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Sample records for molecular level processes

  1. Molecular-Level Processes Governing the Interaction of Contaminants with Iron and Manganese Oxides - Final Report

    Brown Jr., G. E.; Chambers, S. A.

    1999-10-31

    Many of the inorganic and organic contaminants present in sediments at DOE sites can be altered or destroyed by reduction and oxidation (redox) reactions occurring at mineral surfaces. A fundamental understanding of such redox processes provided by molecular-level studies on structurally and compositionally well-defined mineral surfaces will lead to: (i) improved models of contaminant fate and transport in geochemical systems, and (ii) optimized manipulation of these processes for remediation purposes. To contribute to this understanding, we will study, both experimentally and theoretically, redox processes involving three important contaminants - chromate ion, carbon tetrachloride, and trichloroethene TCE, on the following iron and manganese oxides - hematite, magnetite, maghemite, and pyrolusite. These oxides and their hydroxylated analogs commonly occur as coatings on minerals or as interfaces in the subsurface environment. Single-crystal surfaces of these oxides will be synthesized in carefully controlled fashion by molecular beam epitaxy. These surfaces, as well as high surface are powdered samples of these oxides, will be used in spectroscopic and kinetic experiments in both aqueous and gas phases. Our goal is to identify products and to determine the kinetics and mechanisms of surface-catalyzed redox reaction of Cr(VI) and CR(III), and the reductive dechlorination of carbon tetrachloride and TCE. The combination of theory and experiment will provide the base information needed to scale from the molecular level to the microscopic grain level minerals.

  2. Molecular Processes Studied at a Single-Molecule Level Using DNA Origami Nanostructures and Atomic Force Microscopy

    Ilko Bald

    2014-09-01

    Full Text Available DNA origami nanostructures allow for the arrangement of different functionalities such as proteins, specific DNA structures, nanoparticles, and various chemical modifications with unprecedented precision. The arranged functional entities can be visualized by atomic force microscopy (AFM which enables the study of molecular processes at a single-molecular level. Examples comprise the investigation of chemical reactions, electron-induced bond breaking, enzymatic binding and cleavage events, and conformational transitions in DNA. In this paper, we provide an overview of the advances achieved in the field of single-molecule investigations by applying atomic force microscopy to functionalized DNA origami substrates.

  3. Molecular-Level Processes Governing the Interaction of Contaminants with Iron and Manganese Oxides - Final Report; FINAL

    Many of the inorganic and organic contaminants present in sediments at DOE sites can be altered or destroyed by reduction and oxidation (redox) reactions occurring at mineral surfaces. A fundamental understanding of such redox processes provided by molecular-level studies on structurally and compositionally well-defined mineral surfaces will lead to: (i) improved models of contaminant fate and transport in geochemical systems, and (ii) optimized manipulation of these processes for remediation purposes. To contribute to this understanding, we will study, both experimentally and theoretically, redox processes involving three important contaminants - chromate ion, carbon tetrachloride, and trichloroethene TCE, on the following iron and manganese oxides - hematite, magnetite, maghemite, and pyrolusite. These oxides and their hydroxylated analogs commonly occur as coatings on minerals or as interfaces in the subsurface environment. Single-crystal surfaces of these oxides will be synthesized in carefully controlled fashion by molecular beam epitaxy. These surfaces, as well as high surface are powdered samples of these oxides, will be used in spectroscopic and kinetic experiments in both aqueous and gas phases. Our goal is to identify products and to determine the kinetics and mechanisms of surface-catalyzed redox reaction of Cr(VI) and CR(III), and the reductive dechlorination of carbon tetrachloride and TCE. The combination of theory and experiment will provide the base information needed to scale from the molecular level to the microscopic grain level minerals

  4. Insights into surface–adsorbate interactions in corrosion inhibition processes at the molecular level

    Graphical abstract: The interaction of 2-((3-methylpyridine-2-imino)methyl)phenol (MPIMP) with the Fe(1 1 0) surface was clarified at the molecular level using density functional theory (DFT). Highlights: •2-((3-Methylpyridine-2-imino)methyl)phenol was tested as a corrosion inhibitor. •Its interaction with the surface was characterized using density functional theory. •Three stable adsorption configurations on Fe(1 1 0) surface were identified. -- Abstract: 2-((3-Methylpyridine-2-imino)methyl)phenol (MPIMP) was investigated as a potential corrosion inhibitor for mild steel in 0.5 M HCl solution using impedance spectroscopy (IS). Changes in impedance parameters indicated that adsorption of MPIMP occurred on the mild steel surface. Three stable adsorption configurations for MPIMP on the Fe(1 1 0) surface were identified as a result of geometry optimization starting from several adsorption geometries using density functional theory (DFT). Involvement of the delocalized π-electrons of the aromatic rings in the interaction provides extra stabilization to the flat adsorption configurations

  5. Molecular level energy and electron transfer processes at nanocrystalline titanium dioxide interfaces

    Farzad, Fereshteh

    This thesis describes photo-induced molecular electron and energy transfer processes occurring at nanocrystalline semiconductor interfaces. The Introductory Chapter provides background and describes how these materials may be useful for solar energy conversion. In Chapter 2, results describing excitation of Ru(deeb)(bpy)2 2+, bis(2,2'-bipyridine)(2,2'-bipyridine-4,4 '-diethylester)ruthenium(II) hexafluorophosphate, bound to nanocrystalline TiO2 thin films, immersed in an acetonitrile bath are presented. The data indicates that light excitation forms predominately long-lived metal-to-ligand charge-transfer, MLCT, excited states under these conditions. Modeling of the data as a function of irradiance has been accomplished assuming parallel unimolecular and bimolecular excited state deactivation processes. The quantum yield for excited state formation depends on the excitation irradiance, consistent with triplet-triplet annihilation processes that occur with k > 1 x 108 s-1. Chapter 3 extends the work described in Chapter 2 to LiClO4 acetonitrile solutions. Li+ addition results in a red shift in the MLCT absorption and photoluminescence, PL, and a concentration dependent quenching of the PL intensity on TiO2. The Li+ induced spectroscopic changes were found to be reversible by varying the electrolyte composition. A second-order kinetic model quantified charge recombination transients. A model is proposed wherein Li+ ion adsorption stabilizes TiO2 acceptor states resulting in energetically more favorable interfacial electron transfer. The photophysical and photoelectrochemical properties of porous nanocrystalline anatase TiO2 electrodes modified with Ru(deeb)(bpy)2 2+, Os(deeb)(bpy)22+, and mixtures of both are described in Chapters 4 and 5. In regenerative solar cells with 0.5 M LiI/0.05 M I2 acetonitrile electrolyte, both compounds efficiently inject electrons into TiO2 producing monochromatic incident photon-to-current efficiencies (IPCE), IPCE (460 nm) = 0.70 + 0

  6. Excited states structure and processes: Understanding organic light-emitting diodes at the molecular level

    Photo- or electro-excited states in polyatomic molecules, aggregates, and conjugated polymers are at the center of organic light-emitting diodes (OLEDs). These can decay radiatively or non-radiatively, determining the luminescence quantum efficiency of molecular materials. According to Kasha’s rule, light-emission is dictated by the lowest-lying excited state. For conjugated polymers, the electron correlation effect can lead the lowest-lying excited state to the even-parity 2Ag state which is non-emissive. To understand the nature of the low-lying excited state structure, we developed the density matrix renormalization group (DMRG) theory and its symmetrization scheme for quantum chemistry applied to calculate the excited states structure. We found there are three types of 1Bu/2Ag crossover behaviors: with electron correlation strength U, with bond length alternation, and with conjugation length. These directly influence the light-emitting property. For the electro-excitation, carriers (electron and hole) are injected independently, forming both singlet and triplet excited bound states with statistically 25% and 75% portions, respectively. We found that the exciton formation rate can depend on spin manifold, and for conjugated polymers, the singlet exciton can have larger formation rate leading to the internal electroluminescence quantum efficiency larger than the 25% spin statistical limit. It is originated from the interchain electron correlation as well as intrachain lattice relaxation. For the dipole allowed emissive state, the radiative decay process via either spontaneous emission or stimulated emission can be computed from electronic structure plus vibronic couplings. The challenging issue lies in the non-radiative decay via non-adiabatic coupling and/or spin–orbit coupling. We developed a unified correlation function formalism for the excited state radiative and non-radiative decay rates. We emphasized the low-frequency mode mixing (Duschinsky rotation

  7. Mathematical model and calculation algorithm of micro and meso levels of separation process of gaseous mixtures in molecular sieves

    Umarova, Zhanat; Botayeva, Saule; Yegenova, Aliya; Usenova, Aisaule [South Kazakhstan State University, 5, Tauke Khan Avenue, 160012 Shymkent (Kazakhstan)

    2015-05-15

    In the given article, the main thermodynamic aspects of the issue of modeling diffusion transfer in molecular sieves have been formulated. Dissipation function is used as a basic notion. The differential equation, connecting volume flow with the change of the concentration of catchable component has been derived. As a result, the expression for changing the concentration of the catchable component and the coefficient of membrane detecting has been received. As well, the system approach to describing the process of gases separation in ultra porous membranes has been realized and micro and meso-levels of mathematical modeling have been distinguished. The non-ideality of the shared system is primarily taken into consideration at the micro-level and the departure from the diffusion law of Fick has been taken into account. The calculation method of selectivity considering fractal structure of membranes has been developed at the meso level. The calculation algorithm and its software implementation have been suggested.

  8. Mathematical model and calculation algorithm of micro and meso levels of separation process of gaseous mixtures in molecular sieves

    Umarova, Zhanat; Botayeva, Saule; Yegenova, Aliya; Usenova, Aisaule

    2015-05-01

    In the given article, the main thermodynamic aspects of the issue of modeling diffusion transfer in molecular sieves have been formulated. Dissipation function is used as a basic notion. The differential equation, connecting volume flow with the change of the concentration of catchable component has been derived. As a result, the expression for changing the concentration of the catchable component and the coefficient of membrane detecting has been received. As well, the system approach to describing the process of gases separation in ultra porous membranes has been realized and micro and meso-levels of mathematical modeling have been distinguished. The non-ideality of the shared system is primarily taken into consideration at the micro-level and the departure from the diffusion law of Fick has been taken into account. The calculation method of selectivity considering fractal structure of membranes has been developed at the meso level. The calculation algorithm and its software implementation have been suggested.

  9. Probing ice-nucleation processes on the molecular level using second harmonic generation spectroscopy

    A. Abdelmonem

    2015-05-01

    Full Text Available We present and characterize a novel setup to apply Second Harmonic Generation (SHG spectroscopy in total internal reflection geometry (TIR to heterogeneous freezing research. It allows to monitor the evolution of water structuring at solid surfaces at low temperatures prior to heterogeneous ice nucleation. Apart from the possibility of investigating temperature dependence, a major novelty in our setup is the ability of measuring sheet-like samples in TIR geometry in a direct way. As a main experimental result, we find that our method can discriminate between good and poor ice nucleating surfaces. While at the sapphire basal plane, which is known to be a poor ice nucleator, no structural rearrangement of the water molecules is found prior to freezing, the basal plane surface of mica, an analogue to ice active mineral dust surfaces, exhibits a strong change in the nonlinear optical properties at temperatures well above the freezing transition. This is interpreted as a pre-activation, i.e. an increase in the local ordering of the interfacial water which is expected to facilitate the crystallization of ice at the surface. The results are in line with recent predictions by Molecular Dynamics simulations on a similar system.

  10. Identification of light absorbing oligomers from glyoxal and methylglyoxal aqueous processing: a comparative study at the molecular level

    Finessi, Emanuela; Hamilton, Jacqueline; Rickard, Andrew; Baeza-Romero, Maria; Healy, Robert; Peppe, Salvatore; Adams, Tom; Daniels, Mark; Ball, Stephen; Goodall, Iain; Monks, Paul; Borras, Esther; Munoz, Amalia

    2014-05-01

    Numerous studies point to the reactive uptake of gaseous low molecular weight carbonyls onto atmospheric waters (clouds/fog droplets and wet aerosols) as an important SOA formation route not yet included in current models. However, the evaluation of these processes is challenging because water provides a medium for a complex array of reactions to take place such as self-oligomerization, aldol condensation and Maillard-type browning reactions in the presence of ammonium salts. In addition to adding to SOA mass, aqueous chemistry products have been shown to include light absorbing, surface-active and high molecular weight oligomeric species, and can therefore affect climatically relevant aerosol properties such as light absorption and hygroscopicity. Glyoxal (GLY) and methylglyoxal (MGLY) are the gaseous carbonyls that have perhaps received the most attention to date owing to their ubiquity, abundance and reactivity in water, with the majority of studies focussing on bulk physical properties. However, very little is known at the molecular level, in particular for MGLY, and the relative potential of these species as aqueous SOA precursors in ambient air is still unclear. We have conducted experiments with both laboratory solutions and chamber-generated particles to simulate the aqueous processing of GLY and MGLY with ammonium sulphate (AS) under typical atmospheric conditions and investigated their respective aging products. Both high performance liquid chromatography coupled with UV-Vis detection and ion trap mass spectrometry (HPLC-DAD-MSn) and high resolution mass spectrometry (FTICRMS) have been used for molecular identification purposes. Comprehensive gas chromatography with nitrogen chemiluminescence detection (GCxGC-NCD) has been applied for the first time to these systems, revealing a surprisingly high number of nitrogen-containing organics (ONs), with a large extent of polarities. GCxGC-NCD proved to be a valuable tool to determine overall amount and rates of

  11. Mechanical and electrical properties of carbon nanotube/Cu nanocomposites by molecular-level mixing and controlled oxidation process.

    Lim, Byung K; Mo, Chan B; Nam, Dong H; Hong, Soon H

    2010-01-01

    A molecular-level mixing and controlled oxidation process is proposed as a novel fabrication technique for the production of CNT/Cu nanocomposite powders. The fabricated CNT/Cu2O nanocomposite powders showed microstructures with homogeneous dispersion of implanted CNTs in a Cu2O matrix. The CNT/Cu2O nanocomposite powders were reduced to CNT/Cu nanocomposite powders with H2 gas and then the as-prepared CNT/Cu nanocomposite powders were spark plasma sintered to fabricate CNT/Cu nanocomposites. The mechanical properties of the Cu and the CNT/Cu nanocomposites were characterized by tensile testing before and after hot compression. Before hot compression, the CNT/Cu nanocomposites were brittle, but after hot compression both yield strength and elongation were increased, while the yield strength of the Cu was decreased after hot compression. Hot compression enhanced the ductility and strength of the CNT/Cu nanocomposites due to alignment of Cu grains and CNTs. Electrical conductivity was also enhanced due to a reduced scattering of electrons because of the alignment of the CNTs and Cu grains as well as the annealing effects of the Cu matrix. PMID:20352814

  12. Water interactions with condensed organic phases: a combined experimental and theoretical study of molecular-level processes

    Johansson, Sofia M.; Kong, Xiangrui; Thomson, Erik S.; Papagiannakopoulos, Panos; Pettersson, Jan B. C.; Lovrić, Josip; Toubin, Céline

    2016-04-01

    Water uptake on aerosol particles modifies their chemistry and microphysics with important implications for air quality and climate. A large fraction of the atmospheric aerosol consists of organic aerosol particles or inorganic particles with condensed organic components. Here, we combine laboratory studies using the environmental molecular beam (EMB) method1 with molecular dynamics (MD) simulations to characterize water interactions with organic surfaces in detail. The over-arching aim is to characterize the mechanisms that govern water uptake, in order to guide the development of physics-based models to be used in atmospheric modelling. The EMB method enables molecular level studies of interactions between gases and volatile surfaces at near ambient pressure,1 and the technique may provide information about collision dynamics, surface and bulk accommodation, desorption and diffusion kinetics. Molecular dynamics simulations provide complementary information about the collision dynamics and initial interactions between gas molecules and the condensed phase. Here, we focus on water interactions with condensed alcohol phases that serve as highly simplified proxies for systems in the environment. Gas-surface collisions are in general found to be highly inelastic and result in efficient surface accommodation of water molecules. As a consequence, surface accommodation of water can be safely assumed to be close to unity under typical ambient conditions. Bulk accommodation is inefficient on solid alcohol and the condensed materials appear to produce hydrophobic surface structures, with limited opportunities for adsorbed water to form hydrogen bonds with surface molecules. Accommodation is significantly more efficient on the dynamic liquid alcohol surfaces. The results for n-butanol (BuOH) are particularly intriguing where substantial changes in water accommodation taking place over a 10 K interval below and above the BuOH melting point.2 The governing mechanisms for the

  13. Design of structure of zeolitic catalysts on a molecular level as a key to highly effective industrial processes

    Sazama, Petr; Wichterlová, Blanka; Dědeček, Jiří; Tvarůžková, Zdenka; Sathu, Naveen Kumar; Kreibich, Viktor; Sobalík, Zdeněk

    Prague: J. Heyrovský Institute of Physical Chemistry of the ASCR, v.v.i, 2011 - (Horáček, M.). P5 ISBN 978-80-87351-14-7. [Czech-Italian-Spanish Symposium on Molecular Sieves and Catalysis /4./. 15.06.2011-18.06.2011, Liblice] Institutional research plan: CEZ:AV0Z40400503 Keywords : zeolites * ZSM-5 Subject RIV: CF - Physical ; Theoretical Chemistry

  14. Photodissociation processes in molecular beams

    A description is presented of a study of the photodissociation dynamics of molecules in a molecular beam. Photo-fragmentation translational spectroscopy has been utilized to observe the photodissociation dynamics of ozone. Using a supersonic molecular beam and a 10 nanosecond pulsed laser at lambda = 266 nm, the velocities of the fragment products are measured by the method of time of flight. The resolution of the time of flight spectrum of ozone is sufficiently high that the electronic and vibrational states are clearly resolved and identified. Above the threshold (lambda 1D) has been estimated in the past to be unity for the process O3 (1A1) + hν)lambda 3(1B2) → O2(1Δ/sub g/) + O(1D). However a small production of O2 (3Σ/sub g/-) + O(3P) has been observed in this study. The O2(1Δ/sub g/) product yields four vibrational states (v = 0, 1, 2, 3) which yields a vibrational temperature of 27000K along with narrow energy distributions of rotational levels. These energy distributions are compared with photodissociation models along with the polarization dependence of the dissociative process which was also measured. 143 references

  15. Atomic and molecular collision processes

    530Accomplishments during the course of a 44-month program of code development and high precision calculations for electron collisions with atoms, atomic ions, and molecules are summarized. In electron-atom and -ion collisions, we were primarily concerned with the fundamental physics of the process that controls excitation in high temperature plasmas. In the molecular work, we pursued the development of techniques for accurate calculations of ro-vibrational excitation of polyatomic molecules, to the modeling of gas-phase laser systems. Highlights from the seven technical paper published as a result of this contract include: The resolution of a long history of unexplained anomalies and experimental/theoretical discrepancies by a demonstration that the Coulomb phase must be included in scattering amplitudes for electron-ion collisions. Definitive close-coupling calculations of cross sections for electron impact excitation of Be+, using a very elaborate expansion for the collision system and inclusion of both one- and two-body terms for the effect of core polarization. Detailed state-of-the-art calculations for electron-impact excitation of the sodium-like ion A ell 2+ that included core-polarization interactions, and which also produced new data on bound-state energy levels for the magnesium-like ion A ell + and oscillator strengths for A ell 2+. Partial cross sections for excitation of the 3p level of sodium at energies just above threshold calculated using a four-state close-coupling approach, including both total cross sections and those for excitation as a function of the change in the spin and orbital angular momentum projection quantum numbers of the target electron. Generalization of our electron-molecule scattering code to carry out full vibrational close-coupling calculations with an exact treatment of exchange and with a parameter-free representation of correlation and polarization interactions, and application to HF and H2

  16. Multiscale Simulation Starting at the Molecular Level for Adsorption Process Development%用于吸附过程开发的从分子水平级开始的多尺度模拟

    Hae-Jeong Son; Young-il Lim

    2008-01-01

    This article presents a multiscale simulation approach starting at the molecular level for the adsorption process development. A grand canonical Monte Carlo method is used for the prediction of adsorption is otherms ofmethanol on an activated carbon at the molecular level. The adsorption isotherms obtained in the linear region (or adsorption constant) are exploited as a model parameter required for the adsorption process simulation. The adsorp-tion process model described by a set of partial differential equations (PDEs) is solved by using the conservation element and solution element method, which produces a fast and an accurate numerical solution to PDEs. The simulation results obtained from the adsorption constant estimated at the molecular level are in good agreement with the experimental results of the pulse response. The systematical multiscale simulation approach addressed in this study may be useful to accelerate the adsorption process development by reducing the number of experiments.

  17. Quantum Control of Molecular Processes

    Shapiro, Moshe

    2012-01-01

    Written by two of the world's leading researchers in the field, this is a systematic introduction to the fundamental principles of coherent control, and to the underlying physics and chemistry.This fully updated second edition is enhanced by 80% and covers the latest techniques and applications, including nanostructures, attosecond processes, optical control of chirality, and weak and strong field quantum control. Developments and challenges in decoherence-sensitive condensed phase control as well as in bimolecular control are clearly described.Indispensable for atomic, molecular and chemical

  18. Changes of anabolic processes at the cellular and molecular level in chronic wounds under topical negative pressure can be revealed by transcriptome analysis

    Leffler, Mareike; Derrick, Kathleen L.; McNulty, Amy; Malsiner, Caye; Dragu, Adrian; Horch, Raymund E.

    2011-01-01

    Abstract Chronic wounds – as defined by the World Union of Wound Healing Societies (WUWHS) – are a considerable worldwide health care expense and impair quality of life. In order for chronic wounds to heal, these wounds must be transformed to a more acute state to begin the healing process. Topical negative pressure (TNP) with reticulated open cell foam (ROCF) is known to promote healing in certain types of chronic wounds. However, little is known about changes at the cellular or molecular le...

