; Chakkaravarthi, A. Arul; Ramasamy, P.

    2001-06-01

    High quality magnetoresistive La{sub (1{minus}x)}Ca{sub x}MnO{sub 3} thin films have been prepared by the chemical solution deposition technique. A solution of propionate precursors of lanthanum, calcium, and manganese in propionic acid was used for this purpose. Films of varying compositions (x varying from 0.1 to 0.4) were spin coated on to LaAlO{sub 3}(100) and SrTiO{sub 3}(100) substrates at room temperature and pyrolyzed in the temperature range 600{endash}850{degree}C. For fixed compositions, annealing at higher temperatures shifts the insulator{endash}metal transition temperature (T{sub I{endash}M}) to higher values accompanied by a reduction in the resistivity values. The T{sub I{endash}M} variation for different x values was found to be less pronounced in the compositions x=0.2, 0.3, and 0.4. Typical T{sub I{endash}M} values of 283 K and 290 K were obtained for La{sub 0.7}Ca{sub 0.3}MnO{sub 3} coated on LaAlO{sub 3} and SrTiO{sub 3} substrates, respectively, when annealed at 850{degree}C. The substrate effect was found to be more pronounced for the x value 0.1 which showed two peaks (one at 271 K and another at 122 K) in the {rho}-T curve. The roles of substrate mismatch, composition variation, and annealing temperatures are discussed. {copyright} 2001 American Institute of Physics.

  4. Femtosecond photodissociation dynamics of I studied by ion imaging

    DEFF Research Database (Denmark)

    Larsen, J.J.; Bjerre, N.; Mørkbak, N.J.;

    1998-01-01

    on imaging is employed to analyze the fragments from timed Coulomb explosion studies of femtosecond (fs) molecular dynamics. The technique provides high detection efficiency and direct recording of the two-dimensional velocity of all ionized fragments. We illustrate the approach by studying...... agreement with quantum mechanical wave packet simulations. We discuss the perspectives for extending the studies to photochemical reactions of small polyatomic molecules...

  5. Femtosecond Transient Absorption Studies in Cadmium Selenide Nanocrystal Thin Films Prepared by Chemical Bath Deposition Method

    Directory of Open Access Journals (Sweden)

    M. C. Rath

    2007-01-01

    Full Text Available Dynamics of photo-excited carrier relaxation processes in cadmium selenide nanocrystal thin films prepared by chemical bath deposition method have been studied by nondegenerate femtosecond transient pump-probe spectroscopy. The carriers were generated by exciting at 400 nm laser light and monitored by several other wavelengths. The induced absorption followed by a fast bleach recovery observed near and above the bandgap indicates that the photo-excited carriers (electrons are first trapped by the available traps and then the trapped electrons absorb the probe light to show a delayed absorption process. The transient decay kinetics was found to be multiexponential in nature. The short time constant, <1 picosecond, was attributed to the trapping of electrons by the surface and/or deep traps and the long time constant, ≥20 picoseconds, was due to the recombination of the trapped carriers. A very little difference in the relaxation processes was observed in the samples prepared at bath temperatures from 25∘C to 60∘C.

  6. Experimental studies of thermal and chemical interactions between oxide and silicide nuclear fuels with water

    Energy Technology Data Exchange (ETDEWEB)

    farahani, A.A.; Corradini, M.L. [Univ. of Wisconsi, Madison, WI (United States)

    1995-09-01

    Given some transient power/cooling mismatch is a nuclear reactor and its inability to establish the necessary core cooling, energetic fuel-coolant interactions (FCI`s commonly called `vapor explosions`) could occur as a result of the core melting and coolant contact. Although a large number of studies have been done on energetic FCI`s, very few experiments have been performed with the actual fuel materials postulated to be produced in severe accidents. Because of the scarcity of well-characterized FCI data for uranium allows in noncommercial reactors (cermet and silicide fuels), we have conducted a series of experiments to provide a data base for the foregoing materials. An existing 1-D shock-tube facility was modified to handle depleted radioactive materials (U{sub 3}O{sub 8}-Al, and U{sub 3}Si{sub 2}-Al). Our objectives have been to determine the effects of the initial fuel composition and temperature and the driving pressure (triggering) on the explosion work output, dynamic pressures, transient temperatures, and the hydrogen production. Experimental results indicate limited energetics, mainly thermal interactions, for these fuel materials as compared to aluminum where more chemical reactions occur between the molten aluminum and water.