  19. Discrete atomic layers at the molecular level

    In this review, we deal with the syntheses of large discrete atomic layers at the molecular level. Spectroscopic measurements as well as X-ray crystallographic analyses lead to unambiguous characterizations of these layers. The molecular atomic layers can be considered to be parts of graphenes and related atomic layers, thereby helping to understand such indefinitely huge atomic layers or serving as seeds for the controlled synthesis of nanocarbons. (author)

  20. Dynamical processes in atomic and molecular physics

    Ogurtsov, Gennadi

    2012-01-01

    Atomic and molecular physics underlie a basis for our knowledge of fundamental processes in nature and technology and in such applications as solid state physics, chemistry and biology. In recent years, atomic and molecular physics has undergone a revolutionary change due to great achievements in computing and experimental techniques. As a result, it has become possible to obtain information both on atomic and molecular characteristics and on dynamics of atomic and molecular processes. This e-book highlights the present state of investigations in the field of atomic and molecular physics. Rece

  1. Atomic and molecular processes in fusion plasmas

    Janev, R.K. [International Atomic Energy Agency, Vienna (Austria)

    1997-01-01

    The role of atomic and molecular processes in achieving and maintaining the conditions for thermonuclear burn in a magnetically confined fusion plasma is described. Emphasis is given to the energy balance and power and particle exhaust issues. The most important atomic and molecular processes which affect the radiation losses and impurity transport in the core plasma, the neutral particle transport in the plasma edge and the radiative cooling of divertor plasmas are discussed in greater detail. (author)

  2. Designing an university-level module on molecular imaging chemistry

    training in radiopharmacy both in theory and hands-on practice. Final-year radiology students in Polytechnic have to go through a series of lectures on radiopharmacy and also practicals in hospital radiopharmacy laboratory. But due to the Government's initiatives on biomedical industries and also due to a global trend, interest in bio/medical imaging is rising among scientists and students. There is a need to fulfil this demand by introducing new course or modules at the University level. Designing an university-level module on molecular imaging chemistry: In National University of Singapore, a graduate student (MSc and PhD) level 5 module on ''Medical Imaging'' has already been introduced and a new module on ''Molecular Imaging Chemistry'' will be introduced soon. A module of this kind should serve as a link between chemistry, molecular imaging and clinical application with emphasis on chemical probe design. And should introduce contemporary topics and emerging concepts in chemistry related to molecular imaging. A brief introduction on different modalities of molecular imaging and principles of biomedical imaging should be introduced including principles of medical imaging equipment. How this knowledge will direct the chemical synthesis should be highlighted (lead directed synthesis). There should be a coverage on pharmacology and drug discovery process as imaging probes could be considered as drugs. Here is an example of an outline for such module: - Introduction: - What is molecular imaging? - Why molecular imaging? - What is biomedical imaging? - Different modalities of molecular imaging; - Different types of molecular imaging; - In vitro, ex vivo, in vivo imaging; Drug discovery process; - Pharmacological basis. Molecular Imaging Chemistry: - general construct of imaging probe (molecular reporter system); - Bioimaging factors influencing chemical probe synthesis; Optical imaging probes; - Radioimaging probes; - MR contrast agents; - Probes for other modalities, X ray

  3. Understanding diseases at a molecular level

    Rosev, Tatjana K [Los Alamos National Laboratory

    2008-01-01

    A group of scientists at Los Alamos National Laboratory in 2008 successfully pioneered a microscope able to track protein-sized, hard to see particles in three dimensions. The 3D Tracking Microscope, designed and developed by James H. Werner, Guillaume A. Lessard, Nathan Wells and Peter M. Goodwin of LANL's Center for Integrated Nanotechnologies, won a 2008 R&D 100 award. The team's invention is a unique confocal 3D tracking microscope capable of following the motion of nanometer-sized objects, such as individual molecules, quantum dots, organic fluorophores and single green fluorescent proteins as they zoom through three-dimensional space at rates faster than many intracellular transport processes. The 3D tracking microscope can follow the transport of nanometer-sized particles at micrometer per second rates. This enables researchers to follow individual protein, ribonucleic acid (RNA), or deoxyribonucleic acid (DNA) motion throughout the full three-dimensional volume of a cell to discover the path a particular biomolecule takes, the method it employs to get there and the specific proteins it may be interacting with along the way. In addition to applications in molecular spectroscopy and materials research, the 3D tracking microscope is a powerful tool primarily in the fields of cellular biology and biomedical research, Werner said. 'The 3D tracking microscope will advance our understanding of the molecular basis and kinetics of many diseases, such as cancer, diabetes, or muscular dystrophy,' he said. 'We anticipate the microscope will become a valuable weapon in the arsenal of biomedical researchers who are fighting to find cures for cancer, heart disease and other protein or DNA-based diseases.'

  4. Soy protein isolate molecular level contributions to bulk adhesive properties

    Shera, Jeanne Norton

    Increasing environmental awareness and the recognized health hazards of formaldehyde-based resins has prompted a strong demand for environmentally-responsible adhesives for wood composites. Soy protein-based adhesives have been shown to be commercially viable with 90-day shelf stability and composite physical properties comparable to those of commercial formaldehyde-based particleboards. The main research focus is to isolate and characterize the molecular level features in soy protein isolate responsible for providing mechanical properties, storage stability, and water resistance during adhesive formulation, processing, and wood composite fabrication. Commercial composite board will be reviewed to enhance our understanding of the individual components and processes required for particleboard production. The levels of protein structure will be defined and an overview of current bio-based technology will be presented. In the process, the logic for utilizing soy protein as a sole binder in the adhesive will be reinforced. Variables such as adhesive components, pH, divalent ions, blend aging, protein molecular weight, formulation solids content, and soy protein functionalization will relate the bulk properties of soy protein adhesives to the molecular configuration of the soybean protein. This work has demonstrated that when intermolecular beta-sheet interactions and protein long-range order is disrupted, viscosity and mechanical properties decrease. Storage stability can be maintained through the stabilization of intermolecular beta-sheet interactions. When molecular weight is reduced through enzymatic digestion, long-range order is disrupted and viscosity and mechanical properties decrease accordingly. Processibility and physical properties must be balanced to increase solids while maintaining low viscosity, desirable mechanical properties, and adequate storage stability. The structure of the soybean protein must be related to the particleboard bulk mechanical

  5. Bibliography of atomic and molecular processes, 1983

    This annotated bibliography includes papers on atomic and molecular processes published during 1983. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

  6. 1982 bibliography of atomic and molecular processes

    This annotated bibliography includes papers on atomic and molecular processes published during 1982. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

  7. 1978 bibliography of atomic and molecular processes

    This annotated bibliography lists 2557 works on atomic and molecular processes reported in publications dated 1978. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors

  8. 1982 bibliography of atomic and molecular processes

    Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.; Gregory, D.C.; Kirkpatrick, M.I.; McDaniel, E.W.; McKnight, R.H.; Meyer, F.W.; Morgan, T.J.; Phaneuf, R.A. (comps.)

    1984-05-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1982. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  9. Bibliography of atomic and molecular processes, 1983

    Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.; Gregory, D.C.; Kirkpatrick, M.I.; McDaniel, E.W.; McKnight, R.H.; Meyer, F.W.; Morgan, T.J.; Phaneuf, R.A. (comps.)

    1984-10-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1983. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  10. 1984 Bibliography of atomic and molecular processes

    Barnett, C.F.; Gilbody, H.B.; Gregory, D.C.; Griffin, P.M.; Havener, C.C.; Howard, A.M.; Kirkpatrick, M.I.; McDaniel, E.W.; Meyer, F.W.; Morgan, T.J. (comps.)

    1985-04-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1984. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  11. 1985 bibliography of atomic and molecular processes

    This annotated bibliography includes papers on atomic and molecular processes published during 1985. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

  12. 1985 bibliography of atomic and molecular processes

    Barnett, C.F.; Gilbody, H.B.; Gregory, D.C.; Griffin, P.M.; Havener, C.C.; Howald, A.M.; Kirkpatrick, M.I.; McDaniel, E.W.; Meyer, F.W.; Morgan, T.J. (comps.)

    1986-06-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1985. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  13. 1979 bibliography of atomic and molecular processes

    This annotated bibliography lists 2146 works on atomic and molecular processes reported in publications dated 1979. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory, to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors

  14. 1984 Bibliography of atomic and molecular processes

    This annotated bibliography includes papers on atomic and molecular processes published during 1984. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

  15. 1980 bibliography of atomic and molecular processes

    This annotated bibliography lists 2866 works on atomic and molecular processes reported in publications dated 1980. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory, to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors

  16. Systemic structural modular generalization of the crystallography of bound water applied to study the mechanisms of processes in biosystems at the atomic and molecular level

    The main reasons of the modern scientific revolution, one of the consequences of which are nanotechnologies and the development of interdisciplinary overall natural science (which can build potentially possible atomic structures and study the mechanisms of the processes occurring in them), are considered. The unifying role of crystallography in the accumulation of interdisciplinary knowledge is demonstrated. This generalization of crystallography requires the introduction of a new concept: a module which reflects the universal condition for stability of all real and potential and equilibrium and nonequilibrium structures of matter (their connectivity). A modular generalization of crystallography covers all forms of solids, including the structure of bound water (a system-forming matrix for the self-organization and morphogenesis of hierarchical biosystems which determines the metric selection of all other structural components of these systems). A dynamic model of the water surface layer, which serves as a matrix in the formation of Langmuir monolayers and plays a key role in the occurrence of life on the Earth, is developed.

  17. Quantum mechanics of molecular rate processes

    Levine, Raphael D

    1999-01-01

    This survey of applications of the theory of collisions and rate processes to molecular problems explores collisions of molecules with internal structure, generalized Ehrenfest theorem, theory of reactive collisions, and role of symmetry. It also reviews partitioning technique, equivalent potentials and quasibound states, theory of direct reactions, more. 1969 edition.

  18. Radiation damage at the molecular level: Nanodosimetry

    One of the main practical use of the model is its use as a tool of nanodosimetry which basically consists in characterizing the effect of radiation on nano volumes (comparable to the DNA of volumes) in terms of link breaks and molecular dissociations. (Author)

  19. Levels of Processing in Mild Disabilities.

    Al-Hilawani, Yasser A.; And Others

    This study examined the effects of the second level (intermediate acoustical processing of rhyming words) and the third level (deep-semantic processing of words in sentences) of the "levels of processing" framework on memory performance of four types of intermediate-grade students (52 "normal" students, 50 students with learning disabilities, 25…

  20. Mirror symmetry breaking at the molecular level.

    Avetisov, V; Goldanskii, V.

    1996-01-01

    Reasoning from two basic principles of molecular physics, P invariance of electromagnetic interaction and the second law of thermodynamics, one would conclude that mirror symmetry retained in the world of chiral molecules. This inference is fully consistent with what is observed in inorganic nature. However, in the bioorganic world, the reverse is true. Mirror symmetry there is definitely broken. Is it possible to account for this phenomenon without going beyond conventional concepts of the k...

  1. Molecular dynamics simulations using graphics processing units

    Baker, J.A.; Hirst, J.D.

    2011-01-01

    It is increasingly easy to develop software that exploits Graphics Processing Units (GPUs). The molecular dynamics simulation community has embraced this recent opportunity. Herein, we outline the current approaches that exploit this technology. In the context of biomolecular simulations, we discuss some of the algorithms that have been implemented and some of the aspects that distinguish the GPU from previous parallel environments. The ubiquity of GPUs and the ingenuity of the simulation com...

  2. A model for processivity of molecular motors

    Xie Ping; Dou Shuo-Xing; Wang Peng-Ye

    2004-01-01

    We propose a two-dimensional model for a complete description of the dynamics of molecular motors, including both the processive movement along track filaments and the dissociation from the filaments. Theoretical results on the distributions of the run length and dwell time at a given adenosine triphosphate (ATP) concentration, the dependences of mean run length, mean dwell time and mean velocity on ATP concentration and load are in good agreement with the previous experimental results.

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

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

    2008-01-01

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

  4. Uncovering molecular processes in crystal nucleation and growth by using molecular simulation.

    Anwar, Jamshed; Zahn, Dirk

    2011-02-25

    Exploring nucleation processes by molecular simulation provides a mechanistic understanding at the atomic level and also enables kinetic and thermodynamic quantities to be estimated. However, whilst the potential for modeling crystal nucleation and growth processes is immense, there are specific technical challenges to modeling. In general, rare events, such as nucleation cannot be simulated using a direct "brute force" molecular dynamics approach. The limited time and length scales that are accessible by conventional molecular dynamics simulations have inspired a number of advances to tackle problems that were considered outside the scope of molecular simulation. While general insights and features could be explored from efficient generic models, new methods paved the way to realistic crystal nucleation scenarios. The association of single ions in solvent environments, the mechanisms of motif formation, ripening reactions, and the self-organization of nanocrystals can now be investigated at the molecular level. The analysis of interactions with growth-controlling additives gives a new understanding of functionalized nanocrystals and the precipitation of composite materials. PMID:21271625

  5. Plasma detachment with molecular processes in divertor plasmas

    Molecular processes in detached recombining plasmas are briefly reviewed. Several reactions with vibrationally excited hydrogen molecule related to recombination processes are described. Experimental evidence of molecular activated recombination observed in a linear divertor plasma simulator is also shown. (author)

  6. Optical processes in OLEDs: Molecular photonics

    Flaemmich, Michael; Michaelis, Dirk; Danz, Norbert [Fraunhofer Institute for Applied Optics and Precision Engineering, 07745 Jena (Germany)

    2011-07-01

    Following the OLED display market take-off, huge world wide efforts are spent to develop OLEDs towards competitive sources for general lighting applications. In this context, the light outcoupling problem is well known as the key parameter to improve OLED efficiency in order to tackle existing lighting schemes. From the optical point of view, the device performance is driven (i) by the architecture of the OLEDs layered system and (ii) by the internal features of the emissive material. Studies in recent years have shown that the latter attributes (which are the internal electroluminescence spectrum, the profile of the emission zone, the orientation of the transition dipole moments and the internal luminescence quantum efficiency q) can be determined in situ by measurements of the far-field emission pattern generated by active OLEDs (i.e. in electrical operation) and corresponding optical reverse simulations. Starting from basic considerations of the dipole radiation characteristics, we elaborate specifically how the orientation distribution of the dipole transition moments in the layered system can be analyzed in situ, providing insight into the internal photo-physical processes on the molecular scale of the emitter.

  7. Level crossings and other level functionals of stationary Gaussian processes

    Kratz, Marie F.

    2006-01-01

    This paper presents a synthesis on the mathematical work done on level crossings of stationary Gaussian processes, with some extensions. The main results [(factorial) moments, representation into the Wiener Chaos, asymptotic results, rate of convergence, local time and number of crossings] are described, as well as the different approaches [normal comparison method, Rice method, Stein-Chen method, a general $m$-dependent method] used to obtain them; these methods are also very useful in the g...

  8. Biodiversity at the Ecosystem Level - Patterns and Processes

    levels of organization? How may GBIF (Global Biodiversity Information Facility) deal with ecosystem level data and informatics? The conference had two important goals. The first was to present an overview of contemporary research related to ecosystem level biodiversity and the second was to help GBIF......This publication contains the presentations and discussions from the second DanBIF conference, entitled Biodiversity at the Ecosystem Level – Patterns and Processes. The questions asked at this conference were: What is biodiversity at the ecosystem level? How is it related to biodiversity at other...... formulate a strategy for dealing with biodiversity above the species and molecular levels and make data available for the end-users....

  9. Towards an upper level ontology for molecular biology.

    Schulz, Stefan; Beisswanger, Elena; Wermter, Joachim; Hahn, Udo

    2006-01-01

    There is a growing need for the general-purpose description of the basic conceptual entities in the life sciences. Up until now, upper level models have mainly been purpose-driven, such as the GENIA ontology, originally devised as a vocabulary for corpus annotation. As an alternative,we here present BioTop, a description-logic-based top level ontology for molecular biology, which we consider as an ontologically conscious redesign of the GENIA ontology. PMID:17238430

  10. Towards an Upper-Level Ontology for Molecular Biology

    Schulz, Stefan; Beisswanger, Elena; Wermter, Joachim; Hahn, Udo

    2006-01-01

    There is a growing need for the general-purpose description of the basic ontological entities in the life sciences domain. Up until now, upper-level models are mainly purpose-driven, such as the GENIA ontology, originally devised as a vocabulary for corpus annotation. As an alternative, we here present BioTop, a description-logic-based top-level ontology for molecular biology, as an ontologically more conscious re-design of the GENIA ontology.

  11. Features, Events, and Processes: system Level

    The purpose of this analysis report is to evaluate and document the inclusion or exclusion of the system-level features, events, and processes (FEPs) with respect to modeling used to support the total system performance assessment for the license application (TSPA-LA). A screening decision, either Included or Excluded, is given for each FEP along with the technical basis for screening decisions. This information is required by the U.S. Nuclear Regulatory Commission (NRC) at 10 CFR 63.113 (d, e, and f) (DIRS 156605). The system-level FEPs addressed in this report typically are overarching in nature, rather than being focused on a particular process or subsystem. As a result, they are best dealt with at the system level rather than addressed within supporting process-level or subsystem-level analyses and models reports. The system-level FEPs also tend to be directly addressed by regulations, guidance documents, or assumptions listed in the regulations; or are addressed in background information used in development of the regulations. For included FEPs, this analysis summarizes the implementation of the FEP in the TSPA-LA (i.e., how the FEP is included). For excluded FEPs, this analysis provides the technical basis for exclusion from the TSPA-LA (i.e., why the FEP is excluded). The initial version of this report (Revision 00) was developed to support the total system performance assessment for site recommendation (TSPA-SR). This revision addresses the license application (LA) FEP List (DIRS 170760)

  12. Features, Events, and Processes: system Level

    D. McGregor

    2004-10-15

    The purpose of this analysis report is to evaluate and document the inclusion or exclusion of the system-level features, events, and processes (FEPs) with respect to modeling used to support the total system performance assessment for the license application (TSPA-LA). A screening decision, either Included or Excluded, is given for each FEP along with the technical basis for screening decisions. This information is required by the U.S. Nuclear Regulatory Commission (NRC) at 10 CFR 63.113 (d, e, and f) (DIRS 156605). The system-level FEPs addressed in this report typically are overarching in nature, rather than being focused on a particular process or subsystem. As a result, they are best dealt with at the system level rather than addressed within supporting process-level or subsystem-level analyses and models reports. The system-level FEPs also tend to be directly addressed by regulations, guidance documents, or assumptions listed in the regulations; or are addressed in background information used in development of the regulations. For included FEPs, this analysis summarizes the implementation of the FEP in the TSPA-LA (i.e., how the FEP is included). For excluded FEPs, this analysis provides the technical basis for exclusion from the TSPA-LA (i.e., why the FEP is excluded). The initial version of this report (Revision 00) was developed to support the total system performance assessment for site recommendation (TSPA-SR). This revision addresses the license application (LA) FEP List (DIRS 170760).

  13. A Process Calculus for Molecular Interaction Maps

    Roberto Barbuti; Andrea Maggiolo-Schettini; Paolo Milazzo; Giovanni Pardini; Aureliano Rama

    2009-01-01

    We present the MIM calculus, a modeling formalism with a strong biological basis, which provides biologically-meaningful operators for representing the interaction capabilities of molecular species. The operators of the calculus are inspired by the reaction symbols used in Molecular Interaction Maps (MIMs), a diagrammatic notation used by biologists. Models of the calculus can be easily derived from MIM diagrams, for which an unambiguous and executable interpretation is thus obtained. We give...

  14. Nanoparticles of copper stimulate angiogenesis at systemic and molecular level.

    Mroczek-Sosnowska, Natalia; Sawosz, Ewa; Vadalasetty, Krishna Prasad; Łukasiewicz, Monika; Niemiec, Jan; Wierzbicki, Mateusz; Kutwin, Marta; Jaworski, Sławomir; Chwalibog, André

    2015-01-01

    Copper is a key element affecting blood vessel growth and muscle development. However, the ions released from Cu salts are toxic. Given their specific physicochemical properties, nanoparticles of Cu (NanoCu) may have different bioactivity and affect the development of blood vessel and muscles in a different manner than Cu salts. The objective of the study was to evaluate the influence of NanoCu on embryo development and angiogenesis at the systemic and molecular level, in experiments using a chick embryo model. Fertilized chicken eggs were divided into a control group, and groups injected with a placebo, CuSO4 or NanoCu. Embryo development at the whole body level and molecular indices using an embryo chorioallantoic membrane model were measured during embryogenesis. The present study indicated for the first time that NanoCu have pro-angiogenic properties at the systemic level, to a greater degree than CuSO4 salt. The properties of NanoCu were confirmed at the molecular level, demonstrating significant effects on mRNA concentration and on mRNA gene expression of all pro-angiogenic and pro-proliferative genes measured herein. PMID:25741768

  15. Nanoparticles of Copper Stimulate Angiogenesis at Systemic and Molecular Level

    Natalia Mroczek-Sosnowska

    2015-03-01

    Full Text Available Copper is a key element affecting blood vessel growth and muscle development. However, the ions released from Cu salts are toxic. Given their specific physicochemical properties, nanoparticles of Cu (NanoCu may have different bioactivity and affect the development of blood vessel and muscles in a different manner than Cu salts. The objective of the study was to evaluate the influence of NanoCu on embryo development and angiogenesis at the systemic and molecular level, in experiments using a chick embryo model. Fertilized chicken eggs were divided into a control group, and groups injected with a placebo, CuSO4 or NanoCu. Embryo development at the whole body level and molecular indices using an embryo chorioallantoic membrane model were measured during embryogenesis. The present study indicated for the first time that NanoCu have pro-angiogenic properties at the systemic level, to a greater degree than CuSO4 salt. The properties of NanoCu were confirmed at the molecular level, demonstrating significant effects on mRNA concentration and on mRNA gene expression of all pro-angiogenic and pro-proliferative genes measured herein.

  16. Wafer level 3-D ICs process technology

    Tan, Chuan Seng; Reif, L Rafael

    2009-01-01

    This book focuses on foundry-based process technology that enables the fabrication of 3-D ICs. The core of the book discusses the technology platform for pre-packaging wafer lever 3-D ICs. However, this book does not include a detailed discussion of 3-D ICs design and 3-D packaging. This is an edited book based on chapters contributed by various experts in the field of wafer-level 3-D ICs process technology. They are from academia, research labs and industry.

  17. Wiped-Film Molecular Distillation Process

    LI Guobing; ZHANG Xubin; XU Chunjian; ZHOU Ming

    2005-01-01

    Based on the Bhatnagar-Gross-Krook equation, a new scheme of wiped-film molecular distillation for two components in the presenceof inert gas is developed. The equations in the scheme are solved numerically by the method of finite difference and iteration. The new scheme is used to simulate the molecular distillation of dibutyl phthalate and dibutyl sebacate (DBP-DBS) mixture. The effects of the inert gas pressure, the distance between the evaporation surface and condensation surface, the rotation rate of blade, and the number of blades on the distillation rate and separation factor are discussed.

  18. The level of motivation process in company

    HAVLÍČKOVÁ, Eliška

    2014-01-01

    The aim of this diploma thesis is to analyze and assess the level of the motivation process in the company Elektrárny Opatovice, a.s. This thesis is divided into two sections, theoretical and practial. The theoretical section, contains literature data related to management and motivation. Information expressed in the theoretical section, is based on literature contained in the literature review. In the practical section, information is applied from the theoretical section. Concurrently, there...

  19. Molecular-level investigation on electrochemical interfaces by Raman spectroscopy

    TIAN, Zhong-Qun; REN, Bin

    2000-01-01

    The structure and dynamics of electrode/liquid interfaces play an increasingly important role in electrochemistry. Raman spectroscopy is capable of providing detailed structural information at molecular level and new insight into the interfacial structure, adsorption, reaction, electrocatalysis and corrosion. In this account we will summarize some progresses of surface Raman spectroscopy in the study of electrochemical interfaces, mainly based on our group's work, laying emphasis on the detection sensitivity, spectral resolution, time resolution and spatial resolution as well as the hyphenated technique.

  20. Multi-level molecular modelling for plasma medicine

    Modelling at the molecular or atomic scale can be very useful for obtaining a better insight in plasma medicine. This paper gives an overview of different atomic/molecular scale modelling approaches that can be used to study the direct interaction of plasma species with biomolecules or the consequences of these interactions for the biomolecules on a somewhat longer time-scale. These approaches include density functional theory (DFT), density functional based tight binding (DFTB), classical reactive and non-reactive molecular dynamics (MD) and united-atom or coarse-grained MD, as well as hybrid quantum mechanics/molecular mechanics (QM/MM) methods. Specific examples will be given for three important types of biomolecules, present in human cells, i.e. proteins, DNA and phospholipids found in the cell membrane. The results show that each of these modelling approaches has its specific strengths and limitations, and is particularly useful for certain applications. A multi-level approach is therefore most suitable for obtaining a global picture of the plasma–biomolecule interactions. (paper)

  1. Multi-level molecular modelling for plasma medicine

    Bogaerts, Annemie; Khosravian, Narjes; Van der Paal, Jonas; Verlackt, Christof C. W.; Yusupov, Maksudbek; Kamaraj, Balu; Neyts, Erik C.

    2016-02-01

    Modelling at the molecular or atomic scale can be very useful for obtaining a better insight in plasma medicine. This paper gives an overview of different atomic/molecular scale modelling approaches that can be used to study the direct interaction of plasma species with biomolecules or the consequences of these interactions for the biomolecules on a somewhat longer time-scale. These approaches include density functional theory (DFT), density functional based tight binding (DFTB), classical reactive and non-reactive molecular dynamics (MD) and united-atom or coarse-grained MD, as well as hybrid quantum mechanics/molecular mechanics (QM/MM) methods. Specific examples will be given for three important types of biomolecules, present in human cells, i.e. proteins, DNA and phospholipids found in the cell membrane. The results show that each of these modelling approaches has its specific strengths and limitations, and is particularly useful for certain applications. A multi-level approach is therefore most suitable for obtaining a global picture of the plasma-biomolecule interactions.

  2. Processing system for low level radioactive waste

    Low level radioactive wastes are successively charged into a container while sliding a partition plate such that the wastes are kept substantially in a fully charged state in the direction of the height. Radiation rays from the low level radioactive wastes contained in the container are measured by a radiation dose measuring means constituted so as to be slidable together with the partition plate. Further, the weight of the low level radioactive wastes in the container is measured by the weight measuring means, and the radioactivity concentration per unit container is calculated by a calculation means based on the result of the measurement. Accordingly, the optimum storage period and the radioactivity level can be estimated on every containers. Further, since the measuring vessel is used also as a storage vessel, long time measurement can be conducted by measuring the radioactivity for the wastes successively to enable exact evaluation. Accordingly, it is possible to save the labors for processing operation and save the storage facility. (T.M.)

  3. Improving Molecular Level Chemical Speciation of Organic Aerosols

    Worton, D. R.; Decker, M.; Isaacman, G. A.; Chan, A.; Wilson, K. R.; Goldstein, A. H.

    2013-12-01

    A substantial fraction of fine mode aerosols are organic with the majority formed in the atmosphere through oxidation of gas phase compounds emitted from a variety of natural and man-made sources. As a result, organic aerosols are comprised of thousands of individual organic species whose complexity increases exponentially with carbon number and degree of atmospheric oxidation. Chemical characterization of individual compounds present in this complex mixture provides information on sources and transformation processes that are critical for apportioning organic carbon from an often convoluted mixture of sources and to constrain oxidation mechanisms needed for atmospheric models. These compounds also affect the physical and optical properties of the aerosol but the vast majority remain unidentified and missing from published mass spectral libraries because of difficulties in separating and identifying them. We have developed improved methodologies for chemical identification in order to better understand complex environmental mixtures. Our approach has been to combine two-dimensional gas chromatography with high resolution time of flight mass spectrometry (GC×GC-HRTOFMS) and both traditional electron ionization (EI) and vacuum ultraviolet (VUV) photoionization. GC×GC provides improved separation of individual compounds over traditional one dimensional GC and minimizes co-elution of peaks resulting in mass spectra that are virtually free of interferences. VUV ionization is a ';soft' ionization technique that reduces fragmentation and enhances the abundance of the parent or molecular ion, which when combined with high resolution mass spectrometry can provide molecular formulas for chromatographic peaks. We demonstrate our methodology by applying it to identify more than 500 individual compounds in aerosol filter samples collected at Blodgett Forest, a rural site in the Sierra Nevada Mountains. Using the EI NIST mass spectral library and molecular formulas determined

  4. Molecular solution processing of metal chalcogenide thin film solar cells

    Yang, Wenbing

    The barrier to utilize solar generated electricity mainly comes from their higher cost relative to fossil fuels. However, innovations with new materials and processing techniques can potentially make cost effective photovoltaics. One such strategy is to develop solution processed photovoltaics which avoid the expensive vacuum processing required by traditional solar cells. The dissertation is mainly focused on two absorber material system for thin film solar cells: chalcopyrite CuIn(S,Se)2 (CISS) and kesterite Cu2ZnSn(S,Se) 4 organized in chronological order. Chalcopyrite CISS is a very promising material. It has been demonstrated to achieve the highest efficiency among thin film solar cells. Scaled-up industry production at present has reached the giga-watt per year level. The process however mainly relies on vacuum systems which account for a significant percentage of the manufacturing cost. In the first section of this dissertation, hydrazine based solution processed CISS has been explored. The focus of the research involves the procedures to fabricate devices from solution. The topics covered in Chapter 2 include: precursor solution synthesis with a focus on understanding the solution chemistry, CISS absorber formation from precursor, properties modification toward favorable device performance, and device structure innovation toward tandem device. For photovoltaics to have a significant impact toward meeting energy demands, the annual production capability needs to be on TW-level. On such a level, raw materials supply of rare elements (indium for CIS or tellurium for CdTe) will be the bottleneck limiting the scalability. Replacing indium with zinc and tin, earth abundant kesterite CZTS exhibits great potential to reach the goal of TW-level with no limitations on raw material availability. Chapter 3 shows pioneering work towards solution processing of CZTS film at low temperature. The solution processed devices show performances which rival vacuum

  5. Molecular Thermodynamics for Chemical Process Design

    Prausnitz, J. M.

    1976-01-01

    Discusses that aspect of thermodynamics which is particularly important in chemical process design: the calculation of the equilibrium properties of fluid mixtures, especially as required in phase-separation operations. (MLH)

  6. Key processes from tree to stand level

    Changes in six factors have been identified as having potential major future impacts on the productivity and survival of forest trees and stands. These factors are atmospheric carbon dioxide concentration, tropospheric ozone concentration, mean annual air temperature and precipitation, extremes in temperature and precipitation, and levels of ultraviolet radiation. Except for precipitation, all of these factors are expected to increase with climatic change. However, the likelihood of their increase or change ranges from the given to the unknown. The way in which one or more of these factors might individually or in combination affect the productivity and survival of trees is discussed, and particularly sensitive physiological processes are identified. For example, increases in winter temperature and a doubling of CO2 will result in early budburst in many species and therefore increase the risk of frost damage. In other species or locations, warm winters may mean insufficient chilling hours and the requirements for release from bud dormancy may not be met. The interaction of these processes with current species distribution, genotype selection, and management alternatives is reviewed. 52 refs., 1 fig., 1 tab

  7. A Multi-step and Multi-level approach for Computer Aided Molecular Design

    A general multi-step approach for setting up, solving and solution analysis of computer aided molecular design (CAMD) problems is presented. The approach differs from previous work within the field of CAMD since it also addresses the need for a computer aided problem formulation and result analysis....... The problem formulation step incorporates a knowledge base for the identification and setup of the design criteria. Candidate compounds are identified using a multi-level generate and test CAMD solution algorithm capable of designing molecules having a high level of molecular detail. A post solution...... step using an Integrated Computer Aided System (ICAS) for result analysis and verification is included in the methodology. Keywords: CAMD, separation processes, knowledge base, molecular design, solvent selection, substitution, group contribution, property prediction, ICAS Introduction The use of...

  8. VUV diagnostic of electron impact processes in low temperature molecular hydrogen plasma

    Komppula, J

    2015-01-01

    Novel methods for diagnostics of molecular hydrogen plasma processes, such as ionization, production of high vibrational levels, dissociation of molecules via excitation to singlet and triplet states and production of metastable states, are presented for molecular hydrogen plasmas in corona equilibrium. The methods are based on comparison of rate coefficients of plasma processes and optical emission spectroscopy of lowest singlet and triplet transitions, i.e. Lyman-band ($B^1\\Sigma^+_u \\rightarrow X^1\\Sigma^+_g$) and molecular continuum ($a^3\\Sigma^+_g \\rightarrow b^3\\Sigma^+_u$), of the hydrogen molecule in VUV wavelength range. Comparison of rate coefficients of spin-allowed and/or spin-forbidden excitations reduces the uncertainty caused by the non-equilibrium distributions of electron energy and molecular vibrational level, which are typically known poorly in plasma sources. The described methods are applied to estimate the rates of various plasma processes in a filament arc discharge.

  9. Laser-enhanced dynamics in molecular rate processes

    George, T. F.; Zimmerman, I. H.; Devries, P. L.; Yuan, J.-M.; Lam, K.-S.; Bellum, J. C.; Lee, H.-W.; Slutsky, M. S.

    1978-01-01

    The present discussion deals with some theoretical aspects associated with the description of molecular rate processes in the presence of intense laser radiation, where the radiation actually interacts with the molecular dynamics. Whereas for weak and even moderately intense radiation, the absorption and stimulated emission of photons by a molecular system can be described by perturbative methods, for intense radiation, perturbation theory is usually not adequate. Limiting the analysis to the gas phase, an attempt is made to describe nonperturbative approaches applicable to the description of such processes (in the presence of intense laser radiation) as electronic energy transfer in molecular (in particular atom-atom) collisions; collision-induced ionization and emission; and unimolecular dissociation.

  10. Unified treatment of dissociation and ionization processes in molecular hydrogen

    A theoretical procedure is introduced which yields eigenvalues and eigenvectors of the reactance matrix pertaining to competing dissociation and ionization processes in molecular Rydberg states. A calculation is set up in terms of adiabatic (nuclear-coordinate dependent) quantum defects μ(R) which contain the essence of the physics of the excited molecular complex at short range. The application to preionized and predissociated resonances in the H2 spectrum yields good agreement with experiment

  11. Line emission processes in atomic and molecular shocks

    The review discusses the observations and theoretical models of interstellar shock waves in diffuse and molecular clouds. After summarizing the relevant gas dynamics, atomic, molecular and grain processes, and physics of radiative and magnetic precursors, the author describes observational diagnostics of shocks. This paper concludes with a discussion of two topics: unstable or non-steady shocks and thermal conduction in metal-rich shocks

  12. Orbital Energy Levels in Molecular Hydrogen. A Simple Approach.

    Willis, Christopher J.

    1988-01-01

    Described are the energetics involved in the formation of molecular hydrogen using concepts that should be familiar to students beginning the study of molecular orbital theory. Emphasized are experimental data on ionization energies. Included are two-electron atomic and molecular systems. (CW)

  13. Modelling Molecular Mechanisms: A Framework of Scientific Reasoning to Construct Molecular-Level Explanations for Cellular Behaviour

    van Mil, Marc H. W.; Boerwinkel, Dirk Jan; Waarlo, Arend Jan

    2013-01-01

    Although molecular-level details are part of the upper-secondary biology curriculum in most countries, many studies report that students fail to connect molecular knowledge to phenomena at the level of cells, organs and organisms. Recent studies suggest that students lack a framework to reason about complex systems to make this connection. In this…

  14. Modelling molecular mechanisms: a framework of scientific reasoning to construct molecular-level explanations for cellular behaviour

    van Mil, M.H.W.; Boerwinkel, D.J.; Waarlo, A.J.

    2013-01-01

    Although molecular-level details are part of the upper-secondary biology curriculum in most countries, many studies report that students fail to connect molecular knowledge to phenomena at the level of cells, organs and organisms. Recent studies suggest that students lack a framework to reason about

  15. Simulation and dynamics of entropy-driven, molecular self-assembly processes

    Molecular self-assembly is frequently found to generate higher-order functional structures in biochemical systems. One such example is the self-assembly of lipids in aqueous solution forming membranes, micelles, and vesicles; another is the dynamic formation and rearrangement of the cytoskeleton. These processes are often driven by local, short-range forces and therefore the dynamics is solely based on local interactions. In this paper, we introduce a cellular automata based simulation, the lattice molecular automaton, in which data structures, representing different molecular entities such as water and hydrophilic and hydrophobic monomers, share locally propagated force information on a hexagonal, two-dimensional lattice. The purpose of this level of description is the simulation of entropic and enthalpic flows in a microcanonical, molecular ensemble to gain insight about entropy-driven processes in molecular many-particle systems. Three applications are shown, i.e., modeling structural features of a polar solvent, cluster formation of hydrophobic monomers in a polar environment, and the self-assembly of polymers. Processes leading to phase separation on a molecular level are discussed. A thorough discussion of the computational details, advantages, and limitations of the lattice molecular automaton approach is given elsewhere [B. Mayer and S. Rasmussen (unpublished)]. copyright 1997 The American Physical Society

  16. Design strategies for the molecular level synthesis of supported catalysts.

    Wegener, Staci L; Marks, Tobin J; Stair, Peter C

    2012-02-21

    -resolution solid state NMR, UV-visible diffuse reflectance (DRS), UV-Raman, and X-ray absorption spectroscopies to characterize supported catalysts. We demonstrate that it is possible to tailor and isolate defined surface species using a molecularly oriented approach. We anticipate that advances in catalyst design and synthesis will lead to a better understanding of catalyst structure and function and, thus, to advances in existing catalytic processes and the development of new technologies. PMID:22004451

  17. 1978 bibliography of atomic and molecular processes. [Bibliography

    1980-03-01

    This annotated bibliography lists 2557 works on atomic and molecular processes reported in publications dated 1978. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors.

  18. 1979 bibliography of atomic and molecular processes. [Bibliography

    None

    1980-08-01

    This annotated bibliography lists 2146 works on atomic and molecular processes reported in publications dated 1979. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory, to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors.

  19. Prospects for exploring molecular developmental processes in Haemonchus contortus.

    Nikolaou, S; Gasser, R B

    2006-07-01

    Haemonchus contortus of small ruminants is a parasitic nematode of major socio-economic importance world-wide. While there is considerable knowledge of the morphological changes which take place during the life cycle of H. contortus, very little is understood about the molecular and biochemical processes which govern developmental changes in the parasite. Recent technological advances and the imminent genomic sequence for H. contortus provide unique opportunities to investigate the molecular basis of such processes in parasitic nematodes. This article reviews molecular and biochemical aspects of development in H. contortus, reports on some recent progress on signal transduction molecules in this parasite and emphasises the opportunities that new technologies and the free-living nematode, Caenorhabditis elegans, offer for investigating developmental aspects in H. contortus and related strongylid nematodes, also in relation to developing novel approaches for control. PMID:16759659

  20. A note on processing sea level data

    Breaker, L.C.

    1986-01-01

    Procedures for processing hourly observations of tidal elevation from NOAA/NOS tide gauges for the study of subtidal variability are outlined. Processing procedures include an adjustment for datum reference, low-pass filtering to remove the diurnal and semidiurnal tides, and a static correction for atmospheric pressure. These procedures are illustrated using a sequence of tidal elevation data from Santa Monica, California for the period 15 September to 15 December 1984.

  1. Mapping hydrophobicity on the protein molecular surface at atom-level resolution.

    Dan V Nicolau

    Full Text Available A precise representation of the spatial distribution of hydrophobicity, hydrophilicity and charges on the molecular surface of proteins is critical for the understanding of the interaction with small molecules and larger systems. The representation of hydrophobicity is rarely done at atom-level, as this property is generally assigned to residues. A new methodology for the derivation of atomic hydrophobicity from any amino acid-based hydrophobicity scale was used to derive 8 sets of atomic hydrophobicities, one of which was used to generate the molecular surfaces for 35 proteins with convex structures, 5 of which, i.e., lysozyme, ribonuclease, hemoglobin, albumin and IgG, have been analyzed in more detail. Sets of the molecular surfaces of the model proteins have been constructed using spherical probes with increasingly large radii, from 1.4 to 20 Å, followed by the quantification of (i the surface hydrophobicity; (ii their respective molecular surface areas, i.e., total, hydrophilic and hydrophobic area; and (iii their relative densities, i.e., divided by the total molecular area; or specific densities, i.e., divided by property-specific area. Compared with the amino acid-based formalism, the atom-level description reveals molecular surfaces which (i present an approximately two times more hydrophilic areas; with (ii less extended, but between 2 to 5 times more intense hydrophilic patches; and (iii 3 to 20 times more extended hydrophobic areas. The hydrophobic areas are also approximately 2 times more hydrophobicity-intense. This, more pronounced "leopard skin"-like, design of the protein molecular surface has been confirmed by comparing the results for a restricted set of homologous proteins, i.e., hemoglobins diverging by only one residue (Trp37. These results suggest that the representation of hydrophobicity on the protein molecular surfaces at atom-level resolution, coupled with the probing of the molecular surface at different geometric

  2. Information processing at single neuron level

    Vidybida, A. K.

    2007-01-01

    Based on numerical simulation of Hodgkin and Huxley type neuron stimulated from many synaptic inputs, an abstract concept of signal processing in individual neuron is proposed. In the concept proposed, neuron performs binding of synaptic inputs into a single output event, based on the degree of temporal coherence between the inputs. Inhibition serves as controlling factor of this type of binding.

  3. Formation of a molecular ion by photoassociative Raman processes

    Sardar, Dibyendu; Pal, Arpita; Deb, Bimalendu

    2016-01-01

    We show theoretically that it is possible to form a cold molecular ion from a pair of colliding atom and ion at low energy by photoassociative two-photon Raman processes. We explore the possibility of stimulated Raman adiabatic passage (STIRAP) from the continuum of ion-atom scattering states to an ionic molecular state. We provide physical conditions under which coherent population transfer is possible in stimulated Raman photoassociation. Our results are important for experimental realization of PA in ion-atom cold collisions.

  4. Manipulating the conduction process of a molecular resonant tunneling diode

    In this work we propose two methods to manipulate the conduction process in a molecular resonant tunneling diode. In the first proposal we make use of the fact that by twisting the molecule along the long axis, we can generate a nonlinear coupling between the conduction electrons and the phonons. In the second proposal, we allow a light of appropriate frequency to pump the electrons from the ground state to the first excited state. This mechanism generates an additional current across the molecular resonant tunneling diode. (author)

  5. Molecular barriers to processes of genetic reprogramming and cell transformation.

    Chestkov, I V; Khomyakova, E A; Vasilieva, E A; Lagarkova, M A; Kiselev, S L

    2014-12-01

    Genetic reprogramming by ectopic expression of transcription factor genes induces the pluripotent state in somatic cells. This technology provides an opportunity to establish pluripotent stem cells for each person, as well as to get better understanding of epigenetic mechanisms controlling cell state. Interestingly, some of the molecular processes that accompany somatic cell reprogramming in vitro are also characteristic for tumor manifestation. Thus, similar "molecular barriers" that control the stability of epigenetic state exist for both processes of pluripotency induction and malignant transformation. The reprogramming of tumor cells is interesting in two aspects: first, it will determine the contribution of epigenetic changes in carcinogenesis; second, it gives an approach to evaluate tumor stem cells that are supposed to form the entire cell mass of the tumor. This review discusses the key stages of genetic reprogramming, the similarity and difference between the reprogramming process and malignant transformation. PMID:25716723

  6. Theoretical analysis of dynamic processes for interacting molecular motors

    Biological transport is supported by the collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the fundamental role of these interactions by carrying out an analysis of a new class of totally asymmetric exclusion processes, in which interactions are accounted for in a thermodynamically consistent fashion. This allows us to explicitly connect microscopic features of motor proteins with their collective dynamic properties. A theoretical analysis that combines various mean-field calculations and computer simulations suggests that the dynamic properties of molecular motors strongly depend on the interactions, and that the correlations are stronger for interacting motor proteins. Surprisingly, it is found that there is an optimal strength of interactions (weak repulsion) that leads to a maximal particle flux. It is also argued that molecular motor transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed. (paper)

  7. Atomic and molecular processes in JT-60U divertor plasmas

    Takenaga, H.; Shimizu, K.; Itami, K. [Japan Atomic Energy Research Inst., Naka, Ibaraki (Japan). Naka Fusion Research Establishment] [and others

    1997-01-01

    Atomic and molecular data are indispensable for the understanding of the divertor characteristics, because behavior of particles in the divertor plasma is closely related to the atomic and molecular processes. In the divertor configuration, heat and particles escaping from the main plasma flow onto the divertor plate along the magnetic field lines. In the divertor region, helium ash must be effectively exhausted, and radiation must be enhanced for the reduction of the heat load onto the divertor plate. In order to exhaust helium ash effectively, the difference between behavior of neutral hydrogen (including deuterium and tritium) and helium in the divertor plasma should be understood. Radiation from the divertor plasma generally caused by the impurities which produced by the erosion of the divertor plate and/or injected by gas-puffing. Therefore, it is important to understand impurity behavior in the divertor plasma. The ions hitting the divertor plate recycle through the processes of neutralization, reflection, absorption and desorption at the divertor plates and molecular dissociation, charge-exchange reaction and ionization in the divertor plasma. Behavior of hydrogen, helium and impurities in the divertor plasmas can not be understood without the atomic and molecular data. In this report, recent results of the divertor study related to the atomic and molecular processes in JT-60U were summarized. Behavior of neural deuterium and helium was discussed in section 2. In section 3, the comparisons between the modelling of the carbon impurity transport and the measurements of C II and C IV were discussed. In section 4, characteristics of the radiative divertor using Ne puffing were reported. The new diagnostic method for the electron density and temperature in the divertor plasmas using the intensity ratios of He I lines was described in section 5. (author)

  8. Molecular-Level Design of Heterogeneous Chiral Catalysis

    Francisco Zaera

    2012-03-21

    , and the development of ways to imprint chiral centers on achiral solid surfaces. Chiral catalysis is not only a problem of great importance in its own right, but also the ultimate test of how to control selectivity in catalysis. The time is ripe for fundamental work in heterogeneous chiral catalysis to provide the U.S. with a leadership role in developing the next generation of catalytic processes for medicinal and agrochemical manufacturing. Our team provides the required expertise for a synergistic and comprehensive integration of physical and chemical experimentation with solid state and molecular reactivity theories to solve this problem.

  9. Molecular-Level Design of Heterogeneous Chiral Catalysis

    , and the development of ways to imprint chiral centers on achiral solid surfaces. Chiral catalysis is not only a problem of great importance in its own right, but also the ultimate test of how to control selectivity in catalysis. The time is ripe for fundamental work in heterogeneous chiral catalysis to provide the U.S. with a leadership role in developing the next generation of catalytic processes for medicinal and agrochemical manufacturing. Our team provides the required expertise for a synergistic and comprehensive integration of physical and chemical experimentation with solid state and molecular reactivity theories to solve this problem.

  10. Accelerating Molecular Dynamic Simulation on Graphics Processing Units

    Friedrichs, Mark S.; Eastman, Peter; Vaidyanathan, Vishal; Houston, Mike; Legrand, Scott; Beberg, Adam L.; Ensign, Daniel L.; Bruns, Christopher M.; Pande, Vijay S.

    2009-01-01

    We describe a complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core.

  11. Graphics processing units accelerated semiclassical initial value representation molecular dynamics

    Tamascelli, Dario; Dambrosio, Francesco S.; Conte, Riccardo; Ceotto, Michele

    2013-01-01

    This paper presents a Graphics Processing Units (GPUs) implementation of the Semiclassical Initial Value Representation (SC-IVR) propagator for vibrational molecular spectroscopy calculations. The time-averaging formulation of the SC-IVR for power spectrum calculations is employed. Details about the GPU implementation of the semiclassical code are provided. Four molecules with an increasing number of atoms are considered and the GPU-calculated vibrational frequencies perfectly match the bench...

  12. Molecular Dynamics Simulation of Macromolecules Using Graphics Processing Unit

    Xu, Ji; Ren, Ying; Ge, Wei; Yu, Xiang; Yang, Xiaozhen; Li, Jinghai

    2010-01-01

    Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In recent years, graphics processing unit (GPU) provides unprecedented computational power for scientific applications. Many MD algorithms suit with the multithread nature of GPU. In this paper, MD algorithms for macromolecular systems that run entirely on GPU ar...

  13. Automated processing of data generated by molecular dynamics

    A new integrated tool for automated processing of data generated by molecular dynamics packages and programs have been developed. The program allows to calculate important quantities such as pair correlation function, the analysis of common neighbors, counting nanoparticles and their size distribution, conversion of output files between different formats. The work explains in detail the modules of the tool, the interface between them. The uses of program are illustrated in application examples in the calculation of various properties of silver nanoparticles. (author)

  14. Ultrafast molecular processes at the short-wavelength regime

    Picon, A.; Lehmann, C. S.; Bostedt, C.; Rudenko, A.; Rolles, D.; Marinelli, A.; Young, L.; Pratt, S. T.; Southworth, S. H.