  7. Undisclosed chemicals--implications for risk assessment: a case study from the mining industry.

    Science.gov (United States)

    Singh, Khareen; Oates, Christopher; Plant, Jane; Voulvoulis, Nikolaos

    2014-07-01

    Many of the chemicals used in industry can be hazardous to human health and the environment, and some formulations can have undisclosed ingredients and hazards, increasing the uncertainty of the risks posed by their use. The need for a better understanding of the extent of undisclosed information in chemicals arose from collecting data on the hazards and exposures of chemicals used in typical mining operations (copper, platinum and coal). Four main categories of undisclosed chemicals were defined (incomplete disclosure; chemicals with unspecific identities; relative quantities of ingredients not stated; and trade secret ingredients) by reviewing material safety data sheet (MSDS) omissions in previous studies. A significant number of chemicals (20% of 957 different chemicals) across the three sites had a range of undisclosed information, with majority of the chemicals (39%) having unspecific identities. The majority of undisclosed information was found in commercially available motor oils followed by cleaning products and mechanical maintenance products, as opposed to reagents critical to the main mining processes. All three types of chemicals had trade secrets, unspecific chemical identities and incomplete disclosures. These types of undisclosed information pose a hindrance to a full understanding of the hazards, which is made worse when combined with additional MSDS omissions such as acute toxicity endpoints (LD50) and/or acute aquatic toxicity endpoints (LC50), as well as inadequate hazard classifications of ingredients. The communication of the hazard information in the MSDSs varied according to the chemical type, the manufacturer and the regulations governing the MSDSs. Undisclosed information can undermine occupational health protection, compromise the safety of workers in industry, hinder risk assessment procedures and cause uncertainty about future health. It comes down to the duty of care that industries have towards their employees. With a wide range of

  8. Lipid Dynamics Studied by Calculation of 31P Solid-State NMR Spectra Using Ensembles from Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Hansen, Sara Krogh; Vestergaard, Mikkel; Thøgersen, Lea;

    2014-01-01

    We present a method to calculate 31P solid-state NMR spectra based on the dynamic input from extended molecular dynamics (MD) simulations. The dynamic information confered by MD simulations is much more comprehensive than the information provided by traditional NMR dynamics models based on......, for example, order parameters. Therefore, valuable insight into the dynamics of biomolecules may be achieved by the present method. We have applied this method to study the dynamics of lipid bilayers containing the antimicrobial peptide alamethicin, and we show that the calculated 31P spectra obtained...

  9. Bauschinger effect in thin metal films: Discrete dislocation dynamics study

    NARCIS (Netherlands)

    Davoudi, K.M.; Nicola, L.; Vlassak, J.J.

    2014-01-01

    The effects of dislocation climb on plastic deformation during loading and unloading are studied using a two-dimensional discrete dislocation dynamics model. Simulations are performed for polycrystalline thin films passivated on both surfaces. Dislocation climb lowers the overall level of the stress

  10. COMPARISON OF SAMPLING TECHNIQUES USED IN STUDYING LEPIDOPTERA POPULATION DYNAMICS

    Science.gov (United States)

    Four methods (light traps, foliage samples, canvas bands, and gypsy moth egg mass surveys) that are used to study the population dynamics of foliage-feeding Lepidoptera were compared for 10 species, including gypsy moth, Lymantria dispar L. Samples were collected weekly at 12 sit...

  11. Exploring Dynamism in Willingness to Communicate: A Longitudinal Case Study

    Science.gov (United States)

    Cao, Yiqian Katherine

    2013-01-01

    This paper examines dynamism in students' situational willingness to communicate (WTC) within a second language classroom. This longitudinal study involved twelve English as a Second Language (ESL) participants who enrolled in an English for Academic Purposes (EAP) programme in New Zealand for five months. Based on data from classroom…

  12. The dynamics of hydrophobic interaction : A microwave dielectric study

    NARCIS (Netherlands)

    Hallenga, Klaas

    1972-01-01

    To investigate the relation between the structure of liquid water and hydrophobic interaction the dielectric relaxation of water in dilute aqueous solutions has been studied. After an introduction of the problem in which the dynamic aspects of water structure are emphasized, a theoretical analysis o

  13. Quasi-elastic neutron scattering studies of protein dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Rorschach, H.E.

    1991-03-20

    The techniques of X-ray and neutron scattering that have been so successfully applied to the study of the structure of biological macromolecules have in recent years been also used for the study of the thermal motion of these molecules. The diffraction of X-rays has been widely used to investigate the high-frequency motion of the heavy-atom residues of proteins. In these studies, the mean-square thermal amplitudes can be determined from the intensities of the sharp structural lines obtained from single crystals of the hydrated proteins. Similar information can be obtained on lighter atoms from the study of the neutron scattering from single crystals. The results of these measurements are coupled closely to the rapidly developing field of theoretical molecular dynamics which is now being applied to study the dynamics of large biological molecules. This report discusses research in this area.

  14. Ab initio molecular dynamics study of liquid methanol

    CERN Document Server

    Handgraaf, J W; Meijer, E J; Handgraaf, Jan-Willem; Erp, Titus S. van; Meijer, Evert Jan

    2003-01-01

    We present a density-functional theory based molecular-dynamics study of the structural, dynamical, and electronic properties of liquid methanol under ambient conditions. The calculated radial distribution functions involving the oxygen and hydroxyl hydrogen show a pronounced hydrogen bonding and compare well with recent neutron diffraction data, except for an underestimate of the oxygen-oxygen correlation. We observe that, in line with infrared spectroscopic data, the hydroxyl stretching mode is significantly red-shifted in the liquid. A substantial enhancement of the dipole moment is accompanied by significant fluctuations due to thermal motion. Our results provide valuable data for improvement of empirical potentials.

  15. Ultrafast X-ray Studies of Structural Dynamics at SLAC

    Energy Technology Data Exchange (ETDEWEB)

    Gaffney, K.J.; Lindenberg, A.M.; /SLAC, SSRL; Larsson, J.; /Lund Inst. Tech.; Sokolowski-Tinten, K.; /Jena U. /Duisburg U.; Blome, C.; /DESY; Synnergren, O.; /Lund Inst.; Sheppard, J.; /Oxford U.; Reis, D.A.; /Michigan U.; Hastings, J.B.; /SLAC, SSRL

    2005-09-30

    The melting dynamics of laser excited InSb have been studied with femtosecond x-ray diffraction. These measurements demonstrate that the initial stage of crystal disordering results from inertial motion on a laser softened potential energy surface. These inertial dynamics dominate for the first half picosecond following laser excitation, indicating that interatomic forces minimally influence atomic excursions from the equilibrium lattice positions, even for motions in excess of an {angstrom}. This also indicates that the atoms disorder initially without losing memory of their lattice reference.

  16. Chemical Risk Evaluation: A Case Study in an Automotive Air Conditioner Production Facility

    Directory of Open Access Journals (Sweden)

    Tengku Hanidza T.I.

    2010-01-01

    Full Text Available There has been limited knowledge on worker’s exposure to chemicals used in the automotive industries. The purpose of this study is to assess chemical risk and to determine the adequacy of the existing control measures to reduce chemical exposure. A cross sectional survey was conducted in a factory involving installation and servicing of automotive air conditioner units. Qualitative exposure assessment was carried out following the Malaysian Chemical Health Risk Assessment Manual (CHRA. There were 180 employees, 156 workers worked in the production line, which constitutes six work units Tube fin pressed, Brazing, Welding, Final assembly, Piping and Kit II. From the chemical risk evaluation for each work unit, 26 chemical compounds were used. Most of the chemicals were irritants (eye and skin and some were asphyxiants and sensitizers. Based on the work assignment, 93 out of 180 (51.67% of the workers were exposed to chemicals. The highest numbers of workers exposed to chemicals were from the Brazing section (22.22% while the Final Assembly section was the lowest (1.67%. Health survey among the workers showed occurrence of eye irritation, skin irritation, and respiratory irritation, symptoms usually associated with chemical exposure. Using a risk rating matrix, several work process were identified as having ‘significant risk’. For these areas, the workers are at risk of adverse health effects since chemical exposure is not adequately controlled. This study recommends corrective actions be taken in order to control the level of exposure and to provide a safe work environment for workers.

  17. Mixed quantum/semiclassical studies of condensed-phase dynamics and spectroscopy

    Science.gov (United States)

    Cina, Jeffrey A.; Kovac, Philip A.

    We report on theoretical and computational studies of molecular-level chemical dynamics and their time-resolved spectroscopic signatures for small molecules embedded in low-temperature crystalline-host environments. Our calculations are based on a mixed quantum mechanical/semiclassical theory, referred to as the variational fixed vibrational basis/Gaussian bath theory (v-FVB/GB), in which certain optically addressed coordinates driven to large-amplitude motion by laser pulses are treated fully quantum mechanically and a larger number of others executing small-amplitude motion are treated semiclassically. Model systems under investigation incorporate a dihalogen molecule isolated in a symmetrical cluster of rare-gas atoms, with the outer layer of host atoms bound together in a harmonic net that preserves the initial equilibrium structure, but emulates an extended medium by preventing dynamical reconstruction and host-atom evaporation. Supported by the US NSF.