    2016-05-01

    Fundamental molecular processes that underlie chemical reactivity and biological processes typically involve intramolecular dynamics consisting of nuclear motion and the flow of charge and energy across atomic sites. Examples include photosynthesis, electron transfer in biomolecules, and molecular fragmentation. Molecular phenomena initiated by the absorption of an XUV/x-ray photon is one of the most challenging questions for the new generation of XUV/x-ray sources. New capabilities at accelerator-based are continuously being developed, being possible to nowadays generate two-color XUV/x-ray pulses with controlled time delay. The site-specificity of those photons allow the excitation of inner-shell electrons in a particular site of the molecule and, with a controlled time delay, the probing of the induced intramolecular dynamics in another site of the same molecule, opening the door to the unexplored field of intramolecular processes initiated by short-wavelength photons. Also, novel XUV/x-ray sources allow the generation of two-color pulses with a high spatio-temporal degree of coherence, suitable for quantum control schemes involving inner-shell electrons. In this talk, we present new theoretical and experimental results towards this direction. This work is funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division, under Contract No. DE-AC02-06CH11357.

  15. Secondary ionization process in laser induced breakdown of molecular gases

    We studied the separate effect of photo-ionization and collisional ionization of the molecular electronic excited states on the ionization growth rate of nitrogen irradiated with 10 ns pulse of Nd-YAG laser radiation at pressures 7.6x102, 1.79x103 and 5.34x103 Torr. It was found that photo-ionization processes play an important role in enhancing the ionization growth rate at pressures of 7.6x102 Torr. At higher pressures, where there is excess of electron density and hence excited molecule density, collisional ionization processes are dominant. (author). 6 refs, 3 figs

  16. Large scale molecular dynamics modeling of materials fabrication processes

    Belak, J.; Glosli, J.N.; Boercker, D.B.; Stowers, I.F.

    1994-02-01

    An atomistic molecular dynamics model of materials fabrication processes is presented. Several material removal processes are shown to be within the domain of this simulation method. Results are presented for orthogonal cutting of copper and silicon and for crack propagation in silica glass. Both copper and silicon show ductile behavior, but the atomistic mechanisms that allow this behavior are significantly different in the two cases. The copper chip remains crystalline while the silicon chip transforms into an amorphous state. The critical stress for crack propagation in silica glass was found to be in reasonable agreement with experiment and a novel stick-slip phenomenon was observed.

  17. Molecular-level Design of Heterogeneous Chiral Catalysts

    Gellman, Andrew John [Carnegie Mellon University; Sholl, David S. [Georgia Institute of Technology; Tysoe, Wilfred T. [University of Wisconsin - Milwaukee; Zaera, Francisco [University of California at Riverside

    2013-04-28

    Understanding and controlling selectivity is one of the key challenges in heterogeneous catalysis. Among problems in catalytic selectivity enantioselectivity is perhaps the most the most challenging. The primary goal of the project on “Molecular-level Design of Heterogeneous Chiral Catalysts” is to understand the origins of enantioselectivity on chiral heterogeneous surfaces and catalysts. The efforts of the project team include preparation of chiral surfaces, characterization of chiral surfaces, experimental detection of enantioselectivity on such surfaces and computational modeling of the interactions of chiral probe molecules with chiral surfaces. Over the course of the project period the team of PI’s has made some of the most detailed and insightful studies of enantioselective chemistry on chiral surfaces. This includes the measurement of fundamental interactions and reaction mechanisms of chiral molecules on chiral surfaces and leads all the way to rationale design and synthesis of chiral surfaces and materials for enantioselective surface chemistry. The PI’s have designed and prepared new materials for enantioselective adsorption and catalysis. Naturally Chiral Surfaces • Completion of a systematic study of the enantiospecific desorption kinetics of R-3-methylcyclohexanone (R-3-MCHO) on 9 achiral and 7 enantiomeric pairs of chiral Cu surfaces with orientations that span the stereographic triangle. • Discovery of super-enantioselective tartaric acid (TA) and aspartic acid (Asp) decomposition as a result of a surface explosion mechanism on Cu(643)R&S. Systematic study of super-enantiospecific TA and Asp decomposition on five enantiomeric pairs of chiral Cu surfaces. • Initial observation of the enantiospecific desorption of R- and S-propylene oxide (PO) from Cu(100) imprinted with {3,1,17} facets by L-lysine adsorption. Templated Chiral Surfaces • Initial observation of the enantiospecific desorption of R- and S-PO from Pt(111) and Pd(111

  18. Molecular and Supramolecular Information Processing From Molecular Switches to Unconventional Computing

    Katz, Evgeny

    2012-01-01

    Edited by a renowned and much cited chemist, this book covers the whole span of molecular computers that are based on non-biological systems. The contributions by all the major scientists in the field provide an excellent overview of the latest developments in this rapidly expanding area. A must-have for all researchers working on this very hot topic. Perfectly complements Biomolecular Information Processing, also by Prof. Katz, and available as a two-volume set.

  19. Effect of processing on carbon molecular sieve structure and performance

    Das, Mita

    2010-11-01

    Sub-micron sized carbon molecular sieve (CMS) materials were produced via ball milling for subsequent use in hybrid material formation. A detailed analysis of the effects of the milling process in the presence of different milling environments is reported. The milling process apparently alters the molecular scale structure and properties of the carbon material. Three cases: unmilled, air milled and nitrogen milled, were analyzed in this work. The property changes were probed using equilibrium sorption experiments with different gases. Furthermore, WAXD and BET results also showed differences between milling processes. Finally in order to improve the interfacial polymer-sieve region of hybrid membranes, the CMS surface was chemically modified with a linkage unit capable of covalently bonding the polymer to the sieve. A published single-wall carbon nanotube (SWCNTs) modification method was adopted to attach a primary aromatic amine to the surface. Several aspects including rigidity, chemical composition, bulky groups and length were considered in selecting the preferred linkage unit. Fortunately kinetic and equilibrium sorption properties of the modified sieves showed very little difference from unmodified samples, suggesting that the linkage unit is not excessively filling or obstructing access to the pores of the CMSs during the modification process. © 2010 Elsevier Ltd. All rights reserved.

  20. A Complex Approach for Unravelling Musaceae Phylogeny at Molecular Level

    Němcová, Pavla; Hřibová, Eva; Valárik, Miroslav; Doležel, Jaroslav

    2011-01-01

    Roč. 897, SEP 14 (2011), s. 139-142. ISSN 0567-7572. [INTERNATIONAL ISHS-PROMUSA SYMPOSIUM ON GLOBAL PERSPECTIVES ON ASIAN CHALLENGES. Guangzhou, 14.08.2009-16.08.2009] R&D Projects: GA AV ČR IAA600380703 Institutional support: RVO:61389030 Keywords : DArT * low-copy genes * molecular phylogenetics Subject RIV: EF - Botanics http://www.actahort.org/books/897/897_14.htm

  1. Biotin Sensing at the Molecular Level1–3

    Beckett, Dorothy

    2009-01-01

    Biotin influences transcription in organisms from bacteria to humans. The enzyme, biotin protein ligase, which catalyzes post-transcriptional biotin addition to biotin-dependent carboxylases, plays a central roll in transmitting the demand for biotin to gene expression. The molecular mechanism of this communication in bacteria is well understood and involves competing protein:protein interactions. Biochemical measurements indicate that this competition is kinetically controlled. In humans, th...

  2. Application of statistical process control to qualitative molecular diagnostic assays

    O'Brien, Cathal P.

    2014-11-01

    Modern pathology laboratories and in particular high throughput laboratories such as clinical chemistry have developed a reliable system for statistical process control (SPC). Such a system is absent from the majority of molecular laboratories and where present is confined to quantitative assays. As the inability to apply SPC to an assay is an obvious disadvantage this study aimed to solve this problem by using a frequency estimate coupled with a confidence interval calculation to detect deviations from an expected mutation frequency. The results of this study demonstrate the strengths and weaknesses of this approach and highlight minimum sample number requirements. Notably, assays with low mutation frequencies and detection of small deviations from an expected value require greater sample numbers to mitigate a protracted time to detection. Modeled laboratory data was also used to highlight how this approach might be applied in a routine molecular laboratory. This article is the first to describe the application of SPC to qualitative laboratory data.

  3. QUALITY IMPROVEMENT MODEL AT THE MANUFACTURING PROCESS PREPARATION LEVEL

    Dusko Pavletic; Mirko Sokovic

    2009-01-01

    The paper expresses base for an operational quality improvement model at the manufacturing process preparation level. A numerous appropriate related quality assurance and improvement methods and tools are identified. Main manufacturing process principles are investigated in order to scrutinize one general model of manufacturing process and to define a manufacturing process preparation level. Development and introduction of the operational quality improvement model is based on a research condu...

  4. BUSINESS PROCESS MANAGEMENT MATURITY MODEL - SERBIAN ENTERPRISES' MATURITY LEVEL

    Marija Anđelković Pešić; Vesna Janković Milić; Aleksandra Anđelković

    2012-01-01

    Business process management maturity model enables description of "as-is" enterprise's state, in terms of presence and acceptance of process approach.The heart of this model includes five factors or levers, critical for successful implementation of business process management. These factors are: strategic approach, process management, technology, employee management, and business culture. The above-mentioned factors influence the level of enterprise's maturity. At each level, an enterprise is...

  5. Some considerations on coastal processes relevant to sea level rise

    Mehta, Ashish J.; Dean, Robert G.; Dally, William R.; Montague, Clay L.

    1987-01-01

    The effects of potential sea level rise on the shoreline and shore environment have been briefly examined by considering the interactions between sea level rise and relevant coastal processes. These interactions have been reviewed beginning with a discussion of the need to reanalyze previous estimates of eustatic sea level rise and compaction effects in water level measurement. This is followed by considerations on sea level effects on coastal and estuarine tidal ranges, storm ...

  6. A Study of molecular cooling via Sisyphus processes

    COMPARAT, Daniel

    2014-01-01

    We present a study of Sisyphus cooling of molecules: the scattering of a single-photon remove a substantial amount of the molecular kinetic energy and an optical pumping step allow to repeat the process. A review of the produced cold molecules so far indicates that the method can be implemented for most of them, making it a promising method able to produce a large sample of molecules at sub-mK temperature. Considerations of the required experimental parameters, for instance the laser power an...

  7. Molecular collision processes in the presence of picosecond laser pulses

    Lee, H. W.; George, T. F.

    1979-01-01

    Radiative transitions in molecular collision processes taking place in the presence of picosecond pulses are studied within a semiclassical formalism. An expression for adiabatic potential surfaces in the electronic-field representation is obtained, which directly leads to the evaluation of transition probabilities. Calculations with a Landau-Zener-type model indicate that picosecond pulses can be much more effective in inducing transitions than a single long pulse of the same intensity and the same total energy, if the intensity is sufficiently high that the perturbation treatment is not valid.

  8. Oxidized phosphatidylcholines in membrane-level cellular signaling: from biophysics to physiology and molecular pathology.

    Volinsky, Roman; Kinnunen, Paavo K J

    2013-06-01

    The oxidation of lipids has been shown to impact virtually all cellular processes. The paradigm has been that this involvement is due to interference with the functions of membrane-associated proteins. It is only recently that methodological advances in molecular-level detection and identification have begun to provide insights into oxidative lipid modification and its involvement in cell signaling as well as in major diseases and inflammation. Extensive evidence suggests a correlation between lipid peroxidation and degenerative neurological diseases such as Parkinson's and Alzheimer's, as well as type 2 diabetes and cancer. Despite the obvious relevance of understanding the molecular basis of the above ailments, the exact modes of action of oxidized lipids have remained elusive. In this minireview, we summarize recent findings on the biophysical characteristics of biomembranes following oxidative derivatization of their lipids, and how these altered properties are involved in both physiological processes and major pathological conditions. Lipid-bearing, oxidatively truncated and functionalized acyl chains are known to modify membrane bulk physical properties, such as thermal phase behavior, bilayer thickness, hydration and polarity profiles, as manifest in the altered structural dynamics of lipid bilayers, leading to augmented membrane permeability, fast lipid transbilayer diffusion (flip-flop), loss of lipid asymmetry (scrambling) and phase segregation (the formation of 'rafts'). These changes, together with the generated reactive lipid derivatives, can be further expected to interfere with lipid-protein interactions, influencing metabolic pathways, causing inflammation, the execution phase in apoptosis and initiating pathological processes. PMID:23506295

  9. A Note on the Level of Recall, Level of Processing, and Imagery Hypotheses of Hypermnesia.

    Erdelyi, Matthew

    1982-01-01

    Reviews empirical evidence which suggests that level of recall does not determine hypermnesia (increased recall with repeated testing). Discusses the problem of deciding between a levels-of-processing and an imagery hypothesis of hypermnesia. (EKN)

  10. Developing HR processes at group level: Case Halton Group

    Sorvari, Iina

    2016-01-01

    The case company, Halton Group, as many other global technology companies worldwide, is investigating the possibility of taking a global human resource information system into use globally. In order to have a successful implementation process for the project, it is essential to have human resource processes described at the group level. This study aimed to develop the key HR processes in a global technology organization at the group level in order to enable modelling the group’s HR proce...

  11. Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units—Radial Distribution Function Histogramming

    Levine, Benjamin G.; Stone, John E.; Kohlmeyer, Axel

    2011-01-01

    The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory data is a common and computationally expensive analysis task. The rate limiting step in the calculation of the RDF is building a histogram of the distance between atom pairs in each trajectory frame. Here we present an implementation of this histogramming scheme for multiple graphics processing units (GPUs). The algorithm features a tiling scheme to maximize the reuse of data at the fastest levels of th...

  12. Molecular dynamics simulations of cluster fission and fusion processes

    Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia;

    2004-01-01

    groups of atoms from the parent cluster is largely independent of the isomer form of the parent cluster. The importance of rearrangement of the cluster structure during the fission process is elucidated. This rearrangement may include transition to another isomer state of the parent cluster before actual......Results of molecular dynamics simulations of fission reactions Na_10^2+ --> Na_7^+ +Na_3^+ and Na_18^2+ --> 2Na_9^+ are presented. The dependence of the fission barriers on the isomer structure of the parent cluster is analyzed. It is demonstrated that the energy necessary for removing homothetic...... separation of the daughter fragments begins and/or forming a "neck" between the separating fragments. A novel algorithm for modeling the cluster growth process is described. This approach is based on dynamic search for the most stable cluster isomers and allows one to find the optimized cluster geometries...

  13. A novel purification process for dodecanedioic acid by molecular distillation

    Jiang Yu; Xigang Yuan; Aiwu Zeng

    2015-01-01

    A novel purification process is involved to obtain the high purity [N 99%(by mass)] dodecanedioic acid (DC12). It involves a re-crystal ization followed by molecular distil ation from the crude product. The objective of this study is to investigate general conditions, feed rate, distil ing temperature and vacuum, necessary for centrifugal distil-lation of DC12. Under the optimum conditions, distilling temperature 180 °C, pressure 30 Pa and feed flow rate 700 ml·h−1, the purity of DC12 in the residence reached 97.55%with a yield of 53.18%by the analysis of gas chromatography. Multiple-pass distillation made a considerable contribution by improving the purity to 99.22%. Additionally, the effect of pretreatment (re-crystallization) on distillation process was revealed through a series of comparative experiments.

  14. 77 FR 47337 - Project-Level Predecisional Administrative Review Process

    2012-08-08

    ... Forest Service 36 CFR Part 218 RIN 0596-AD07 Project-Level Predecisional Administrative Review Process... establishes the sole process by which the public may file objections seeking predecisional administrative... Appeal Reform Act (ARA), which provided for a postdecisional administrative appeal process. The...

  15. 78 FR 18481 - Project-Level Predecisional Administrative Review Process

    2013-03-27

    ... Forest Service 36 CFR Part 218 RIN 0596-AD07 Project-Level Predecisional Administrative Review Process... postdecisional administrative appeal process for projects and activities implementing land management plans. The... administrative review process for hazardous fuel reduction projects authorized by the HFRA. The interim...

  16. Molecular processes of transgenerational acclimation to a warming ocean

    Veilleux, Heather D.

    2015-07-20

    Some animals have the remarkable capacity to acclimate across generations to projected future climate change1, 2, 3, 4; however, the underlying molecular processes are unknown. We sequenced and assembled de novo transcriptomes of adult tropical reef fish exposed developmentally or transgenerationally to projected future ocean temperatures and correlated the resulting expression profiles with acclimated metabolic traits from the same fish. We identified 69 contigs representing 53 key genes involved in thermal acclimation of aerobic capacity. Metabolic genes were among the most upregulated transgenerationally, suggesting shifts in energy production for maintaining performance at elevated temperatures. Furthermore, immune- and stress-responsive genes were upregulated transgenerationally, indicating a new complement of genes allowing the second generation of fish to better cope with elevated temperatures. Other differentially expressed genes were involved with tissue development and transcriptional regulation. Overall, we found a similar suite of differentially expressed genes among developmental and transgenerational treatments. Heat-shock protein genes were surprisingly unresponsive, indicating that short-term heat-stress responses may not be a good indicator of long-term acclimation capacity. Our results are the first to reveal the molecular processes that may enable marine fishes to adjust to a future warmer environment over multiple generations.

  17. Coalescence process of two cooper nanoparticles: molecular dynamics simulation

    Molecular Dynamics simulation, using an empirical potential EAM for the modeling of the atomic interaction, have been performed to study the coalescence process of two spherical Cu nanoparticles that contains equal number of atoms N = 736. The simulation is made with md step equal to 1.6 fs without applying periodic boundary conditions. The previously optimized nanoparticles has bounding energy -3.2805 eV/atom and melting temperature 989 K. The coalescence process with collision velocity of 400 and 800 m/s is analyzed at temperatures 300 and 600 K. The geometric and structural changes, that undergo particles during the collision process and sintering as well as the variation of number of atoms in the neck of the system are analyzed. It is observed that even at relatively low temperatures as 300 K nanoparticles are crowded together forming a single particle, but the final geometric form and the kinetic of the process is different at different temperatures and collision energies. The faceting surface of nanoparticles obeys the dynamics of the coalescence process. (author)

  18. Radiation damage at the molecular level: Nanodosimetry; Dano por radiacion a nivel molecular: nanodosimetria

    Blanco, F.; Munoz, A.; Lagares, J. I.; Nunez, L.; Garcia, G.

    2013-07-01

    One of the main practical use of the model is its use as a tool of nanodosimetry which basically consists in characterizing the effect of radiation on nano volumes (comparable to the DNA of volumes) in terms of link breaks and molecular dissociations. (Author)

  19. Molecular-Level Organization of the Tear Film Lipid Layer: A Molecular Dynamics Simulation Study

    Wizert, A.; Iskander, D. R.; Jungwirth, Pavel; Cwiklik, Lukasz

    Elsevier. Roč. 106, č. 2 (2014), 710A. ISSN 0006-3495. [Annual Meeting of the Biophysical Society /58./. 15.02.2014-19.02.2014, San Francisco] Institutional support: RVO:61388963 ; RVO:61388955 Keywords : tear film * lipid layer * molecular dynamics simulations Subject RIV: BO - Biophysics

  20. Renormalized molecular levels in a Sc3N@C-80 molecular electronic device

    Larade, Brian; Taylor, Jeremy Philip; Zheng, Q. R.;

    2001-01-01

    We address several general questions about quantum transport through molecular systems by an ab initio analysis of a scandium-nitrogen doped C-80 metallofullerene device. Charge transfer from the Sc3N is found to drastically change the current-voltage characteristics: the current through the Sc3N...

  1. Managing the high level waste nuclear regulatory commission licensing process

    This paper reports that the process for obtaining Nuclear Regulatory Commission permits for the high level waste storage facility is basically the same process commercial nuclear power plants followed to obtain construction permits and operating licenses for their facilities. Therefore, the experience from licensing commercial reactors can be applied to the high level waste facility. Proper management of the licensing process will be the key to the successful project. The management of the licensing process was categorized into four areas as follows: responsibility, organization, communication and documentation. Drawing on experience from nuclear power plant licensing and basic management principles, the management requirement for successfully accomplishing the project goals are discussed

  2. Molecular and cellular level of action of digitalis.

    Charlemagne, D

    1993-04-01

    The pharmacological receptor of cardiac glycosides is the Na+/K(+)-ATPase which consists of a catalytic alpha (M(r) = 112,000) and glycosylated beta (M(r) = 35,000) subunit. The enzyme is responsible for the vectorial transport across the sarcolemma of three Na+ ions outward and two K+ ions inward against their electrochemical gradient. Specific inhibition of the Na+ pump by digitalis induces a positive inotropic effect by increasing the intracellular Na+ concentration which in turn induces an increase in the intracellular Ca2+ concentration by the Na+/Ca2+ exchange and an increase in the Ca2+ pool of the sarcoplasmic reticulum; toxic effects are observed at higher doses of cardiac glycosides leading to spontaneous calcium release from the sarcoplasmic reticulum. Three isoforms of the alpha catalytic subunit have been identified by molecular cloning. They share a high homology in the deduced amino acid sequence with eight transmembrane domains. The ouabain binding domain is located on the extracellular side and ouabain sensitivity depends mainly on the two residues at the border of the first extracellular domain. The isoforms differed by their ouabain sensitivity, are expressed in a tissue-specific and hormonally-regulated manner. Moreover, expression of the isoforms and their ouabain sensitivity vary from species to species with an alpha 1 isoform of very low affinity being the major isoform (80%) in the adult rat heart and an alpha 1 isoform of high affinity representing 50% of total alpha mRNA abundance in the human heart. Therefore the effect of digitalis on the heart depends mainly on the isoform which is expressed and on the regulation of their expression according to age, hormonal influence and pathology. PMID:7684015

  3. Molecular dynamics simulations of thermal effects in nanometric cutting process

    2010-01-01

    Understanding the basic action of how material removing in nanoscale is a critical issue of producing well-formed components.In order to clarify thermal effects on material removal at atomic level,molecular dynamics(MD)simulations of nanometric cutting of mono-crystalline copper are performed with Morse,EAM and Tersoff potential.The effects of cutting speed on temperature distribution are investigated.The simulation results demonstrate that the temperature distribution shows a roughly concentric shape around shear zone and a steep temperature gradient lies in diamond tool,a relative high temperature is located in shear zone and machined surface,but the highest temperature is found in chip.At a high cutting speed mode,the atoms in shear zone with high temperature implies a large stress is built up in a local region.

  4. Hierarchical Three-level Ontology for Text Processing

    Gladun, Victor; Velychko, Vitalii; Svyatogor, Leonid

    2008-01-01

    The principal feature of ontology, which is developed for a text processing, is wider knowledge representation of an external world due to introduction of three-level hierarchy. It allows to improve semantic interpretation of natural language texts.

  5. In-silico design of computational nucleic acids for molecular information processing.

    Ramlan, Effirul Ikhwan; Zauner, Klaus-Peter

    2013-01-01

    Within recent years nucleic acids have become a focus of interest for prototype implementations of molecular computing concepts. During the same period the importance of ribonucleic acids as components of the regulatory networks within living cells has increasingly been revealed. Molecular computers are attractive due to their ability to function within a biological system; an application area extraneous to the present information technology paradigm. The existence of natural information processing architectures (predominately exemplified by protein) demonstrates that computing based on physical substrates that are radically different from silicon is feasible. Two key principles underlie molecular level information processing in organisms: conformational dynamics of macromolecules and self-assembly of macromolecules. Nucleic acids support both principles, and moreover computational design of these molecules is practicable. This study demonstrates the simplicity with which one can construct a set of nucleic acid computing units using a new computational protocol. With the new protocol, diverse classes of nucleic acids imitating the complete set of boolean logical operators were constructed. These nucleic acid classes display favourable thermodynamic properties and are significantly similar to the approximation of successful candidates implemented in the laboratory. This new protocol would enable the construction of a network of interconnecting nucleic acids (as a circuit) for molecular information processing. PMID:23647621

  6. High-Level Waste System Process Interface Description

    d' Entremont, P.D.