  18. Autoinhibitory mechanisms of ERG studied by molecular dynamics simulations

    Science.gov (United States)

    Lu, Yan; Salsbury, Freddie R.

    2015-01-01

    ERG, an ETS-family transcription factor, acts as a regulator of differentiation of early hematopoietic cells. It contains an autoinhibitory domain, which negatively regulates DNA-binding. The mechanism of autoinhibitory is still illusive. To understand the mechanism, we study the dynamical properties of ERG protein by molecular dynamics simulations. These simulations suggest that DNA binding autoinhibition associates with the internal dynamics of ERG. Specifically, we find that (1), The N-C terminal correlation in the inhibited ERG is larger than that in uninhibited ERG that contributes to the autoinhibition of DNA-binding. (2), DNA-binding changes the property of the N-C terminal correlation from being anti-correlated to correlated, that is, changing the relative direction of the correlated motions and (3), For the Ets-domain specifically, the inhibited and uninhibited forms exhibit essentially the same dynamics, but the binding of the DNA decreases the fluctuation of the Ets-domain. We also find from PCA analysis that the three systems, even with quite different dynamics, do have highly similar free energy surfaces, indicating that they share similar conformations.

  19. A study of dynamic filtration; Um estudo sobre filtracao dinamica

    Energy Technology Data Exchange (ETDEWEB)

    Girao, Joaquim Helder S. [PETROBRAS, Natal, RN (Brazil). Distrito de Perfuracao da Bacia Potiguar. Div. de Tecnicas de Perfuracao

    1989-12-31

    The problems that cause cost increase such as: formation damage and borehole swelling or caving lead us to study the filtration of the liquid part of formation drilling fluid. With the aim of comparing static and dynamic filtration rates, we developed a modest dynamic filtration equipment, consisting of a modified API filter, connected to reservoir by means of a positive injection pump. We carried out various tests, and the results were set in charts and tables. Through these, it is possible to notice how the static and dynamic filtration curves come apart for a same pressure value. We also evaluated the effects of circulation speed, starch concentration and counter pressure. This paper does not include calculations or mathematical models accounting for filtrate invasion radii, but it demonstrates, for example, that cleaning circulation will cause lower filtration rates at lower flows. (author) 5 refs., 11 figs., 14 tabs.

  20. Effect of temperature, pressure, and cosolvents on structural and dynamic properties of the hydration shell of SNase: a molecular dynamics computer simulation study.

    Science.gov (United States)

    Smolin, Nikolai; Winter, Roland

    2008-01-24

    It is now generally agreed that the hydration water and solvational properties play a crucial role in determining the dynamics and hence the functionality of proteins. We present molecular dynamics computer simulation studies on staphylococcal nuclease (SNase) at various temperatures and pressures as well as in different cosolvent solutions containing various concentrations of urea and glycerol. The aim is to provide a molecular level understanding of how different types of cosolvents (chaotropic and kosmotropic) as well as temperature and high hydrostatic pressure modify the structure and dynamics of the hydration water. Taken together, these three intrinsic thermodynamic variables, temperature, pressure, and chemical potential (or activity) of the solvent, are able to influence the stability and function of the protein by protein-solvent dynamic coupling in different ways. A detailed analysis of the structural and dynamical properties of the water and cosolvents at the protein surface (density profile, coordination numbers, hydrogen-bond distribution, average H-bond lifetimes (water-protein and water-water), and average residence time of water in the hydration shell) was carried out, and differences in the structural and dynamical properties of the hydration water in the presence of the different cosolvents and at temperatures between 300 and 400 K and pressures up to 5000 bar are discussed. Furthermore, the results obtained help understand various thermodynamic properties measured for the protein.

  1. Surface variations affecting human dental enamel studied using nanomechanical and chemical analysis

    Science.gov (United States)

    Dickinson, Michelle Emma

    The enamel surface is the interface between the tooth and its ever changing oral environment. Cavity (caries) formation and extrinsic tooth staining are due, respectively, to degradation of the enamel structure under low pH conditions and interactions between salivary pellicle and dietary elements. Both of these occur at the enamel surface and are caused by the local environment changing the chemistry of the surface. The results can be detrimental to the enamel's mechanical integrity and aesthetics. Incipient carious lesions are the precursor to caries and form due to demineralisation of enamel. These carious lesions are a reversible structure where ions (e.g. Ca2+, F -) can diffuse in (remineralisation) to preserve the tooth's structural integrity. This investigation used controlled in vitro demineralisation and remineralisation to study artificial carious lesion formation and repair. The carious lesions were cross-sectioned and characterised using nanoindentation, electron probe micro-analysis and time of flight secondary ion mass spectrometry. Mechanical and chemical maps showed the carious lesion had a significantly reduced hardness and elastic modulus, and the calcium and phosphate content was lower than in sound enamel. Fluoride based remineralisation treatments gave a new phase (possibly fluorohydroxyapatite) within the lesion with mechanical properties higher than sound enamel. The acquired salivary pellicle is a protein-rich film formed by the physisorption of organic molecules in saliva onto the enamel surface. Its functions include lubrication during mastication and chemical protection. However, pellicle proteins react with dietary elements such as polyphenols (tannins in tea) causing a brown stain. This study has used in vitro dynamic nanoindentation and atomic force microscopy to examine normal and stained pellicles formed in vivo. The effects of polyphenols on the pellicle's mechanical properties and morphology have been studied. It was found that the

  2. Model reduction for dynamic real-time optimization of chemical processes

    NARCIS (Netherlands)

    Van den Berg, J.

    2005-01-01

    The value of models in process industries becomes apparent in practice and literature where numerous successful applications are reported. Process models are being used for optimal plant design, simulation studies, for off-line and online process optimization. For online optimization applications th

  3. Non-allergic cutaneous reactions in airborne chemical sensitivity--a population based study

    DEFF Research Database (Denmark)

    Berg, Nikolaj Drimer; Linneberg, Allan; Thyssen, Jacob Pontoppidan;

    2011-01-01

    Multiple chemical sensitivity (MCS) is characterised by adverse effects due to exposure to low levels of chemical substances. The aetiology is unknown, but chemical related respiratory symptoms have been found associated with positive patch test. The purpose of this study was to investigate...... the relationship between cutaneous reactions from patch testing and self-reported severity of chemical sensitivity to common airborne chemicals. A total of 3460 individuals participating in a general health examination, Health 2006, were patch tested with allergens from the European standard series and screened...... sensitivity. Associations were controlled for the possible confounding effects of sex, age, asthma, eczema, atopic dermatitis, psychological and social factors, and smoking habits. In unadjusted analyses we found associations between allergic and non-allergic cutaneous reactions on patch testing and the two...

  4. Chemical Study of the Essential Oil of Mutisia Friesiana

    Directory of Open Access Journals (Sweden)

    J. De la Fuente

    2000-03-01

    Full Text Available The composition of essential oil of Mutisia friesiana (Asteracae was studied. The oil is a complex system in which 127 compounds were identified. The major components are monoterpenes: b-phellandrene, (Z-β-ocimene, α and β-pinene and sabinene.

  5. Using chemical approaches to study selenoproteins - focus on thioredoxin reductases

    OpenAIRE

    Hondal, Robert J.

    2009-01-01

    The study of selenocysteine-containing proteins is difficult due to the problems associated with the heterologous production of these proteins. These problems are due to the intricate recoding mechanism used by cells to translate the UGA codon as a sense codon for selenocysteine. The process is further complicated by the fact that eukaryotes and prokaryotes have different UGA recoding machineries.

  6. Dynamic CT head phantom for perfusion and angiography studies

    Science.gov (United States)

    Russell, K.; Blazeski, A.; Dannecker, K.; Lee, Q. Y.; Holscher, C.; Donahue, C.; van Kampen, W.

    2010-03-01

    Contrast imaging is a compelling enhancement for the portable, flat panel-based brain CT scanner currently under development at Xoran. Due to the relative low temporal resolution of flat panel detectors, enabling tomographic imaging on such platform requires optimizing the imaging and injection protocols. A dynamic CT head phantom was designed to facilitate this task. The Dynamic Perfusion and Angiography Model (PAM), mimics tissue attenuation in CT images, provides physiological timing for angiography and perfusion studies, and moves fluid with properties similar to those of blood. The design consists of an arterial system, which contains bifurcating vessels that feed into perfusion chambers, mimicking blood flow through capillaries and smaller vessels, and a venous system, which is symmetrical to the arterial side and drains the perfusion chambers. The variation of geometry and flow rate in the phantom provides the physiological total time that fluid spends in the head, and the difference in material densities correlates to CT numbers for biological tissues. This paper discusses the design of Dynamic PAM and shows experimental results demonstrating its ability to realistically simulate blood flow. Results of dynamic imaging studies of the phantom are also presented.

  7. Chemical gas-dynamics beyond Wang Chang-Uhlenbeck's kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Kolesnichenko, Evgeniy G. [Gas Kinetics Lab, Moscow State University, Institute for Mechanics, Moscow, 117192 (Russian Federation); Gorbachev, Yuriy E. [Research Department, Coddan Technologies LLC, St. Petersburg, 197342 (Russian Federation)

    2014-12-09

    Wang Chang-Uhlenbeck equation does not give possibility to take into account intermolecular processes such as redistribution of the energy among different degrees of freedom. The modification of the generalized Wang Chang-Uhlenbeck equation including such processes is proposed. It allows to study for instance the kinetics of non-radiative transitions. Limitations of this approach are connected with the requirements of absence of polarization of rotational momentum and phases of intermolecular vibrations.