    1999-01-14

    The High-Level Waste System is a set of six different processes interconnected by pipelines. These processes function as one large treatment plant that receives, stores, and treats high-level wastes from various generators at SRS and converts them into forms suitable for final disposal. The three major forms are borosilicate glass, which will be eventually disposed of in a Federal Repository, Saltstone to be buried on site, and treated water effluent that is released to the environment.

  7. High-Level Waste System Process Interface Description

    The High-Level Waste System is a set of six different processes interconnected by pipelines. These processes function as one large treatment plant that receives, stores, and treats high-level wastes from various generators at SRS and converts them into forms suitable for final disposal. The three major forms are borosilicate glass, which will be eventually disposed of in a Federal Repository, Saltstone to be buried on site, and treated water effluent that is released to the environment

  8. Fine-tuning molecular energy levels by nonresonant laser pulses

    Lemeshko, Mikhail

    2010-01-01

    We evaluate the shifts imparted to vibrational and rotational levels of a linear molecule by a nonresonant laser field at intensities of up to 10^12 W/cm^2. Both types of shift are found to be either positive or negative, depending on the initial rotational state acted upon by the field. An adiabatic field-molecule interaction imparts a rotational energy shift which is negative and exceeds the concomitant positive vibrational shift by a few orders of magnitude. The rovibrational states are thus pushed downward in such a field. A nonresonant pulsed laser field that interacts nonadiabatically with the molecule is found to impart rotational and vibrational shifts of the same order of magnitude. The nonadiabatic energy transfer occurs most readily at a pulse duration which amounts to about a tenth of the molecule's rotational period, and vanishes when the sudden regime is attained for shorter pulses. We applied our treatment to the much studied 87Rb_2 molecule in the last bound vibrational levels of its lowest si...

  9. The effects of melatonin on a molecular level

    M. Haag

    1992-07-01

    Full Text Available The indole hormone melatonin is secreted in a biphasic circadian rhythm by the pineal gland. This review presents a summary of recent results concerning — (i factors that influence melatonin synthesis; (ii the existence of melatonin receptors in brain tissue; (iii the effects of melatonin as a modulator of dopaminergic, noradrenergic, GABAergic and opioidergic neurotransmitter processes; (iv the influence of melatonin on the electric activity and metabolic rate of certain brain nuclei; and (v melatonin effects on hormone secretion in the hypothalamic-pituitary axis. A basic mechanism of melatonin action via cyclic nucleotides and thus protein phosphorylation is presented.

  10. Molecular Dynamics Simulation of Macromolecules Using Graphics Processing Unit

    Xu, Ji; Ge, Wei; Yu, Xiang; Yang, Xiaozhen; Li, Jinghai

    2010-01-01

    Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In recent years, graphics processing unit (GPU) provides unprecedented computational power for scientific applications. Many MD algorithms suit with the multithread nature of GPU. In this paper, MD algorithms for macromolecular systems that run entirely on GPU are presented. Compared to the MD simulation with free software GROMACS on a single CPU core, our codes achieve about 10 times speed-up on a single GPU. For validation, we have performed MD simulations of polymer crystallization on GPU, and the results observed perfectly agree with computations on CPU. Therefore, our single GPU codes have already provided an inexpensive alternative for macromolecular simulations on traditional CPU clusters and they can also be used as a basis to develop parallel GPU programs to further spee...

  11. Graphics processing units accelerated semiclassical initial value representation molecular dynamics

    This paper presents a Graphics Processing Units (GPUs) implementation of the Semiclassical Initial Value Representation (SC-IVR) propagator for vibrational molecular spectroscopy calculations. The time-averaging formulation of the SC-IVR for power spectrum calculations is employed. Details about the GPU implementation of the semiclassical code are provided. Four molecules with an increasing number of atoms are considered and the GPU-calculated vibrational frequencies perfectly match the benchmark values. The computational time scaling of two GPUs (NVIDIA Tesla C2075 and Kepler K20), respectively, versus two CPUs (Intel Core i5 and Intel Xeon E5-2687W) and the critical issues related to the GPU implementation are discussed. The resulting reduction in computational time and power consumption is significant and semiclassical GPU calculations are shown to be environment friendly

  12. Roles of upper-level processes in tropical cyclogenesis

    Zhang, Da-Lin; Zhu, Lin

    2012-09-01

    Previous studies have focused mostly on the impact of lower-level vorticity growth and other lower-level processes on tropical cyclogenesis (TCG). In this study, the importance of upper-level processes in TCG is studied in terms of the minimum sea-level pressure (MSLP) changes with two cases exhibiting different warm-core heights and vorticity structures due to their developments in the respective weak- and strong-sheared environment. Results show that the upper-level warming could account for more than 75% the MSLP changes in both cases. Widespread deep convection during the early TCG stage tends to warm the upper troposphere and induce meso-α-scale surface pressure falls. Upper-level flow and vertical wind shear (VWS) will suppress the formation of a warm core due to the presence of weak inertial stability, whereas the development of upper-level divergent outflows favors its formation. Results also show that TCG is triggered when the upper-level warming amplitude and depth increase as a result of weak or significantly reduced ventilation and VWS aloft. Results suggest that both the upper- and low-level processes be considered in the understanding and prediction of TCG.

  13. Molecular-Level Simulations of Shock Generation and Propagation in Soda-Lime Glass

    Grujicic, M.; Bell, W. C.; Pandurangan, B.; Cheeseman, B. A.; Fountzoulas, C.; Patel, P.

    2012-08-01

    A non-equilibrium molecular dynamics method is employed to study the mechanical response of soda-lime glass (a material commonly used in transparent armor applications) when subjected to the loading conditions associated with the generation and propagation of planar shock waves. Specific attention is given to the identification and characterization of various (inelastic-deformation and energy-dissipation) molecular-level phenomena and processes taking place at, or in the vicinity of, the shock front. The results obtained revealed that the shock loading causes a 2-4% (shock strength-dependent) density increase. In addition, an increase in the average coordination number of the silicon atoms is observed along with the creation of smaller Si-O rings. These processes are associated with substantial energy absorption and dissipation and are believed to greatly influence the blast/ballistic impact mitigation potential of soda-lime glass. The present work was also aimed at the determination of the shock Hugoniot (i.e., a set of axial stress vs. density/specific-volume vs. internal energy vs. particle velocity vs. temperature) material states obtained in soda-lime glass after the passage of a shock wave of a given strength (as quantified by the shock speed). The availability of a shock Hugoniot is critical for construction of a high deformation-rate, large-strain, high pressure material model which can be used within a continuum-level computational analysis to capture the response of a soda-lime glass based laminated transparent armor structure (e.g., a military vehicle windshield, door window, etc.) to blast/ballistic impact loading.

  14. Region Division and Stress Analysis for Plate Roller Leveling Process

    ZHOU Cun-long; WANG Guo-dong; LIU Xiang-hua; QIN Jian-ping

    2005-01-01

    The flatness of leveled plate is settled by residual stress. According to stress distribution simulated by FEM software ANSYS/LS-DYNA, the plate can be divided into non-steady region and steady region. The nonsteady region is composed of four zones, two of which are about half of leveling roller pitch at leading and end edges and other two are about 10% of the width at lateral edges. The steady region is the rest part enclosed by the non-steady regions. It is helpful to improve the leveling process by analyzing forming mechanism of each region and selecting suitable processes settings.

  15. High-Level Waste (HLW) Feed Process Control Strategy

    The primary purpose of this document is to describe the overall process control strategy for monitoring and controlling the functions associated with the Phase 1B high-level waste feed delivery. This document provides the basis for process monitoring and control functions and requirements needed throughput the double-shell tank system during Phase 1 high-level waste feed delivery. This document is intended to be used by (1) the developers of the future Process Control Plan and (2) the developers of the monitoring and control system

  16. Levels of processing and Eye Movements: A Stimulus driven approach

    Mulvey, Fiona Bríd

    2014-01-01

    to investigate individual differences in levels of processing within the normal population using existing constructs and tests of cognitive style. Study 4 investigates these stimuli and the eye movements of a clinical group with known interruption to the dorsal stream of processing, and subsequent isolated....... This series of studies attempts to provide explanatory information for previous findings that saccade amplitude and fixation duration are indicative of levels of processing and to isolate top down influences on eye movements with a stimulus driven approach. This approach involves developing measures suitable...... for studying individual differences in attention in large sample groups, using stimulus pairs which are similar in terms of bottom up properties but different in terms of higher level processing. These methods are presented in study 1, stimuli are developed and tested in Study 2. Study 3 uses these stimuli...

  17. Regulation of leaf hydraulics: from molecular to whole plant levels

    Karine ePrado

    2013-07-01

    Full Text Available The water status of plant leaves is dependent on both stomatal regulation and water supply from the vasculature to inner tissues. The present review addresses the multiple physiological and mechanistic facets of the latter process. Inner leaf tissues contribute to at least a third of the whole resistance to water flow within the plant. Physiological studies indicated that leaf hydraulic conductance (Kleaf is highly dependent on the anatomy, development and age of the leaf and can vary rapidly in response to physiological or environmental factors such as leaf hydration, light, temperature or nutrient supply. Differences in venation pattern provide a basis for variations in Kleaf during development and between species. On a short time (hour scale, the hydraulic resistance of the vessels can be influenced by transpiration-induced cavitations, wall collapses and changes in xylem sap composition. The extravascular compartment includes all living tissues (xylem parenchyma, bundle sheath and mesophyll that transport water from xylem vessels to substomatal chambers. Pharmacological inhibition and reverse genetics studies have shown that this compartment involves water channel proteins called aquaporins (AQP that facilitate water transport across cell membranes. In many plant species, AQPs are present in all leaf tissues with a preferential expression in the vascular bundles. The various mechanisms that allow adjustment of Kleaf to specific environmental conditions include transcriptional regulation of AQPs and changes in their abundance, trafficking and intrinsic activity. Finally, the hydraulics of inner leaf tissues can have a strong impact on the dynamic responses of leaf water potential and stomata, and as a consequence on plant carbon economy and leaf expansion growth. The manipulation of these functions could help optimize the entire plant performance and its adaptation to extreme conditions over short and long time scales.

  18. Impact of Educational Level on Performance on Auditory Processing Tests.

    Murphy, Cristina F B; Rabelo, Camila M; Silagi, Marcela L; Mansur, Letícia L; Schochat, Eliane

    2016-01-01

    Research has demonstrated that a higher level of education is associated with better performance on cognitive tests among middle-aged and elderly people. However, the effects of education on auditory processing skills have not yet been evaluated. Previous demonstrations of sensory-cognitive interactions in the aging process indicate the potential importance of this topic. Therefore, the primary purpose of this study was to investigate the performance of middle-aged and elderly people with different levels of formal education on auditory processing tests. A total of 177 adults with no evidence of cognitive, psychological or neurological conditions took part in the research. The participants completed a series of auditory assessments, including dichotic digit, frequency pattern and speech-in-noise tests. A working memory test was also performed to investigate the extent to which auditory processing and cognitive performance were associated. The results demonstrated positive but weak correlations between years of schooling and performance on all of the tests applied. The factor "years of schooling" was also one of the best predictors of frequency pattern and speech-in-noise test performance. Additionally, performance on the working memory, frequency pattern and dichotic digit tests was also correlated, suggesting that the influence of educational level on auditory processing performance might be associated with the cognitive demand of the auditory processing tests rather than auditory sensory aspects itself. Longitudinal research is required to investigate the causal relationship between educational level and auditory processing skills. PMID:27013958

  19. QUALITY IMPROVEMENT MODEL AT THE MANUFACTURING PROCESS PREPARATION LEVEL

    Dusko Pavletic

    2009-12-01

    Full Text Available The paper expresses base for an operational quality improvement model at the manufacturing process preparation level. A numerous appropriate related quality assurance and improvement methods and tools are identified. Main manufacturing process principles are investigated in order to scrutinize one general model of manufacturing process and to define a manufacturing process preparation level. Development and introduction of the operational quality improvement model is based on a research conducted and results of methods and tools application possibilities in real manufacturing processes shipbuilding and automotive industry. Basic model structure is described and presented by appropriate general algorithm. Operational quality improvement model developed lays down main guidelines for practical and systematic application of quality improvements methods and tools.

  20. Molecular control of electron and hole transfer processes: Theory and applications

    Newton, M.D. [Brookhaven National Lab., Upton, NY (United States). Dept. of Chemistry; Cave, R.J. [Harvey Mudd Coll., Claremont, CA (United States). Dept. of Chemistry

    1996-02-01

    Recent decades have seen remarkable advances in microscopic understanding of electron transfer (ET) processes in widely ranging contexts, including solid-state, liquid solution, and complex biological assemblies. The primary goal of this chapter is to report recent advances in the modeling, calculation, and analysis of electronic coupling in complex molecular aggregates, thereby allowing an assessment of current progress toward the goal of molecular-level control and design. The control of electron transfer kinetics (i.e., enhancing desired processes, while inhibiting others) involves, of course, system energetics (especially activation and reorganization energies) as well as electronic coupling, which is most directly relevant only after the system has reached the appropriate point (or region) along the reaction coordinate. Nevertheless, to focus the discussion in this chapter, the authors will consider such energetics, and the associated molecular and solvent coordinates which control then, only to the extent that they bear on the analysis of the electronic coupling. In the following sections they first discuss the formulation of basic ET models, including the definition of initial and final states, the role of orbitals and 1-particle models in a many-electron context, the utility of various effective Hamiltonians, and the role of vibronic as well as purely electronic effects. With these theoretical tools in hand, they then examine very recent applications to complex molecular systems using the techniques of computational quantum chemistry, followed by detailed analysis of the numerical results. They then conclude with some comments regarding the current ``state of the art`` and remaining challenges.

  1. 0-level Vacuum Packaging RT Process for MEMS Resonators

    Abelé, N; Hibert, C; Casset, F; Ancey, P; Ionescu, A

    2008-01-01

    A new Room Temperature (RT) 0-level vacuum package is demonstrated in this work, using amorphous silicon (aSi) as sacrificial layer and SiO2 as structural layer. The process is compatible with most of MEMS resonators and Resonant Suspended-Gate MOSFET [1] fabrication processes. This paper presents a study on the influence of releasing hole dimensions on the releasing time and hole clogging. It discusses mass production compatibility in terms of packaging stress during back-end plastic injection process. The packaging is done at room temperature making it fully compatible with IC-processed wafers and avoiding any subsequent degradation of the active devices.

  2. Method of processing high level radioactive liquid waste

    High level radioactive liquid wastes formed from re-processing plants are cleaned being frozen in a freezing step. Frozen products of high level radioactive liquid wastes are put to a heated, pressurized and evacuated state in a sublimation step and nitric acid, water, subliming nuclides, etc. are sublimated from the frozen products. They are condensated in a condenser into liquid condensates. Then, a solution of sodium hydroxide is added to the residues and they are separated in a solid-liquid separation step into solutions such as of sodium nitrate and sodium hydroxide and residues mainly comprising nuclear fission products, actinoide elements and corrosion products in the re-processing step. Then, the residues are dried and calcined to form nitrates, drying and calcinating products, etc. of such shape and volume as easy to be stored. Accordingly, as compared with the case of directly processing high level radioactive liquid wastes, the amount of solidification products can be reduced remarkably. (I.N.)

  3. Duration perception: assessing contributions of lower and higher level processes

    Kliegl, Katrin M.

    2015-01-01

    Although time perception in the milliseconds to seconds range is crucial for human perception and performance, it is known that time perception is prone to distortions. In current models of duration perception, effects of arousal and attention are stressed. In the present work, the contributions of lower level sensory and higher level cognitive processes are assessed, and methods are developed helping to disentangle these influences. In a first series of experiments, effects of the retinal...

  4. Level sets and extrema of random processes and fields

    Azais, Jean-Marc

    2009-01-01

    A timely and comprehensive treatment of random field theory with applications across diverse areas of study Level Sets and Extrema of Random Processes and Fields discusses how to understand the properties of the level sets of paths as well as how to compute the probability distribution of its extremal values, which are two general classes of problems that arise in the study of random processes and fields and in related applications. This book provides a unified and accessible approach to these two topics and their relationship to classical theory and Gaussian processes and fields, and the most modern research findings are also discussed. The authors begin with an introduction to the basic concepts of stochastic processes, including a modern review of Gaussian fields and their classical inequalities. Subsequent chapters are devoted to Rice formulas, regularity properties, and recent results on the tails of the distribution of the maximum. Finally, applications of random fields to various areas of mathematics a...

  5. Molecular processes from the AGB to the PN stage

    Garcia-Hernandez, D A

    2011-01-01

    Many complex organic molecules and inorganic solid-state compounds have been observed in the circumstellar shell of stars (both C-rich and O-rich) in the transition phase between Asymptotic Giant Branch (AGB) stars and Planetary Nebulae (PNe). This short (~100-10.000 years) phase of stellar evolution represents a wonderful laboratory for astrochemistry and provides severe constraints on any model of gas-phase and solid-state chemistry. One of the major challenges of present day astrophysics and astrochemistry is to understand the formation pathways of these complex organic molecules and inorganic solid-state compounds (e.g., polycyclic aromatic hydrocarbons, fullerenes, and graphene in the case of a C-rich chemistry and oxides and crystalline silicates in O-rich environments) in space. In this review, I present an observational review of the molecular processes in the late stages of stellar evolution with a special emphasis on the first detections of fullerenes and graphene in PNe.

  6. Complex physiological and molecular processes underlying root gravitropism

    Chen, Rujin; Guan, Changhui; Boonsirichai, Kanokporn; Masson, Patrick H.

    2002-01-01

    Gravitropism allows plant organs to guide their growth in relation to the gravity vector. For most roots, this response to gravity allows downward growth into soil where water and nutrients are available for plant growth and development. The primary site for gravity sensing in roots includes the root cap and appears to involve the sedimentation of amyloplasts within the columella cells. This process triggers a signal transduction pathway that promotes both an acidification of the wall around the columella cells, an alkalinization of the columella cytoplasm, and the development of a lateral polarity across the root cap that allows for the establishment of a lateral auxin gradient. This gradient is then transmitted to the elongation zones where it triggers a differential cellular elongation on opposite flanks of the central elongation zone, responsible for part of the gravitropic curvature. Recent findings also suggest the involvement of a secondary site/mechanism of gravity sensing for gravitropism in roots, and the possibility that the early phases of graviresponse, which involve differential elongation on opposite flanks of the distal elongation zone, might be independent of this auxin gradient. This review discusses our current understanding of the molecular and physiological mechanisms underlying these various phases of the gravitropic response in roots.

  7. Levels-of-processing effects in subject-performed tasks.

    Zimmer, H D; Engelkamp, J

    1999-09-01

    In memory for subject-performed tasks (SPTs), subjects encode a list of simple action phrases (e.g., thumb through a book, knock at the door) by performing these actions during learning. In three experiments, we investigated the size of the levels-of-processing effects in SPTs as compared with those in standard verbal learning tasks (VTs). Subjects under SPT and VT conditions learned lists of action phrases in a surface or a conceptual orienting task. Under both encoding conditions, the subjects recalled fewer items with surface orienting tasks than with conceptual orienting tasks, but the levels-of-processing effects were strongly reduced in the SPT condition. In the SPT condition, items that were encoded in a surface orienting task were still substantially recalled. The items were recalled almost as well as the conceptually encoded items in the VT condition. The distinct reduction of the levels-of-processing effect is caused by the fact that, in SPT encoding even with a verbal surface orienting task, subjects process conceptual information in order to perform the denoted action. We attribute the small conceptual advantage, which remains with SPT despite the conceptual processing for performing, to the fact that items are not as well integrated into memory as they are when conceptual processing is focused on the action component, rather than on the semantic contexts. This lower integration reduces the accessibility of items in the verbal surface task, even with SPT encoding. PMID:10540819

  8. Tip-induced gating of molecular levels in carbene-based junctions.

    Foti, Giuseppe; Vázquez, Héctor

    2016-03-29

    We study the conductance of N-heterocyclic carbene-based (NHC) molecules on gold by means of first-principles calculations based on density-functional theory and non-equilibrium Green's functions. We consider several tip structures and find a strong dependence of the position of the NHC molecular levels with the atomistic structure of the tip. The position of the lowest unoccupied molecular orbital (LUMO) can change by almost 0.8 eV with tip shape. Through an analysis of the net charge transfer, electron redistribution and work function for each tip structure, we rationalize the LUMO shifts in terms of the sum of the work function and the maximum electrostatic potential arising from charge rearrangement. These differences in the LUMO position, effectively gating the molecular levels, result in large conductance variations. These findings open the way to modulating the conductance of NHC-based molecular circuits through the controlled design of the tip atomistic structure. PMID:26891059

  9. Molecular processes affecting the macroscopic tribological behavior of surfaces

    The purpose of this study was to investigate the influence of various additives on the tribological properties of a system in the macro and nanoscale, as well as clarify lubricant interactions with surfaces and materials. To accomplish that a wide range of lubricants and additives were considered. Moreover, a detail chemical analysis was carried out, in order to explain the effect on the friction coefficient, wear mechanisms and corrosion process in lubricated tribosystems. This research was mainly focused on additives for water based lubricants. Solutions of anti-corrosion and anti-foaming agents - amines, friction modifiers - glycols and amines derivatives with longer hydrocarbon chains were investigated. The results showed that the additives build chemisorbed mono-molecular films on surfaces, what was verified by AFM, AR-XPS and AES analysis, and compared with SESSA simulation. Investigated tribo-films affect the friction coefficient in nanoscale, however during tribological test in the macroscale, they showed different results depending on contact situation (rolling and/or sliding). The conclusion states that the differences in tribological behavior might be due to the orientation of amine and hydroxyl groups on the surfaces. Furthermore, lubricants for rolling bearing elements such as polar and non polar oils with zinc dialkyldithiophosphate (ZDDP) additives were studied. The results demonstrated that a reaction layer formation is strongly dependent on the molecular polarity of the oils and additives. The evolution of the topography and mechanical properties of the ZDDP-derived tribo-layer with rubbing time showed that initially a thin and soft ZDDP reaction layer develops very quick. The second part of this work was addressed on chemical vapor deposited (CVD) diamond films and transition metal dichalcogenides (TMD) in consideration of desired properties for micro electro mechanical systems (MEMS). The main scientific goal of this part of the work was to

  10. Molecular-Level Simulation of Reacting Systems in Bulk and Confinement

    Lísal, Martin; Smith, W. R.; Brennan, J. K.

    Praha : Process Engineering Publisher, 2004, s. 502. ISBN 80-86059-40-5. [International Congress of Chemical and Process Engineering CHISA 2004 /16./. Praha (CZ), 22.08.2004-26.08.2004] Institutional research plan: CEZ:AV0Z4072921 Keywords : molecular simulation * bulk and confinement * reacting systems Subject RIV: CF - Physical ; Theoretical Chemistry

  11. Effects of molecular structural variants on serum Krebs von den Lungen-6 levels in sarcoidosis

    Shigemura Masahiko

    2012-07-01

    Full Text Available Abstract Background Serum Krebs von den Lungen-6 (KL-6, which is classified as human mucin-1 (MUC1, is used as a marker of sarcoidosis and other interstitial lung diseases. However, there remain some limitations due to a lack of information on the factors contributing to increased levels of serum KL-6. This study was designed to investigate the factors contributing to increased levels of serum KL-6 by molecular analysis. Methods Western blot analysis using anti-KL-6 antibody was performed simultaneously on the bronchoalveolar lavage fluid (BALF and serum obtained from 128 subjects with sarcoidosis. Results KL-6/MUC1 in BALF showed three bands and five band patterns. These band patterns were associated with the MUC1 genotype and the KL-6 levels. KL-6/MUC1 band patterns in serum were dependent on molecular size class in BALF. Significantly increased levels of serum KL-6, serum/BALF KL-6 ratio and serum soluble interleukin 2 receptor were observed in the subjects with influx of high molecular size KL-6/MUC1 from the alveoli to blood circulation. The multivariate linear regression analysis involving potentially relevant variables such as age, gender, smoking status, lung parenchymal involvement based on radiographical stage and molecular size of KL-6/MUC1 in serum showed that the molecular size of KL-6/MUC1 in serum was significant independent determinant of serum KL-6 levels. Conclusions The molecular structural variants of KL-6/MUC1 and its leakage behavior affect serum levels of KL-6 in sarcoidosis. This information may assist in the interpretation of serum KL-6 levels in sarcoidosis.