  8. Study of dynamic strain aging in dual phase steel

    Energy Technology Data Exchange (ETDEWEB)

    Queiroz, R.R.U. [Instituto Federal de Minas Gerais. Rua Pandia Calogeras, 898, Bauxita, Ouro Preto, MG (Brazil); Cunha, F.G.G. [Department of Metallurgical and Materials Engineering, Universidade Federal de Minas Gerais, Av. Antonio Carlos, 6627, Pampulha, Belo Horizonte, MG (Brazil); Gonzalez, B.M., E-mail: gonzalez@demet.ufmg.br [Department of Metallurgical and Materials Engineering, Universidade Federal de Minas Gerais, Av. Antonio Carlos, 6627, Pampulha, Belo Horizonte, MG (Brazil)

    2012-05-01

    Highlights: Black-Right-Pointing-Pointer Characterization of the high temperature mechanical behavior of a dual phase steel. Black-Right-Pointing-Pointer Determination of the effect of dynamic strain aging on the strain hardening rate. Black-Right-Pointing-Pointer Identification of the mechanism associated with dynamic strain aging. Black-Right-Pointing-Pointer The value of the interaction energy carbon-dislocation in ferrite was confirmed. - Abstract: The susceptibility to dynamic strain aging of a dual phase steel was evaluated by the variation of mechanical properties in tension with the temperature and the strain rate. The tensile tests were performed at temperatures varying between 25 Degree-Sign C and 600 Degree-Sign C and at strain rates ranging from 10{sup -2} to 5 Multiplication-Sign 10{sup -4} s{sup -1}. The studied steel presented typical manifestations related to dynamic strain aging: serrated flow (the Portevin-Le Chatelier effect) for certain combinations of temperature and strain rates; the presence of a plateau in the variation of yield stress with temperature; a maximum in the curves of tensile strength, flow stress, and work hardening exponent as a function of temperature; and a minimum in the variation of total elongation with temperature. The determined apparent activation energy values, associated with the beginning of the Portevin-Le Chatelier effect and the maximum in the variation of flow stress with temperature, were 83 kJ/mol and 156 kJ/mol, respectively. These values suggest that the mechanism responsible for dynamic strain aging in the dual phase steel is the locking of dislocations by carbon atoms in ferrite and that the formation of clusters and/or transition carbides and carbide precipitation in martensite do not interfere with the dynamic strain aging process.

  9. Physico-Chemical Studies of the Pvc K+ - Selective Membrane

    Directory of Open Access Journals (Sweden)

    Ana COROIAN

    2002-12-01

    Full Text Available A plasticized ion-selective membrane based on PVC matrix which tricrezylphosphate (TCP and containing K+ - ionophores (dibenzo-18-crown-6 and decyl-18-crown-6 was used to obtain a potentiometric potassium sensor. The potassium selective membranes were characterized in terms of their electrochemical and physical properties, surface morphology and structural parameters. The a.c. impedance, UV/VIS analysis of the membranes was also studied.

  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. Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci.

    Directory of Open Access Journals (Sweden)

    Christopher L Schardl

    Full Text Available The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species, which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some-including the infamous ergot alkaloids-have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne, and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species, a morning-glory symbiont (Periglandula ipomoeae, and a bamboo pathogen (Aciculosporium take, and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories

  12. Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci.

    Science.gov (United States)

    Schardl, Christopher L; Young, Carolyn A; Hesse, Uljana; Amyotte, Stefan G; Andreeva, Kalina; Calie, Patrick J; Fleetwood, Damien J; Haws, David C; Moore, Neil; Oeser, Birgitt; Panaccione, Daniel G; Schweri, Kathryn K; Voisey, Christine R; Farman, Mark L; Jaromczyk, Jerzy W; Roe, Bruce A; O'Sullivan, Donal M; Scott, Barry; Tudzynski, Paul; An, Zhiqiang; Arnaoudova, Elissaveta G; Bullock, Charles T; Charlton, Nikki D; Chen, Li; Cox, Murray; Dinkins, Randy D; Florea, Simona; Glenn, Anthony E; Gordon, Anna; Güldener, Ulrich; Harris, Daniel R; Hollin, Walter; Jaromczyk, Jolanta; Johnson, Richard D; Khan, Anar K; Leistner, Eckhard; Leuchtmann, Adrian; Li, Chunjie; Liu, JinGe; Liu, Jinze; Liu, Miao; Mace, Wade; Machado, Caroline; Nagabhyru, Padmaja; Pan, Juan; Schmid, Jan; Sugawara, Koya; Steiner, Ulrike; Takach, Johanna E; Tanaka, Eiji; Webb, Jennifer S; Wilson, Ella V; Wiseman, Jennifer L; Yoshida, Ruriko; Zeng, Zheng

    2013-01-01

    The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some-including the infamous ergot alkaloids-have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the

  13. Chemical Dynamics of State-Selected Atomic and Diatomic Ions of Aerospace Relevance

    Science.gov (United States)

    2008-11-01

    modified the triple - quadrupole -double-octopole y<t&te Cy» LJMW • • Figure 1. Schematic diagram of the comprehensive VUV laser system, which...H. Xu, and C. Y. Ng, "The Study of State-Selected Ion-Molecule Reactions using the Pulsed-Field Ionization- Photoion Technique ", J. Chem. Phys...8217==0-4) + He collisions in the ET range of 0-3 eV have also been measured using the VUV-photoionization-guided-ion beam mass spectrometric technique

  14. The interplay between dynamic heterogeneities and structure of bulk liquid water: A molecular dynamics simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Demontis, Pierfranco; Suffritti, Giuseppe B. [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Gulín-González, Jorge [Grupo de Matemática y Física Computacionales, Universidad de las Ciencias Informáticas (UCI), Carretera a San Antonio de los Baños, Km 21/2, La Lisa, La Habana (Cuba); Masia, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Istituto Officina dei Materiali del CNR, UOS SLACS, Via Vienna 2, 07100 Sassari (Italy); Sant, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy)

    2015-06-28

    In order to study the interplay between dynamical heterogeneities and structural properties of bulk liquid water in the temperature range 130–350 K, thus including the supercooled regime, we use the explicit trend of the distribution functions of some molecular properties, namely, the rotational relaxation constants, the atomic mean-square displacements, the relaxation of the cross correlation functions between the linear and squared displacements of H and O atoms of each molecule, the tetrahedral order parameter q and, finally, the number of nearest neighbors (NNs) and of hydrogen bonds (HBs) per molecule. Two different potentials are considered: TIP4P-Ew and a model developed in this laboratory for the study of nanoconfined water. The results are similar for the dynamical properties, but are markedly different for the structural characteristics. In particular, for temperatures higher than that of the dynamic crossover between “fragile” (at higher temperatures) and “strong” (at lower temperatures) liquid behaviors detected around 207 K, the rotational relaxation of supercooled water appears to be remarkably homogeneous. However, the structural parameters (number of NNs and of HBs, as well as q) do not show homogeneous distributions, and these distributions are different for the two water models. Another dynamic crossover between “fragile” (at lower temperatures) and “strong” (at higher temperatures) liquid behaviors, corresponding to the one found experimentally at T{sup ∗} ∼ 315 ± 5 K, was spotted at T{sup ∗} ∼ 283 K and T{sup ∗} ∼ 276 K for the TIP4P-Ew and the model developed in this laboratory, respectively. It was detected from the trend of Arrhenius plots of dynamic quantities and from the onset of a further heterogeneity in the rotational relaxation. To our best knowledge, it is the first time that this dynamical crossover is detected in computer simulations of bulk water. On the basis of the simulation results, the possible

  15. Modelling of Mass Transfer Phenomena in Chemical and Biochemical Reactor Systems using Computational Fluid Dynamics

    DEFF Research Database (Denmark)

    Larsson, Hilde Kristina

    are subsequently evaluated based on their applicability in the four case studies. The evaluations especially focus on the impact of the choice of turbulence model and other modelling decisions made by the user. The conclusion is that CFD is a highly valuable tool for modelling several important parameters...... are presented as well as the theory behind the SST and the k-ε turbulence models. Modelling of additional variables, porous materials and twophase flows are also introduced. The two-phase flows are modelled using the Euler-Euler method, and both dispersed and free-surface flows are simulated. The importance...... of mass transfer with a focus on mixing, gas-liquid transfer of oxygen, and heterogeneous reactor systems is reviewed and mathematical models for these applications are presented. A review of how these mass transfer phenomena have been modelled in the scientific literature is also included. The models...