  12. Level 5: user refinement to aid the fusion process

    Blasch, Erik P.; Plano, Susan

    2003-04-01

    The revised JDL Fusion model Level 4 process refinement covers a broad spectrum of actions such as sensor management and control. A limitation of Level 4 is the purpose of control - whether it be for user needs or system operation. Level 5, User Refinement, is a modification to the Revised JDL model that distinguishes between machine process refinement and user refinement. User refinement can either be human control actions or refinement of the user's cognitive model. In many cases, fusion research concentrates on the machine and does not take full advantage of the human as not only a qualified expert to refine the fusion process, but also as customer for whom the fusion system is designed. Without user refinement, sensor fusion is incomplete, inadequate, and the user neglects its worthiness. To capture user capabilities, we explore the concept of user refinement through decision and action based on situational leadership models. We develop a Fuse-Act Situational User Refinement (FASUR) model that details four refinement behaviors: Neglect, Consult, Rely, and Interact and five refinement functions: Planning, Organizing, Coordinating, Directing, and Controlling. Process refinement varies for different systems and different user information needs. By designing a fusion system with a specific user in mind, vis Level 5, a fusion architecture can meet user's information needs for varying situations, extend user sensing capabilities for action, and increase the human-machine interaction.

  13. Process Analysis and Level Measurement of Textbooks Use by Teachers

    Kong, Fanzhe; Shi, Ningzhong

    2009-01-01

    Teachers and textbooks are two important elements in curriculum implementation. Based on Concerns-Based Adoption Model (CBAM), a curriculum implementation measurement model designed by G. Hall and S. M. Hord, this paper analyzes the general process of curriculum implementation in terms of textbook use, establishes a model that gauges the level of…

  14. Dislocation processes in the deformation of nanocrystalline aluminum by molecular-dynamics simulation.

    Yamakov, V.; Wolf, D.; Phillpot, S. R.; Mukherjee, A. K.; Gleiter, H.; Materials Science Division; Univ. of California; Forschungszentrum Karlsruhe

    2002-09-01

    The mechanical behaviour of nanocrystalline materials (that is, polycrystals with a grain size of less than 100 nm) remains controversial. Although it is commonly accepted that the intrinsic deformation behaviour of these materials arises from the interplay between dislocation and grain-boundary processes, little is known about the specific deformation mechanisms. Here we use large-scale molecular-dynamics simulations to elucidate this intricate interplay during room-temperature plastic deformation of model nanocrystalline Al microstructures. We demonstrate that, in contrast to coarse-grained Al, mechanical twinning may play an important role in the deformation behaviour of nanocrystalline Al. Our results illustrate that this type of simulation has now advanced to a level where it provides a powerful new tool for elucidating and quantifying-in a degree of detail not possible experimentally-the atomic-level mechanisms controlling the complex dislocation and grain-boundary processes in heavily deformed materials with a submicrometre grain size.

  15. Dislocation processes in the deformation of nanocrystalline aluminium by molecular-dynamics simulation.

    Yamakov, Vesselin; Wolf, Dieter; Phillpot, Simon R; Mukherjee, Amiya K; Gleiter, Herbert

    2002-09-01

    The mechanical behaviour of nanocrystalline materials (that is, polycrystals with a grain size of less than 100 nm) remains controversial. Although it is commonly accepted that the intrinsic deformation behaviour of these materials arises from the interplay between dislocation and grain-boundary processes, little is known about the specific deformation mechanisms. Here we use large-scale molecular-dynamics simulations to elucidate this intricate interplay during room-temperature plastic deformation of model nanocrystalline Al microstructures. We demonstrate that, in contrast to coarse-grained Al, mechanical twinning may play an important role in the deformation behaviour of nanocrystalline Al. Our results illustrate that this type of simulation has now advanced to a level where it provides a powerful new tool for elucidating and quantifying--in a degree of detail not possible experimentally--the atomic-level mechanisms controlling the complex dislocation and grain-boundary processes in heavily deformed materials with a submicrometre grain size. PMID:12618848

  16. Prediction of organic molecular crystal geometries from MP2-level fragment quantum mechanical/molecular mechanical calculations

    Nanda, Kaushik D.; Beran, Gregory J. O.

    2012-11-01

    The fragment-based hybrid many-body interaction (HMBI) model provides a computationally affordable means of applying electronic structure wavefunction methods to molecular crystals. It combines a quantum mechanical treatment of individual molecules in the unit cell and their short-range pairwise interactions with a polarizable molecular mechanics force-field treatment of long-range and many-body interactions. Here, we report the implementation of analytic nuclear gradients for the periodic model to enable full relaxation of both the atomic positions and crystal lattice parameters. Using a set of five, chemically diverse molecular crystals, we compare the quality of the HMBI MP2/aug-cc-pVDZ-level structures with those obtained from dispersion-corrected periodic density functional theory, B3LYP-D*, and from the Amoeba polarizable force field. The MP2-level structures largely agree with the experimental lattice parameters to within 2%, and the root-mean-square deviations in the atomic coordinates are less than 0.2 Å. These MP2 structures are almost as good as those predicted from periodic B3LYP-D*/TZP and are significantly better than those obtained with B3LYP-D*/6-31G(d,p) or with the Amoeba force field.

  17. Process for Selecting System Level Assessments for Human System Technologies

    Watts, James; Park, John

    2006-01-01

    The integration of many life support systems necessary to construct a stable habitat is difficult. The correct identification of the appropriate technologies and corresponding interfaces is an exhaustive process. Once technologies are selected secondary issues such as mechanical and electrical interfaces must be addressed. The required analytical and testing work must be approached in a piecewise fashion to achieve timely results. A repeatable process has been developed to identify and prioritize system level assessments and testing needs. This Assessment Selection Process has been defined to assess cross cutting integration issues on topics at the system or component levels. Assessments are used to identify risks, encourage future actions to mitigate risks, or spur further studies.

  18. Machine learning for molecular scattering dynamics: Gaussian Process models for improved predictions of molecular collision observables

    Krems, Roman; Cui, Jie; Li, Zhiying

    2016-05-01

    We show how statistical learning techniques based on kriging (Gaussian Process regression) can be used for improving the predictions of classical and/or quantum scattering theory. In particular, we show how Gaussian Process models can be used for: (i) efficient non-parametric fitting of multi-dimensional potential energy surfaces without the need to fit ab initio data with analytical functions; (ii) obtaining scattering observables as functions of individual PES parameters; (iii) using classical trajectories to interpolate quantum results; (iv) extrapolation of scattering observables from one molecule to another; (v) obtaining scattering observables with error bars reflecting the inherent inaccuracy of the underlying potential energy surfaces. We argue that the application of Gaussian Process models to quantum scattering calculations may potentially elevate the theoretical predictions to the same level of certainty as the experimental measurements and can be used to identify the role of individual atoms in determining the outcome of collisions of complex molecules. We will show examples and discuss the applications of Gaussian Process models to improving the predictions of scattering theory relevant for the cold molecules research field. Work supported by NSERC of Canada.

  19. INTEGRATING CMMI MATURITY LEVEL-3 IN TRADITIONAL SOFTWARE DEVELOPMENT PROCESS

    Reena Dadhich

    2012-02-01

    Full Text Available CMMI defines the practices that are specially implemented by software development businesses to achievesuccess. Practices includes topics that direct about eliciting and managing requirements, decision making,measuring performance, planning work, handling risks, and more. In this paper we will discuss CapabilityMaturity Model Integration (CMMI software process improvement maturity model and the process areasat various levels of CMMI in brief. The main emphasis of the paper is to discuss about the RiskManagement (RSKM which is one of process area at CMMI level-3. The purpose of Risk Management(RSKM processes is to identify potential problems before they occur so that risk-handling activities can beplanned and invoked as needed across the life of the product or project to mitigate adverse impacts onachieving objectives. The main aim of the paper is to analyse the effect of integrating the CMMI maturitylevel-3(process area -RSKM with the traditional software development process. It represents an attempt toorganize the sources of software development risk around the principal aspects of the softwaredevelopment cycle.

  20. A Multi-Step and Multi-Level Approach for Computer Aided Molecular Design

    Harper, Peter Mathias; Gani, Rafiqul

    . The problem formulation step incorporates a knowledge base for the identification and setup of the design criteria. Candidate compounds are identified using a multi-level generate and test CAMD solution algorithm capable of designing molecules having a high level of molecular detail. A post solution......A general multi-step approach for setting up, solving and solution analysis of computer aided molecular design (CAMD) problems is presented. The approach differs from previous work within the field of CAMD since it also addresses the need for a computer aided problem formulation and result analysis...

  1. Calculation of energy levels and wavefunctions of hydrogen molecular ion using B-splines function

    Energy levels and wavefunctions of the ground state and the first excited state of hydrogen molecular ion are calculated by solving stationary Schrodinger equation with B-splines functions. By adopting nuclear positions as knots of B-splines basis, high accuracy of energy levels of the ground state and the first excited state for hydrogen molecular ion can be reached even for the larger internuclear separations, and our ι dependent radial wavefunctions of the ground state are in a good agreement with those computed from GAUSSIAN chemistry software. (authors)

  2. A Multi-Step and Multi-Level Approach for Computer Aided Molecular Design

    Harper, Peter Mathias; Gani, Rafiqul

    A general multi-step approach for setting up, solving and solution analysis of computer aided molecular design (CAMD) problems is presented. The approach differs from previous work within the field of CAMD since it also addresses the need for a computer aided problem formulation and result analysis....... The problem formulation step incorporates a knowledge base for the identification and setup of the design criteria. Candidate compounds are identified using a multi-level generate and test CAMD solution algorithm capable of designing molecules having a high level of molecular detail. A post solution...... step for result analysis and verification is included in the methodology. (C) 2000 Elsevier Science Ltd. All rights reserved....

  3. Surface encapsulation process for managing low-level radioactive wastes

    Current processes for low-level radioactive waste (LLRW) stabilization involve mixing contaminants with a fixative such as cement, asphalt, polyethylene, or vinyl monomers, and subsequently curing the mixtures in containers. These methods give rise to processing difficulties and yield products lacking performance to assure long-term LLRW immobilization. Mixing of LLRW into fixatives is impeded by viscous media and the curing reaction is inhibited by LLRW constituents. Product performance is affected by corrosion of the containers which ultimately expose the cured mixtures to environmental stresses. This process, termed the ''Surface Encapsulation Process,'' circumvents these problems. A thermosetting fixative is employed that mixes readily with LLRW and is highly insensitive to inhibition in curing. The agglomerated mixtures are further stabilized by encapsulation with seamless jackets of corrosion resistant plastic, such as polyethylene. In laboratory-scale investigations, feasibility of the technique was demonstrated for managing a broad spectrum of LLRW simulants including ion-exchange resins, beads, and glasses, and sodium salts. Products tested to date meet all relevant NRC and DOT regulations governing waste fixation. The high waste loadings of the products, use of commodity resins, and processing simplicity indicated our process would provide high performance LLRW stabilization at costs that are competitive to those for processes employing state-of-the-art fixatives. An economic analysis based on managing LLRW generated by commercial power plants (≅1,000 MeW) substantiates the competitive process costs advantages

  4. Low level radwaste management and processing in Maanshan NPP

    Nuclear power plant like as the other power plant will generate technology waste. Owing to Nuclear still is a debatable topic for discussion, Nuclear radwaste including low level radwaste, high level spent fuel and nuclear operate safety become a focus point in Taiwan also in all world. Maanshan NPP is the only one PWR unit in Taiwan. In common understand, the Low Level radwaste generate from PWR unit is less than BWR. No matter what LLW generate quantity is reduced obviously, the government asks seriously restrain LLW quantity year by year. Maanshan NPP had reach a stable level in solidification waste, system spent resin, combustible and incombustible radwaste that generate from necessary maintenance. The further aim is keep waste generate under control, stable operate processing system and make a new processing technical to dispose spent resin. Maanshan NPP via technical cooperation to set HESS system with INER in one decade. Nowadays there are about 18 55 gallon drums per year in Maanshan NPP. LLW incinerator equipment designed by Maanshan and install at 7 years ago, there almost burns up all the combustible LLW that generate from commercial operation. The new equipment, wet-oxidation solidification process for treatment of spent radioactive ion-exchange resins plan will cooperate with INER and complete in 2014. It is estimated that the generation of solidified wastes of the NPS will be reduced to about 1/3 volume of that currently generated. (author)

  5. Separation processes for high-level radioactive waste treatment

    During World War II, production of nuclear materials in the United States for national defense, high-level waste (HLW) was generated as a byproduct. Since that time, further quantities of HLW radionuclides have been generated by continued nuclear materials production, research, and the commercial nuclear power program. In this paper HLW is defined as the highly radioactive material resulting from the processing of spent nuclear fuel. The HLW is the liquid waste generated during the recovery of uranium and plutonium in a fuel processing plant that generally contains more than 99% of the nonvolatile fission products produced during reactor operation. Since this paper deals with waste separation processes, spent reactor fuel elements that have not been dissolved and further processed are excluded

  6. Elevated levels of high-molecular-weight adiponectin in type 1 diabetes

    Leth, H.; Andersen, K.K.; Frystyk, J.;

    2008-01-01

    BACKGROUND: Several studies have shown that type 1 diabetic patients have elevated total levels of the adipocyte-derived adipocytokine adiponectin. However, adiponectin circulates in three different subforms, and the high-molecular-weight (HMW) subform is believed to be the primary biologically...... active form. The effects of the medium-molecular-weight (MMW) subform and the low-molecular-weight (LMW) subform are still unresolved. PURPOSE: The objective of the study was to investigate the distribution of the three molecular subforms of adiponectin in well-characterized groups of type 1 diabetics...... measured using a validated in-house time-resolved immunoflourometric assay after separation by fast protein liquid chromatography. RESULTS: The absolute concentrations of total adiponectin and all subforms were higher in type 1 diabetic patients than healthy controls. However, the relative HMW fraction was...

  7. Commercial low level waste processing in a competitive market

    In most nations with active nuclear establishments, Low Level Radioactive Waste (LLW) is treated, packaged and disposed of by a single governmental organization or corporation that operates in a monopoly situation. In the US, LLW generated from utility and industry sources is processed at various commercial enterprises throughout the country and buried in commercially owned and operated LLW disposal facilities. These centralized waste processing or 'fixed base' companies provide their services in a competitive, free market environment. This competition has led to the development and use of effective technologies for waste volume reduction. The actual techniques used are chosen based on cost impact to company's financial performance rather than budget considerations

  8. In situ sensing and modeling of molecular events at the cellular level

    Yang, Ruiguo

    We developed the Atomic Force Microscopy (AFM) based nanorobot in combination with other nanomechanical sensors for the investigation of cell signaling pathways. The AFM nanorobotics hinge on the superior spatial resolution of AFM in imaging and extends it into the measurement of biological processes and manipulation of biological matters. A multiple input single output control system was designed and implemented to solve the issues of nanomanipulation of biological materials, feedback, response frequency and nonlinearity. The AFM nanorobotic system therefore provide the human-directed position, velocity and force control with high frequency feedback, and more importantly it can feed the operator with the real-time imaging of manipulation result from the fast-imaging based local scanning. The use of the system has taken the study of cellular process at the molecular scale into a new level. The cellular response to the physiological conditions can be significantly manifested in cellular mechanics. Dynamic mechanical property has been regarded as biomarkers, sometimes even regulators of the signaling and physiological processes, thus the name mechanobiology. We sought to characterize the relationship between the structural dynamics and the molecular dynamics and the role of them in the regulation of cell behavior. We used the AFM nanorobotics to investigate the mechanical properties in real-time of cells that are stimulated by different chemical species. These reagents could result in similar ion channel responses but distinctive mechanical behaviors. We applied these measurement results to establish a model that describes the cellular stimulation and the mechanical property change, a "two-hit" model that comprises the loss of cell adhesion and the initiation of cell apoptosis. The first hit was verified by functional experiments: depletion of Calcium and nanosurgery to disrupt the cellular adhesion. The second hit was tested by a labeling of apoptotic markers that

  9. Mixing Processes in High-Level Waste Tanks - Final Report

    The mixing processes in large, complex enclosures using one-dimensional differential equations, with transport in free and wall jets is modeled using standard integral techniques. With this goal in mind, we have constructed a simple, computationally efficient numerical tool, the Berkeley Mechanistic Mixing Model, which can be used to predict the transient evolution of fuel and oxygen concentrations in DOE high-level waste tanks following loss of ventilation, and validate the model against a series of experiments

  10. Mechanisms of molecular electronic rectification through electronic levels with strong vibrational coupling

    Kuznetsov, A.M.; Ulstrup, Jens

    2002-01-01

    We present a new view and an analytical formalism of electron flow through a donor-acceptor molecule inserted between a pair of metal electrodes. The donor and acceptor levels are strongly coupled to an environmental nuclear continuum. The formalism applies to molecular donor-acceptor systems bot...

  11. Treatment of High Level Waste Arising from Pyrochemical Processes

    The report describes the JSC «SSC RIAR» research experience on management high-level waste (HLW) arising from pyrochemical processes. The laboratory investigations including simulated and real waste forms generated as a result of the experimental reprocessings of spent nuclear fuel (SNF) of fast reactors are summarized. Pyrochemical processes are characterized by a few types and a small volume of the waste, their high specific activity and, practically, absence of the liquid process HLW. The main types of solid process wastes are phosphate and oxide precipitates and spent electrolytes. The investigation included the chemical and radionuclide composition, gas release, chemical durability, thermal stability of the precipitates and spent electrolytes. The results of the analysis suggest that the main waste forms of the pyrochemical processes can be stored for a long time in shielded containers without any chemical conversion and immobilization. To increase the efficiency of the shielded barrier for the purposes of the long-term geological storage, the waste forms of the pyrochemical processes can be transferred into more stable chemical forms. (author)

  12. Gain control in molecular information processing: lessons from neuroscience

    Statistical properties of environments experienced by biological signaling systems in the real world change, which necessitates adaptive responses to achieve high fidelity information transmission. One form of such adaptive response is gain control. Here, we argue that a certain simple mechanism of gain control, understood well in the context of systems neuroscience, also works for molecular signaling. The mechanism allows us to transmit more than 1 bit (on or off) of information about the signal independent of the signal variance. It does not require additional molecular circuitry beyond that already present in many molecular systems, and in particular, it does not depend on existence of feedback loops. The mechanism provides a potential explanation for abundance of ultrasensitive response curves in biological regulatory networks. (paper)

  13. FEATURES, EVENTS, AND PROCESSES: SYSTEM-LEVEL AND CRITICALITY

    D.L. McGregor

    2000-12-20

    The primary purpose of this Analysis/Model Report (AMR) is to identify and document the screening analyses for the features, events, and processes (FEPs) that do not easily fit into the existing Process Model Report (PMR) structure. These FEPs include the 3 1 FEPs designated as System-Level Primary FEPs and the 22 FEPs designated as Criticality Primary FEPs. A list of these FEPs is provided in Section 1.1. This AMR (AN-WIS-MD-000019) documents the Screening Decision and Regulatory Basis, Screening Argument, and Total System Performance Assessment (TSPA) Disposition for each of the subject Primary FEPs. This AMR provides screening information and decisions for the TSPA-SR report and provides the same information for incorporation into a project-specific FEPs database. This AMR may also assist reviewers during the licensing-review process.

  14. FEATURES, EVENTS, AND PROCESSES: SYSTEM-LEVEL AND CRITICALITY

    The primary purpose of this Analysis/Model Report (AMR) is to identify and document the screening analyses for the features, events, and processes (FEPs) that do not easily fit into the existing Process Model Report (PMR) structure. These FEPs include the 3 1 FEPs designated as System-Level Primary FEPs and the 22 FEPs designated as Criticality Primary FEPs. A list of these FEPs is provided in Section 1.1. This AMR (AN-WIS-MD-000019) documents the Screening Decision and Regulatory Basis, Screening Argument, and Total System Performance Assessment (TSPA) Disposition for each of the subject Primary FEPs. This AMR provides screening information and decisions for the TSPA-SR report and provides the same information for incorporation into a project-specific FEPs database. This AMR may also assist reviewers during the licensing-review process

  15. Driving ordering processes in molecular-dynamics simulations.

    Dittmar, Harro; Kusalik, Peter G

    2014-05-16

    Self-organized criticality describes the emergence of complexity in dynamical nonequilibrium systems. In this paper we introduce a unique approach whereby a driven energy conversion is utilized as a sampling bias for ordered arrangements in molecular dynamics simulations of atomic and molecular fluids. This approach gives rise to dramatically accelerated nucleation rates, by as much as 30 orders of magnitude, without the need of predefined order parameters, which commonly employed rare-event sampling methods rely on. The measured heat fluxes suggest how the approach can be generalized. PMID:24877946

  16. Two-level hierarchical fragmentation in the northern filament of the Orion Molecular Cloud 1

    Teixeira, P. S.; Takahashi, S.; Zapata, L. A.; Ho, P. T. P.