  16. Nonequilibrium dynamics of active matter with correlated noise: A dynamical renormalization group study

    Science.gov (United States)

    Kachan, Devin; Levine, Alex; Bruinsma, Robijn

    2014-03-01

    Biology is rife with examples of active materials - soft matter systems driven into nonequilibrium steady states by energy input at the micro scale. For example, solutions of active micron scale swimmers produce active fluids showing phenomena reminiscent of turbulent convection at low Reynolds number; cytoskeletal networks driven by endogenous molecular motors produce active solids whose mechanics and low frequency strain fluctuations depend sensitively on motor activity. One hallmark of these systems is that they are driven at the micro scale by temporally correlated forces. In this talk, we study how correlated noise at the micro scale leads to novel long wavelength and long time scale dynamics at the macro scale in a simple model system. Specifically, we study the fluctuations of a ϕ4 scalar field obeying model A dynamics and driven by noise with a finite correlation time τ. We show that the effective dynamical system at long length and time scales is driven by white noise with a renormalized amplitude and renormalized transport coefficients. We discuss the implications of this result for a broad class of active matter systems driven at the micro scale by colored noise.

  17. Study on New Approaches for extended chemical management and REACH

    DEFF Research Database (Denmark)

    Lee, Jihyun

    2014-01-01

    , additional analysis has been performed. The analysis of the current mass flow of plastics and paper in Europe shows that with the recycling of 60% of paper and 26% of plastic wastes, approximately 4% to 18% of the above mentioned phthalates are re-entering the product cycle through recycling. Moreover......, a case study on the childhood phthalate exposures from food packaging made from recycled materials, and a simulation of the flows of phthalates in 2020 - under the assumption that the recycling rate of plastic and paper products will increase with the full implementation of EU waste legislations by 2020...... - have been performed. Even under the 50% reduction of phthalates production, the increased recycling rate of plastic and paper in 2020 might lead to an increase of unwanted recycling of DEHP and BBP to 110 and 40% respectively, while recycling of DBP will decrease by 15%. The results demonstrate...

  18. Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation

    DEFF Research Database (Denmark)

    Wedberg, Nils Hejle Rasmus Ingemar; Abildskov, Jens; Peters, Günther H.J.

    2012-01-01

    In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method...... relies on determining the water content of the bulk phase and uses a combination of Kirkwood−Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents...... methanol, tert-butyl alcohol, methyl tert-butyl ether, and hexane, each mixture at five different water activities. It is shown that similar water activity yields similar enzyme hydration in the different solvents. However, both solvent and water activity are shown to have profound effects on enzyme...

  19. Role of conical intersections in molecular spectroscopy and photoinduced chemical dynamics.

    Science.gov (United States)

    Domcke, Wolfgang; Yarkony, David R

    2012-01-01

    This review describes how conical intersections affect measured molecular spectra and simple photofragmentation processes. We consider excitations that result in electron ejection, that is, photoionization or photodetachment, as well as photoinduced H-atom elimination. Section 1 presents a brief overview of the history of conical intersections and their rise from an arcane theoretical concept to a major paradigm in nonadiabatic chemistry. In Section 2, the generic properties of conical intersections are discussed, as well as their characterization with modern electronic-structure methods. Section 3 briefly discusses computational tools used to compute the nuclear motion involving conical intersections. Section 4 describes how the ideas of Sections 2 and 3 are combined to simulate molecular spectra impacted by conical intersections. Section 5 describes selected recent experimental and computational studies of photoelectron, photodetachment, and photofragment spectra. Rather than providing an encyclopedic bibliography of the previous and current literature, we illustrate significant problems currently being addressed and describe what can be accomplished with current computational techniques and how these results are achieved. Section 6 suggests future directions in this field.

  20. Chemical dynamics of acidity and heavy metals in a mine water-polluted soil during decontamination using clean water.

    Science.gov (United States)

    Chen, A; Lin, C; Lu, W; Ma, Y; Bai, Y; Chen, H; Li, J

    2010-03-15

    A column leaching experiment was conducted to investigate the chemical dynamics of the percolating water and washed soil during decontamination of an acidic mine water-polluted soil. The results show that leaching of the contaminated soil with clean water rapidly reduced soluble acidity and ion concentrations in the soils. However, only water over a long period of time. During the column leaching, dissolved Cu and Pb were rapidly leached out, followed by mobilization of colloidal Cu and Pb from the exchangeable and the oxide-bound fractions as a result of reduced ionic strength in the soil solution. The soluble Fe contained in the soil was rare, probably because the soil pH was not sufficiently low; marked mobility of colloidal Fe took place after the ionic strength of the percolating water was weakened and the mobilized Fe was mainly derived from iron oxides. In contrast with Cu, Pb and Fe, the concentration of leachate Zn and Mn showed a continuously decreasing trend during the entire period of the experiment.