    2016-03-01

    -equidistant length of ≈30' (0.06 pc). This separation is dominated by the Jeans length and therefore indicates that the main physical process in the filament evolution was thermal fragmentation. Within the protostellar groups, the typical separation is ≈6'' (~2500 au), which is a factor 2-3 smaller than the Jeans length of the parental clumps within which the protostars are embedded. These results point to a hierarchical (two-level) thermal fragmentation process of the OMC 1n filament. The reduced continuun map (FITS file) is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/587/A47

  17. Molecular responses during cadmium-induced stress in Daphnia magna: Integration of differential gene expression with higher-level effects

    DNA microarrays offer great potential in revealing insight into mechanistic toxicity of contaminants. The aim of the present study was (i) to gain insight in concentration- and time-dependent cadmium-induced molecular responses by using a customized Daphnia magna microarray, and (ii) to compare the gene expression profiles with effects at higher levels of biological organization (e.g. total energy budget and growth). Daphnids were exposed to three cadmium concentrations (nominal value of 10, 50, 100 μg/l) for two time intervals (48 and 96 h). In general, dynamic expression patterns were obtained with a clear increase of gene expression changes at higher concentrations and longer exposure duration. Microarray analysis revealed cadmium affected molecular pathways associated with processes such as digestion, oxygen transport, cuticula metabolism and embryo development. These effects were compared with higher-level effects (energy budgets and growth). For instance, next to reduced energy budgets due to a decline in lipid, carbohydrate and protein content, we found an up-regulated expression of genes related to digestive processes (e.g. α-esterase, cellulase, α-amylase). Furthermore, cadmium affected the expression of genes coding for proteins involved in molecular pathways associated with immune response, stress response, cell adhesion, visual perception and signal transduction in the present study

  18. Molecular alignment effect on the photoassociation process via a pump-dump scheme.

    Wang, Bin-Bin; Han, Yong-Chang; Cong, Shu-Lin

    2015-09-01

    The photoassociation processes via the pump-dump scheme for the heternuclear (Na + H → NaH) and the homonuclear (Na + Na → Na2) molecular systems are studied, respectively, using the time-dependent quantum wavepacket method. For both systems, the initial atom pair in the continuum of the ground electronic state (X(1)Σ(+)) is associated into the molecule in the bound states of the excited state (A(1)Σ(+)) by the pump pulse. Then driven by a time-delayed dumping pulse, the prepared excited-state molecule can be transferred to the bound states of the ground electronic state. It is found that the pump process can induce a superposition of the rovibrational levels |v, j〉 on the excited state, which can lead to the field-free alignment of the excited-state molecule. The molecular alignment can affect the dumping process by varying the effective coupling intensity between the two electronic states or by varying the population transfer pathways. As a result, the final population transferred to the bound states of the ground electronic state varies periodically with the delay time of the dumping pulse. PMID:26342366

  19. Molecular alignment effect on the photoassociation process via a pump-dump scheme

    The photoassociation processes via the pump-dump scheme for the heternuclear (Na + H → NaH) and the homonuclear (Na + Na → Na2) molecular systems are studied, respectively, using the time-dependent quantum wavepacket method. For both systems, the initial atom pair in the continuum of the ground electronic state (X1Σ+) is associated into the molecule in the bound states of the excited state (A1Σ+) by the pump pulse. Then driven by a time-delayed dumping pulse, the prepared excited-state molecule can be transferred to the bound states of the ground electronic state. It is found that the pump process can induce a superposition of the rovibrational levels |v, j〉 on the excited state, which can lead to the field-free alignment of the excited-state molecule. The molecular alignment can affect the dumping process by varying the effective coupling intensity between the two electronic states or by varying the population transfer pathways. As a result, the final population transferred to the bound states of the ground electronic state varies periodically with the delay time of the dumping pulse

  20. Molecular alignment effect on the photoassociation process via a pump-dump scheme

    Wang, Bin-Bin; Han, Yong-Chang, E-mail: ychan@dlut.edu.cn; Cong, Shu-Lin [School of Physics and Optoelectronic Technology, Dalian University of Technology, Dalian 116024 (China)

    2015-09-07

    The photoassociation processes via the pump-dump scheme for the heternuclear (Na + H → NaH) and the homonuclear (Na + Na → Na{sub 2}) molecular systems are studied, respectively, using the time-dependent quantum wavepacket method. For both systems, the initial atom pair in the continuum of the ground electronic state (X{sup 1}Σ{sup +}) is associated into the molecule in the bound states of the excited state (A{sup 1}Σ{sup +}) by the pump pulse. Then driven by a time-delayed dumping pulse, the prepared excited-state molecule can be transferred to the bound states of the ground electronic state. It is found that the pump process can induce a superposition of the rovibrational levels |v, j〉 on the excited state, which can lead to the field-free alignment of the excited-state molecule. The molecular alignment can affect the dumping process by varying the effective coupling intensity between the two electronic states or by varying the population transfer pathways. As a result, the final population transferred to the bound states of the ground electronic state varies periodically with the delay time of the dumping pulse.

  1. Atmospheric processes on ice nanoparticles in molecular beams

    Fárník, Michal; Poterya, Viktoriya

    2014-01-01

    Roč. 2, č. 2014 (2014), s. 4. ISSN 2296-2646 R&D Projects: GA ČR GA203/09/0422; GA ČR GAP208/11/0161 Institutional support: RVO:61388955 Keywords : molecular beams * photodissociation * water clusters Subject RIV: BL - Plasma and Gas Discharge Physics

  2. Molecular dynamics simulations of the nano-droplet impact process on hydrophobic surfaces

    Large-scale molecular dynamics simulations are used to study the dynamic processes of a nano-droplet impacting on hydrophobic surfaces at a microscopic level. Both the impact phenomena and the velocity distributions are recorded and analyzed. According to the simulation results, similar phenomena are obtained to those in macro-experiments. Impact velocity affects the spread process to a greater degree than at a level of contact angle when the velocity is relatively high. The velocity distribution along the X axis during spread is wave-like, either W- or M-shaped, and the velocity at each point is oscillatory; while the edges have the highest spread velocity and there are crests in the distribution curve which shift toward the edges over time. The distribution along the Y axis is <- or >-shaped, and the segments above the middle have the lowest decrease rate in the spreading process and the highest increase rate in the retraction process. (electromagnetism, optics, acoustics, heat transfer, classical mechanics, and fluid dynamics)

  3. Atmospheric processes on ice nanoparticles in molecular beams

    Michal eFárník; Viktoriya ePoterya

    2014-01-01

    This review summarizes some recent experiments with ice nanoparticles (large water clusters) in molecular beams and outlines their atmospheric relevance: (1) Investigation of mixed water–nitric acid particles by means of the electron ionization and sodium doping combined with photoionization revealed the prominent role of HNO3 molecule as the condensation nuclei. (2) The uptake of atmospheric molecules by water ice nanoparticles has been studied, and the pickup cross sections for some molecul...

  4. West Valley demonstration project: alternative processes for solidifying the high-level wastes

    In 1980, the US Department of Energy (DOE) established the West Valley Solidification Project as the result of legislation passed by the US Congress. The purpose of this project was to carry out a high level nuclear waste management demonstration project at the Western New York Nuclear Service Center in West Valley, New York. The DOE authorized the Pacific Northwest Laboratory (PNL), which is operated by Battelle Memorial Institute, to assess alternative processes for treatment and solidification of the WNYNSC high-level wastes. The Process Alternatives Study is the suject of this report. Two pretreatment approaches and several waste form processes were selected for evaluation in this study. The two waste treatment approaches were the salt/sludge separation process and the combined waste process. Both terminal and interim waste form processes were studied. The terminal waste form processes considered were: borosilicate glass, low-alkali glass, marbles-in-lead matrix, and crystallinolecular potential and molecular dynamics calculations of the effect are yet to be completed. Cous oxide was also investigated. The reaction is first order in nitrite ion, second order in hydrogen ion, and between zero and first order in hydroxylamine monosulfonate, depending on the concentration

  5. Molecular characterization of low molecular weight dissolved organic matter in water reclamation processes using Orbitrap mass spectrometry.

    Phungsai, Phanwatt; Kurisu, Futoshi; Kasuga, Ikuro; Furumai, Hiroaki

    2016-09-01

    Reclaimed water has recently become an important water source for urban use, but the composition of dissolved organic matter (DOM) in reclaimed water has rarely been characterized at the compound level because of its complexity. In this study, the transformation and changes in composition of low molecular weight DOM in water reclamation processes, where secondary effluent of the municipal wastewater treatment plant was further treated by biofiltration, ozonation and chlorination, were investigated by "unknown" screening analysis using Orbitrap mass spectrometry (Orbitrap MS). The intense ions were detected over an m/z range from 100 to 450. In total, 2412 formulae with various heteroatoms were assigned, and formulae with carbon (C), hydrogen (H) and oxygen (O) only and C, H, O and sulfur (S) were the most abundant species. During biofiltration, CHO-only compounds with relatively high hydrogen to carbon (H/C) ratio or with saturated structure were preferentially removed, while CHOS compounds were mostly removed. Ozonation induced the greatest changes in DOM composition. CHOS compounds were mostly decreased after ozonation while ozone selectively removed CHO compounds with relatively unsaturated structure and produced compounds that were more saturated and with a higher degree of oxidation. After chlorination, 168 chlorine-containing formulae, chlorinated disinfection by-products (DBPs), were additionally detected. Candidate DBP precursors were determined by tracking chlorinated DBPs formed via electrophilic substitution, half of which were generated during the ozonation. PMID:27235773

  6. Turning randomness into meaning at the molecular level using Muller's morphs

    Kathleen Henson

    2012-02-01

    While evolutionary theory follows from observable facts and logical inferences (Mayr, 1985, historically, the origin of novel inheritable variations was a major obstacle to acceptance of natural selection (Bowler, 1992; Bowler, 2005. While molecular mechanisms address this issue (Jablonka and Lamb, 2005, analysis of responses to the Biological Concept Inventory (BCI (Klymkowsky et al., 2010, revealed that molecular biology majors rarely use molecular level ideas in their discourse, implying that they do not have an accessible framework within which to place evolutionary variation. We developed a “Socratic tutorial” focused on Muller's categorization of mutations' phenotypic effects (Muller, 1932. Using a novel vector-based method to analyzed students' essay responses, we found that a single interaction with this tutorial led to significant changes in thinking toward a clearer articulation of the effects of mutational change. We suggest that Muller's morphs provides an effective framework for facilitating student learning about mutational effects and evolutionary mechanisms.

  7. Tuning molecular level alignment and work function modification through self-assembled monolayers on noble metals: theoretical perspectives

    Full text: There is currently significant interest in highly-ordered, self-assembled monolayers (SAMs) on (noble) metal surfaces, inspired both by the emergence of the field of molecular electronics alongside the high potential for SAMs to improve the properties of more conventional device structures. SAMs are also used to control surface reactivity and for chemical sensing applications. In order to tune the interface properties and to endow the self-assembled systems with functionality suitable for use in either macroscopic or nanoscale devices, the use of π-conjugated systems is highly promising and the focus of intense, multidisciplinary research. The goal of the present study is to provide an in-depth description of the electronic structure of the interface between metallic substrates and covalently bound conjugated molecules. In this way, we expect to devise strategies to tune the interaction and thus the properties of the investigated systems and eventually to gain a full understanding of the processes governing the electronics of metal/organic interfaces. Here, we describe a first step in that direction: we study conjugated SAMs consisting of molecules with widely varied molecular ionization potentials, different conjugated backbones with different polarizabilities, and monolayers with varying degrees of coverage. We consider noble metals with varying work functions such as Au, Ag, and Pt, different molecule docking groups and investigate the effects of mechanical stress on the organic system. Using DFT band-structure-type methods, the details of the interface morphology, charge transfer between the metal and the molecules, interface dipoles, molecular layer depolarization, and work function modifications as well as the alignment between metallic and molecular levels are described. Our thorough analysis provides results that are sometimes a priori unexpected, like the finding that by properly tuning the molecular structure, the level alignment between the

  8. Pseudomonas viridiflava, a multi host plant pathogen with significant genetic variation at the molecular level.

    Panagiotis F Sarris

    Full Text Available The pectinolytic species Pseudomonas viridiflava has a wide host range among plants, causing foliar and stem necrotic lesions and basal stem and root rots. However, little is known about the molecular evolution of this species. In this study we investigated the intraspecies genetic variation of P. viridiflava amongst local (Cretan, as well as international isolates of the pathogen. The genetic and phenotypic variability were investigated by molecular fingerprinting (rep-PCR and partial sequencing of three housekeeping genes (gyrB, rpoD and rpoB, and by biochemical and pathogenicity profiling. The biochemical tests and pathogenicity profiling did not reveal any variability among the isolates studied. However, the molecular fingerprinting patterns and housekeeping gene sequences clearly differentiated them. In a broader phylogenetic comparison of housekeeping gene sequences deposited in GenBank, significant genetic variability at the molecular level was found between isolates of P. viridiflava originated from different host species as well as among isolates from the same host. Our results provide a basis for more comprehensive understanding of the biology, sources and shifts in genetic diversity and evolution of P. viridiflava populations and should support the development of molecular identification tools and epidemiological studies in diseases caused by this species.

  9. Polyelectrolytes processing at pilot scale level by electron beam irradiation

    Three years of research, combined with engineering activities, have culminated in the development of a new method of electron beam processing applicable up to the pilot scale level, namely, the polyelectrolytes (acrylamide - acrylic acid copolymers) electron beam processing. This new radiation processing method has been achieved by bilateral co-operation between the National Institute for Laser, Plasma and Radiation Physics (NILPRP) and the Electrical Design and Research Institute, EDRI - Bucharest. The polyelectrolytes electron beam (EB) processing was put in operation at EDRI, where, recently, an industrial electron accelerator of 2 MeV and 20 kW, manufactured by Institute of Nuclear Physics, Novosibirsk, Russia was installed in a specially designed irradiation facility. Automatic start-up via computer control makes it compatible with industrial processing. According to the first conclusions, which resulted from our experimental research with regard to acrylamide - acrylic acid copolymers production by EB irradiation, the proper physical and chemical characteristics can be well controlled by chemical composition to be treated and by suitable adjustment of absorbed dose and absorbed dose rate. So, it was possible to obtain a very large area of characteristics and therefore a large area of applications. The conversion coefficient is very high (> 98%) and concentration of the residual monomer is under 0.05%. The tests applied to some wastewaters from the vegetable oil plants demonstrated that the fatty substances, matters in suspension, chemical oxygen demand and biological oxygen demand over 5 days were much reduced, in comparison with classical treatment. Also, sedimentation time was around four times smaller and sediment volume was 60% smaller than the values obtained in case of classical treatment. The necessary EB absorbed dose for the acrylamide - acrylic acid aqueous solution polymerization, established by optimization of chemical composition and irradiation

  10. Empoderamiento: Proceso, Nivel y Contexto Empowerment: Process, Level, and Context

    Carmen Silva

    2004-11-01

    Full Text Available En este artículo se discute el fenómeno del empoderamiento y se analiza la distinción teórica entre proceso y resultado de empoderamiento (Zimmerman, 2000. A partir de las formulaciones de este autor y el aporte de una perspectiva interaccional (Bronfenbrenner, 1987, se sostiene que aquella diferenciación es poco viable en términos objetivos y absolutos o de esencia, pero sí útil, en términos analíticos, desde la percepción de la propia comunidad involucrada, que debe ser comprendida por el colaborador externo. También se propone establecer una diferencia entre contexto y nivel de empoderamiento, y analizar el contexto del fenómeno en los niveles individual, organizacional y comunitario del agregado social, lo que aporta claridad a su definición. De esta manera adquiere centralidad la concepción del empoderamiento como proceso en sucesivos contextos que benefician no sólo a los individuos sino que a los colectivos socialesA critical analysis of the concept of empowerment and the theoretical distinction between empowerment process and outcome (Zimmerman, 2000 are presented. Based on Zimmerman's conceptualisation, and the interaccional perspective (Bronfenbrenner, 1987, we argue that the distinction between empowerment process and outcome, though analytically useful (if based on the perception of the community itself from their own experience, which must be understood by professional agent is not always viable in absolute or objective terms. In addition, we suggest to distinguish between context and level of analyses in empowerment theory, and to analyze the context of the empowerment phenomenon at the individual, organizational and community level, which clarifies the definition of each of them. In sum, empowerment is conceived as a process within successive contexts that benefits not only individuals, but also different social aggregate kinds of groups

  11. SENTINEL-2 image quality and level 1 processing

    Meygret, Aimé; Baillarin, Simon; Gascon, Ferran; Hillairet, Emmanuel; Dechoz, Cécile; Lacherade, Sophie; Martimort, Philippe; Spoto, François; Henry, Patrice; Duca, Riccardo

    2009-08-01

    In the framework of the Global Monitoring for Environment and Security (GMES) programme, the European Space Agency (ESA) in partnership with the European Commission (EC) is developing the SENTINEL-2 optical imaging mission devoted to the operational monitoring of land and coastal areas. The Sentinel-2 mission is based on a twin satellites configuration deployed in polar sun-synchronous orbit and is designed to offer a unique combination of systematic global coverage with a wide field of view (290km), a high revisit (5 days at equator with two satellites), a high spatial resolution (10m, 20m and 60 m) and multi-spectral imagery (13 bands in the visible and the short wave infrared spectrum). SENTINEL-2 will ensure data continuity of SPOT and LANDSAT multispectral sensors while accounting for future service evolution. This paper presents the main geometric and radiometric image quality requirements for the mission. The strong multi-spectral and multi-temporal registration requirements constrain the stability of the platform and the ground processing which will automatically refine the geometric physical model through correlation technics. The geolocation of the images will take benefits from a worldwide reference data set made of SENTINEL-2 data strips geolocated through a global space-triangulation. These processing are detailed through the description of the level 1C production which will provide users with ortho-images of Top of Atmosphere reflectances. The huge amount of data (1.4 Tbits per orbit) is also a challenge for the ground processing which will produce at level 1C all the acquired data. Finally we discuss the different geometric (line of sight, focal plane cartography, ...) and radiometric (relative and absolute camera sensitivity) in-flight calibration methods that will take advantage of the on-board sun diffuser and ground targets to answer the severe mission requirements.

  12. Organic conductors as novel ``molecular rulers`` for advanced manufacturing processes

    Williams, J.M.

    1995-12-31

    Future advanced manufacturing equipment used in high technology programs will require ultra-high precision and associated machining tool operations that require placement accuracy of {approximately} 1--100 nm (1 nm = 10 {angstrom}). There is consensus among engineers that this equipment will be based on STM (Scanning Tunneling Microscope) technology. All such STM-based ``drivers`` must contain a metrology system that requires absolute length standards referenced to atomic spacings for calibration. Properly designed organic conductor substrate crystals have the potential to be molecular rulers for STM-based advanced manufacturing equipment. The major challenges in future organic conductor research aimed at STM metrology application are listed.

  13. Molecular solution processing of metal chalcogenide thin film solar cells

    Yang, Wenbing

    2013-01-01

    The barrier to utilize solar generated electricity mainly comes from their higher cost relative to fossil fuels. However, innovations with new materials and processing techniques can potentially make cost effective photovoltaics. One such strategy is to develop solution processed photovoltaics which avoid the expensive vacuum processing required by traditional solar cells. The dissertation is mainly focused on two absorber material system for thin film solar cells: chalcopyrite CuIn(S,Se)2 (C...

  14. Effect of heparin and low-molecular weight heparin on serum potassium and sodium levels

    Girish M Bengalorkar; N Sarala; Venkatrathnamma, P. N.; Kumar, T. N.

    2011-01-01

    Introduction: To study the effects of heparin and low-molecular weight heparin (LMWH) on potassium and sodium levels in patients with cardiovascular diseases (CVDs) and stroke. Materials and Methods : Sixty patients were recruited with 30 patients each receiving heparin and enoxaparin. Patients with CVD and stroke receiving heparin and LMWH were compared for their demographic profile and laboratory data, and this was analyzed by descriptive statistics. Risk factors associated with the develop...

  15. Sources of genetic resistance in maize to Fusarium stalk rot andtheir variations at molecular level

    QURESHI, SAJJAD HUSSAIN; Qayyum, Abdul; FIERS, WILL

    2015-01-01

    Identifying the resistant genotypes is one of the vital strategies to control Fusarium stalk rot disease in maize. Fifty accessions of maize germplasm were evaluated for resistance to stalk rot caused by Fusarium verticillioides at the Maize and Millet Research Institute, Yousafwala, Pakistan, during the spring and autumn of 2010, and their genetic variations were also studied at the molecular level to avoid environmental effects in the Department of Medicinal Chemistry, University of Minneso...

  16. Investigation of variables influencing cognitive inhibition: from the behavioral to the molecular level

    Dieler, Alica Christina

    2011-01-01

    The present work investigated the neural mechanisms underlying cognitive inhibition/thought suppression in Anderson’s and Green’s Think/No-Think paradigm (TNT), as well as different variables influencing these mechanisms at the cognitive, the neurophysiological, the electrophysiological and the molecular level. Neurophysiological data collected with fNIRS and fMRI have added up to the existing evidence of a fronto-hippocampal network interacting during the inhibition of unwanted thoughts. Som...

  17. Molecular-level engineering of protein physical hydrogels for predictive sol-gel phase behavior

    Mulyasasmita, Widya; Lee, Ji Seok; Heilshorn, Sarah C.

    2011-01-01

    Predictable tuning of bulk mechanics from the molecular level remains elusive in many physical hydrogel systems due to the reliance on non-specific and non-stoichiometric chain interactions for network formation. We describe a Mixing-Induced Two-Component Hydrogel (MITCH) system, in which network assembly is driven by specific and stoichiometric peptide-peptide binding interactions. By integrating protein science methodologies with simple polymer physics model, we manipulate the polypeptide b...

  18. Sensing, physiological effects and molecular response to elevated CO2 levels in eukaryotes

    Sharabi, Kfir; Lecuona, Emilia; Helenius, Iiro Taneli; Beitel, Greg J.; Sznajder, Jacob Iasha; Gruenbaum, Yosef

    2009-01-01

    Carbon dioxide (CO2) is an important gaseous molecule that maintains biosphere homeostasis and is an important cellular signalling molecule in all organisms. The transport of CO2 through membranes has fundamental roles in most basic aspects of life in both plants and animals. There is a growing interest in understanding how CO2 is transported into cells, how it is sensed by neurons and other cell types and in understanding the physiological and molecular consequences of elevated CO2 levels (h...

  19. Molecular-Level Insights into Photocatalysis from Scanning Probe Microscopy Studies on TiO2(110)

    Henderson, Michael A.; Lyubinetsky, Igor

    2013-06-12

    The field of heterogeneous photocatalysis has grown considerably in the decades since Fujishima and Honda's ground-breaking publications of photoelectrochemistry on TiO2. Numerous review articles continue to point to both progress made in the use of heterogeneous materials (such as TiO2) to perform photoconversion processes, and the many opportunities and challenges in heterogeneous photocatalysis research such as solar energy conversion and environmental remediation. The past decade has also seen an increase in the use of molecular-level approaches applied to model single crystal surfaces in an effort to obtain new insights into photocatalytic phenomena. In particular, scanning probe techniques (SPM) have enabled researchers to take a ‘nanoscale’ approach to photocatalysis that includes interrogation of the reactivities of specific sites and adsorbates on a model photocatalyst surface. The rutile TiO2(110) surface has become the prototypical oxide single crystal surface for fundamental studies of many interfacial phenomena. In particular, TiO2(110) has become an excellent model surface for probing photochemical and photocatalytic reactions at the molecular level. A variety of experimental approaches have emerged as being ideally suited for studying photochemical reactions on TiO2(110), including desorption-oriented approaches and electronic spectroscopies, but perhaps the most promising techniques for evaluating site-specific properties are those of SPM. In this review, we highlight the growing use of SPM techniques in providing molecular-level insights into surface photochemistry on the model photocatalyst surface of rutile TiO2(110). Our objective is to both illustrate the unique knowledge that scanning probe techniques have already provided the field of photocatalysis, and also to motivate a new generation of effort into the use of such approaches to obtain new insights into the molecular level details of photochemical events occurring at interfaces

  20. HELAC-PHEGAS: A generator for all parton level processes

    Cafarella, Alessandro; Papadopoulos, Costas G.; Worek, Malgorzata

    2009-10-01

    The updated version of the HELAC-PHEGAS event generator is presented. The matrix elements are calculated through Dyson-Schwinger recursive equations using color connection representation. Phase-space generation is based on a multichannel approach, including optimization. HELAC-PHEGAS generates parton level events with all necessary information, in the most recent Les Houches Accord format, for the study of any process within the Standard Model in hadron and lepton colliders. New version program summaryProgram title: HELAC-PHEGAS Catalogue identifier: ADMS_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADMS_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 35 986 No. of bytes in distributed program, including test data, etc.: 380 214 Distribution format: tar.gz Programming language: Fortran Computer: All Operating system: Linux Classification: 11.1, 11.2 External routines: Optionally Les Houches Accord (LHA) PDF Interface library ( http://projects.hepforge.org/lhapdf/) Catalogue identifier of previous version: ADMS_v1_0 Journal reference of previous version: Comput. Phys. Comm. 132 (2000) 306 Does the new version supersede the previous version?: Yes, partly Nature of problem: One of the most striking features of final states in current and future colliders is the large number of events with several jets. Being able to predict their features is essential. To achieve this, the calculations need to describe as accurately as possible the full matrix elements for the underlying hard processes. Even at leading order, perturbation theory based on Feynman graphs runs into computational problems, since the number of graphs contributing to the amplitude grows as n!. Solution method: Recursive algorithms based on Dyson-Schwinger equations have been developed recently in

  1. Modulation of ROS levels in fibroblasts by altering mitochondria regulates the process of wound healing.

    Janda, Jaroslav; Nfonsam, Valentine; Calienes, Fernanda; Sligh, James E; Jandova, Jana

    2016-05-01

    Mitochondria are the major source of reactive oxygen species (ROS) in fibroblasts which are thought to be crucial regulators of wound healing with a potential to affect the expression of nuclear genes involved in this process. ROS generated by mitochondria are involved in all stages of tissue repair process but the regulation of ROS-generating system in fibroblasts still remains poorly understood. The purpose of this study was to better understand molecular mechanisms of how the regulation of ROS levels generated by mitochondria may influence the process of wound repair. Cybrid model system of mtDNA variations was used to study the functional consequences of altered ROS levels on wound healing responses in a uniform nuclear background of cultured ρ(0) fibroblasts. Mitochondrial ROS in cybrids were modulated by antioxidants that quench ROS to examine their ability to close the wound. Real-time PCR arrays were used to investigate whether ROS generated by specific mtDNA variants have the ability to alter expression of some key nuclear-encoded genes central to the wound healing response and oxidative stress. Our data suggest levels of mitochondrial ROS affect expression of some nuclear encoded genes central to wound healing response and oxidative stress and modulation of mitochondrial ROS by antioxidants positively affects in vitro process of wound closure. Thus, regulation of mitochondrial ROS-generating system in fibroblasts can be used as effective natural redox-based strategy to help treat non-healing wounds. PMID:26873374

  2. Effects of molecular structural variants on serum Krebs von den Lungen-6 levels in sarcoidosis

    Shigemura Masahiko; Nasuhara Yasuyuki; Konno Satoshi; Shimizu Chikara; Matsuno Kazuhiko; Yamguchi Etsuro; Nishimura Masaharu

    2012-01-01

    Abstract Background Serum Krebs von den Lungen-6 (KL-6), which is classified as human mucin-1 (MUC1), is used as a marker of sarcoidosis and other interstitial lung diseases. However, there remain some limitations due to a lack of information on the factors contributing to increased levels of serum KL-6. This study was designed to investigate the factors contributing to increased levels of serum KL-6 by molecular analysis. Methods Western blot analysis using anti-KL-6 antibody was performed s...

  3. Effects of molecular structural variants on serum Krebs von den Lungen-6 levels in sarcoidosis

    Shigemura, Masahiko; Nasuhara, Yasuyuki; Konno, Satoshi; Shimizu, Chikara; Matsuno, Kazuhiko; Yamguchi, Etsuro; Nishimura, Masaharu

    2012-01-01

    Background: Serum Krebs von den Lungen-6 (KL-6), which is classified as human mucin-1 (MUC1), is used as a marker of sarcoidosis and other interstitial lung diseases. However, there remain some limitations due to a lack of information on the factors contributing to increased levels of serum KL-6. This study was designed to investigate the factors contributing to increased levels of serum KL-6 by molecular analysis. Methods: Western blot analysis using anti-KL-6 antibody was performed simultan...

  4. Tree-indexed processes: a high level crossing analysis

    Mark Kelbert

    2003-01-01

    Full Text Available Consider a branching diffusion process on R1 starting at the origin. Take a high level u>0 and count the number R(u,n of branches reaching u by generation n. Let Fk,n(u be the probability P(R(u,n

  5. Atmospheric processes on ice nanoparticles in molecular beams

    Michal eFárník

    2014-02-01

    Full Text Available This review summarizes some recent experiments with ice nanoparticles (large water clusters in molecular beams and outlines their atmospheric relevance: (1 Investigation of mixed water–nitric acid particles by means of the electron ionization and sodium doping combined with photoionization revealed the prominent role of HNO3 molecule as the condensation nuclei. (2 The uptake of atmospheric molecules by water ice nanoparticles has been studied, and the pickup cross sections for some molecules exceed significantly the geometrical sizes of the ice nanoparticles. (3 Photodissociation of hydrogen halides on water ice particles has been shown to proceed via excitation of acidically dissociated ion pair and subsequent biradical generation and H3O dissociation. The photodissociation of CF2Cl2 molecule in clusters is also mentioned. Possible atmospheric consequences of all these results are briefly discussed.

  6. Heat impact caused molecular level changes in solid and dissolved soil organic matter

    Hofmann, Diana; Steffen, Bernhard; Eckhardt, Kai-Uwe; Leinweber, Peter

    2015-04-01

    resolution (used 400.000 at m/z 400 Da) and mass accuracy (≤ 1 ppm), simultaneously providing molecular level details of thousands of compounds. The characteristics and differences of the FTICR-MS spectra with as many as ten or more peaks at each nominal mass are discussed: heated samples showed considerable higher intensities of even numbered peaks. An in-house developed, automated post processing was used for further exploitation of the data with the aim of an unambiguous assignment of as many peaks as possible. Obtained mass lists were transformed for sorting and preparation/ interpretation of graphics like Kendrick and van Krevelen plots. The heat-treated solid samples show decreasing C/N ratios and the formation cyclic and N-heterocyclic compounds in good agreement among the various methods (Py-FIMS and C- and N-XANES). Detailed insight into the hot-water extracts by FTICR-MS showed clear qualitative as well as quantitative changes in the number and the intensity of nitrogen and nitrogen + sulfur containing compounds, respectively, which generally became enriched under soil heating. This demonstrates for the first time, that not only the bulk SOM is affected in structure by heat impact but also the more mobile DOM. We assume, that heat impact volatilizes and oxidizes parts of the organic substances is as expected but another part of the substances incorporates (further) nitrogen atom(s) similar to the generation of new compounds under the conditions of plasma etching in nitrogen atmosphere. This would explain to some extent, why soils are e.g. after fire clearing of vegetation are highly fertile for a short period (better plant acceptable compounds) but become more infertile in the long run, especially under tropical conditions with frequently heavy rain that would lead to an increased leaching of compounds with higher polarity.

  7. Molecular imaging with radionuclides, a powerful technique for studying biological processes in vivo

    Cisbani, E.; Cusanno, F.; Garibaldi, F.; Magliozzi, M. L.; Majewski, S.; Torrioli, S.; Tsui, B. M. W.

    2007-02-01

    Our team is carrying on a systematic study devoted to the design of a SPECT detector with submillimeter resolution and adequate sensitivity (1 cps/kBq). Such system will be used for functional imaging of biological processes at molecular level in small animal. The system requirements have been defined by two relevant applications: study of atherosclerotic plaques characterization and stem cells diffusion and homing. In order to minimize costs and implementation time, the gamma detector will be based—as much as possible—on conventional components: scintillator crystal and position sensitive PhotoMultipliers read by individual channel electronics. A coded aperture collimator should be adapted to maximize the efficiency. The optimal selection of the detector components is investigated by systematic use of Monte-Carlo simulations (and laboratory validation tests); and finally preliminary results are presented and discussed here.

  8. Molecular Modeling of Environmentally Important Processes: Reduction Potentials

    Lewis, Anne; Bumpus, John A.; Truhlar, Donald G.; Cramer, Christopher J.

    2004-01-01

    The increasing use of computational quantum chemistry in the modeling of environmentally important processes is described. The employment of computational quantum mechanics for the prediction of oxidation-reduction potential for solutes in an aqueous medium is discussed.

  9. Decontamination processes for low level radioactive waste metal objects

    Disposal and safe storage of contaminated nuclear waste is a problem of international scope. Although the greatest volume of such waste is concentrated in the USA and former Soviet Union, Western Europe and Japan have contaminated nuclear waste requiring attention. Japan's radioactive nuclear waste is principally generated at nuclear power plants since it has no nuclear weapons production. However, their waste reduction, storage and disposal problems may be comparable to that of the USA on an inhabited area basis when consideration is given to population density where Japan's population, half that of the USA, lives in an area slightly smaller than that of California's. If everyone's backyard was in California, the USA might have insoluble radioactive waste reduction, storage and disposal problems. Viewing Japan's contaminated nuclear waste as a national problem requiring solutions, as well as an economic opportunity, Morikawa began research and development for decontaminating low level radioactive nuclear waste seven years ago. As engineers and manufacturers of special machinery for many years Morikawa brings special electro/mechanical/pneumatic Skills and knowledge to solving these unique problems. Genden Engineering Services and Construction Company (GESC), an affiliate of Japan Atomic Power Company, recently joined with Morikawa in this R ampersand D effort to decontaminate low level radioactive nuclear waste (LLW) and to substantially reduce the volume of such nuclear waste requiring long term storage. This paper will present equipment with both mechanical and chemical processes developed over these several years by Morikawa and most recently in cooperation with GESC

  10. Molecular Specificity of Multiple Hippocampal Processes Governing Fear Extinction

    Radulovic, Jelena; Tronson, Natalie C

    2010-01-01

    Over many years, fear extinction has been conceptualized as one dominant process, new inhibitory learning, which serves to dampen previously acquired fear. Here we present an alternative view, that brain region-specific processing of representations, expectations and emotional attributes of the fear-provoking event, recruits unique mechanisms that interdependently contribute to the conditioning and extinction of fear. The co-occurrence of these mechanisms within the fear circuit can thus be t...

  11. Levels and Atypical Evolutions of the Romanian Demographic Processes

    Mirela Ionela Aceleanu

    2007-01-01

    Full Text Available Within the XXth century, especially in the second half thereof, the approach views of the relation between the population and economy (both of them regarded in dynamics have multiplied themselves, the points of view as regards this subject becoming not only much more diverse but also opposite. All these views are characterised by the population transformation in endogenous factor (in internal, intrinsic side of the economic development (of the economic growth, factor that, at its turn, is determined by the economic processes. The double position of the population in the demo-economical relations system - as main production factor and as virtual recipient of produced goods - is a strong argument in the favour of the demographic factor as endogenous factor of growth and economic development. The correlations between the two variables are diverse and very difficultly to be quantified. It is known that the effect of the demographic impact upon the economic factor is felt after many years from the date of the demo-economic phenomenon occurring. So, within the last decades, the research intended to identify certain essential, durable relations between the population evolution and the economic growth became more intensive. On this line there are presented atypical evolutions and levels of demographic processes in Romania.

  12. Direct observation of atomic-level nucleation and growth processes from an ultrathin metallic glass films

    Huang, K. Q.; Cao, C. R.; Sun, Y. T.; Li, J.; Bai, H. Y.; Zheng, D. N., E-mail: l.gu@iphy.ac.cn, E-mail: dzheng@iphy.ac.cn, E-mail: whw@iphy.ac.cn; Wang, W. H., E-mail: l.gu@iphy.ac.cn, E-mail: dzheng@iphy.ac.cn, E-mail: whw@iphy.ac.cn [Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Gu, L., E-mail: l.gu@iphy.ac.cn, E-mail: dzheng@iphy.ac.cn, E-mail: whw@iphy.ac.cn [Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Collaborative Innovation Center of Quantum Matter, Beijing 100190 (China)

    2016-01-07

    Till date, there have been no direct atomic-level experimental observations of the earliest stages of the nucleation and growth processes of nanocrystals formed by thermally induced crystallization in ultrathin metallic glasses (MGs). Here, we present a study of the crystallization process in atomically thin and highly stable MG films using double spherical aberration-corrected scanning transmission electron microscopy (Cs-TEM). Taking advantage of the stability of MG films with a slow crystallization process and the atomic-level high resolution of Cs-TEM, we observe the formation of the nucleus precursor of nanocrystals formed by atom aggregation followed by concomitant coalescence and stepwise evolution of the shape of the nanocrystals with a monodispersed and separated bimodal size distribution. Molecular dynamics simulation of the atomic motion in the glass film on a rigid amorphous substrate confirms the stepwise evolution processes of atom aggregation, cluster formation, cluster movement on the substrate, and cluster coalescence into larger crystalline particles. Our results might provide a better fundamental understanding of the nucleation and growth processes of nanocrystals in thin MG films.

  13. Direct observation of atomic-level nucleation and growth processes from an ultrathin metallic glass films

    Till date, there have been no direct atomic-level experimental observations of the earliest stages of the nucleation and growth processes of nanocrystals formed by thermally induced crystallization in ultrathin metallic glasses (MGs). Here, we present a study of the crystallization process in atomically thin and highly stable MG films using double spherical aberration-corrected scanning transmission electron microscopy (Cs-TEM). Taking advantage of the stability of MG films with a slow crystallization process and the atomic-level high resolution of Cs-TEM, we observe the formation of the nucleus precursor of nanocrystals formed by atom aggregation followed by concomitant coalescence and stepwise evolution of the shape of the nanocrystals with a monodispersed and separated bimodal size distribution. Molecular dynamics simulation of the atomic motion in the glass film on a rigid amorphous substrate confirms the stepwise evolution processes of atom aggregation, cluster formation, cluster movement on the substrate, and cluster coalescence into larger crystalline particles. Our results might provide a better fundamental understanding of the nucleation and growth processes of nanocrystals in thin MG films

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

    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. PMID:27050645

  15. Predicting the residual aluminum level in water treatment process

    J. Tomperi

    2013-06-01

    Full Text Available In water treatment processes, aluminum salts are widely used as coagulation chemical. High dose of aluminum has been proved to be at least a minor health risk and some evidence points out that aluminum could increase the risk of Alzheimer's disease. Thus it is important to minimize the amount of residual aluminum in drinking water and water used at food industry. In this study, the data of a water treatment plant (WTP was analyzed and the residual aluminum in drinking water was predicted using Multiple Linear Regression (MLR and Artificial Neural Network (ANN models. The purpose was to find out which variables affect the amount of residual aluminum and create simple and reliable prediction models which can be used in an early warning system (EWS. Accuracy of ANN and MLR models were compared. The new nonlinear scaling method based on generalized norms and skewness was used to scale all measurement variables to range [−2...+2] before data-analysis and modeling. The effect of data pre-processing was studied by comparing prediction results to ones achieved in an earlier study. Results showed that it is possible to predict the baseline level of residual aluminum in drinking water with a simple model. Variables that affected the most the amount of residual aluminum were among others: raw water temperature, raw water KMnO4 and PAC/KMnO4 (Poly-Aluminum Chloride/Potassium permanganate-ratio. The accuracies of MLR and ANN models were found to be almost the same. Study also showed that data pre-processing affects to the final prediction result.

  16. Predicting the residual aluminum level in water treatment process

    J. Tomperi

    2012-06-01

    Full Text Available In water treatment processes, aluminum salts are widely used as coagulation chemical. High dose of aluminum has been proved to be at least a minor health risk and some evidence points out that aluminum could increase the risk of Alzheimer's disease thus it is important to minimize the amount of residual aluminum in drinking water and water used at food industry. In this study, the data of a water treatment plant (WTP was analyzed and the residual aluminum in drinking water was predicted using Multiple Linear Regression (MLR and Artificial Neural Network (ANN models. The purpose was to find out which variables affect the amount of residual aluminum and create simple and reliable prediction models which can be used in an early warning system (EWS. Accuracy of ANN and MLR models were compared. The new nonlinear scaling method based on generalized norms and skewness was used to scale all measurement variables to range [−2...+2] before data-analysis and modeling. The effect of data pre-processing was studied by comparing prediction results to ones achieved in an earlier study. Results showed that it is possible to predict the baseline level of residual aluminum in drinking water with a simple model. Variables that affected the most the amount of residual aluminum were among others: raw water temperature, raw water KMnO4 and PAC / KMnO4-ratio. The accuracies of MLR and ANN models were found to be almost equal. Study also showed that data pre-processing affects to the final prediction result.

  17. Vibrational Distribution of Hydrogen Molecular Ions in High-Energy Ionization Processes

    CHEN Shao-Hao; HE Chun-Long; CHEN Chao; LI Jia-Ming

    2005-01-01

    @@ A theoretical time-dependent wave-packet dynamics method is applied to calculate the distribution of vibrational states of hydrogen molecular ions produced in high-energy ionization processes of hydrogen molecules. The isotope effect is elucidated in agreement with the available experimental measurements. Our proposed method should be readily applied in other atomic and molecular processes considering great advances in electronic computation science and technology.

  18. Post-processing interstitialcy diffusion from molecular dynamics simulations

    Bhardwaj, U.; Bukkuru, S.; Warrier, M.

    2016-01-01

    An algorithm to rigorously trace the interstitialcy diffusion trajectory in crystals is developed. The algorithm incorporates unsupervised learning and graph optimization which obviate the need to input extra domain specific information depending on crystal or temperature of the simulation. The algorithm is implemented in a flexible framework as a post-processor to molecular dynamics (MD) simulations. We describe in detail the reduction of interstitialcy diffusion into known computational problems of unsupervised clustering and graph optimization. We also discuss the steps, computational efficiency and key components of the algorithm. Using the algorithm, thermal interstitialcy diffusion from low to near-melting point temperatures is studied. We encapsulate the algorithms in a modular framework with functionality to calculate diffusion coefficients, migration energies and other trajectory properties. The study validates the algorithm by establishing the conformity of output parameters with experimental values and provides detailed insights for the interstitialcy diffusion mechanism. The algorithm along with the help of supporting visualizations and analysis gives convincing details and a new approach to quantifying diffusion jumps, jump-lengths, time between jumps and to identify interstitials from lattice atoms.

  19. Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units.

    Lindert, Steffen; Bucher, Denis; Eastman, Peter; Pande, Vijay; McCammon, J Andrew

    2013-11-12

    The accelerated molecular dynamics (aMD) method has recently been shown to enhance the sampling of biomolecules in molecular dynamics (MD) simulations, often by several orders of magnitude. Here, we describe an implementation of the aMD method for the OpenMM application layer that takes full advantage of graphics processing units (GPUs) computing. The aMD method is shown to work in combination with the AMOEBA polarizable force field (AMOEBA-aMD), allowing the simulation of long time-scale events with a polarizable force field. Benchmarks are provided to show that the AMOEBA-aMD method is efficiently implemented and produces accurate results in its standard parametrization. For the BPTI protein, we demonstrate that the protein structure described with AMOEBA remains stable even on the extended time scales accessed at high levels of accelerations. For the DNA repair metalloenzyme endonuclease IV, we show that the use of the AMOEBA force field is a significant improvement over fixed charged models for describing the enzyme active-site. The new AMOEBA-aMD method is publicly available (http://wiki.simtk.org/openmm/VirtualRepository) and promises to be interesting for studying complex systems that can benefit from both the use of a polarizable force field and enhanced sampling. PMID:24634618

  20. Coexistence of spinodal instability and thermal nucleation in thin-film rupture: Insights from molecular levels

    Nguyen, Trung Dac; Fuentes-Cabrera, Miguel; Fowlkes, Jason D.; Rack, Philip D.

    2014-03-01

    Despite extensive investigation using hydrodynamic models and experiments over the past decades, there remain open questions regarding the origin of the initial rupture of thin liquid films. One of the reasons that makes it difficult to identify the rupture origin is the coexistence of two dewetting mechanisms, namely, thermal nucleation and spinodal instability, as observed in many experimental studies. Using a coarse-grained model and large-scale molecular dynamics simulations, we are able to characterize the very early stage of dewetting in nanometer-thick liquid-metal films wetting a solid substrate. We observe the features characteristic of both spinodal instability and thermal nucleation in the spontaneously dewetting films and show that these two macroscopic mechanisms share a common origin at molecular levels.

  1. Evaluation of Phonon-level Density of UO2 by Molecular Dynamics Simulation

    Hui-fen Zhang; Gan Li; Xiao-feng Tian; Tao Gao

    2011-01-01

    Molecular dynamics calculation of UO2 in a wide temperature range are presented and discussed.The calculated lattice parameters,mean square displacements,and dynamic property of phonon-level density of the velocity auto-correlation functions for UO2 are provided.The Morelon potential and the Basak potential are employed.It confirms that the calculated lattice parameters using the Basak potential are in nearly perfect agreement with the reported values.The models successfully predict mean square displacement and Bredig transition.Furthermore,the phonon-level density of uranium dioxide are discussed.The intensity of phonon-level density increases with temperature,and the properties of UO2 are characterized by large thermal vibrations rather than extensive disorder.

  2. Hanford low-level waste process chemistry testing data package

    Recently, the Tri-Party Agreement (TPA) among the State of Washington Department of Ecology, U.S. Department of Energy (DOE) and the US Environmental Protection Agency (EPA) for the cleanup of the Hanford Site was renegotiated. The revised agreement specifies vitrification as the encapsulation technology for low level waste (LLW). A demonstration, testing, and evaluation program underway at Westinghouse Hanford Company to identify the best overall melter-system technology available for vitrification of Hanford Site LLW to meet the TPA milestones. Phase I is a open-quotes proof of principleclose quotes test to demonstrate that a melter system can process a simulated highly alkaline, high nitrate/nitrite content aqueous LLW feed into a glass product of consistent quality. Seven melter vendors were selected for the Phase I evaluation: joule-heated melters from GTS Duratek, Incorporated (GDI); Envitco, Incorporated (EVI); Penberthy Electomelt, Incorporated (PEI); and Vectra Technologies, Incorporated (VTI); a gas-fired cyclone burner from Babcock ampersand Wilcox (BCW); a plasma torch-fired, cupola furnace from Westinghouse Science and Technology Center (WSTC); and an electric arc furnace with top-entering vertical carbon electrodes from the U.S. Bureau of Mines (USBM)

  3. Quantum simulation and quantum information processing with molecular dipolar crystals

    In this thesis interactions between dipolar crystals and neutral atoms or separated molecules have been investigated. They were motivated to realize new kinds of lattice models in mixtures of atoms and polar molecules where an MDC functions as an underlying periodic lattice structure for the second species. Such models bring out the peculiar features of MDC's, that include a controllable, potentially sub-optical wavelength periodicity and strong particle phonon interactions. Only stable collisional configurations have been investigated, excluding chemical reactions between the substituents, and crystal distortions beyond the scope of perturbation theory. The system was treated in the polaron picture where particles of the second species are dressed by surrounding crystal phonons. To describe the competition between coherent and incoherent dynamics of the polarons, a master equation in the Brownian motion limit was used with phonons treated as a thermal heat bath. It was shown analytically that in a wide range of realistic parameters the corrections to the coherent time evolution are small, and that the dynamics of the dressed particles can be described by an effective extended Hubbard model with controllable system parameters. The last chapter of this thesis contains a proposal for QIP with cold polar molecules that, in contrast to previous works, uses an MDC as a quantum register. It was motivated by the unique features of dipolar molecules and to exploit the peculiar physical conditions in dipolar crystals. In this proposal the molecular dipole moments were tailored by non-local fields to include a small, switchable, state-dependent dipole moment in addition to the large internal state independent moment that stabilizes the crystal. It was shown analytically that a controllable, non-trivial phonon-mediated interaction can be generated that exceeds non-trivial, direct dipole-dipole couplings. The addressability problem due to high crystal densities was overcome by

  4. Singlet molecular oxygen generated in dark biological process.

    Di Mascio, Paolo; Medeiros, Marisa H G

    2014-10-01

    Ultraweak chemiluminescence arising from biomolecules oxidation has been attributed to the radiative deactivation of singlet molecular oxygen [(1)O2] and electronically excited triplet carbonyl products involving dioxetane intermediates. As examples, we will discuss the generation of (1)O2 from lipid hydroperoxides, which involves a cyclic mechanism from a linear tetraoxide intermediate. The generation of (1)O2 in aqueous solution via energy transfer from the excited triplet acetone arising from the thermodecomposition of dioxetane a chemical source, and horseradish peroxidase-catalyzed oxidation of 2-methylpropanal, as an enzymatic source, will also be discussed. The approach used to unequivocally demonstrate the generation of (1)O2 in these reactions is the use of (18)O-labeled hydroperoxide / triplet dioxygen ((18)[(3)O2]), the detection of labeled compounds by HPLC coupled to tandem mass spectrometry (HPLC-MS/MS) and the direct spectroscopic detection and characterization of (1)O2 light emission. Characteristic light emission at 1,270nm, corresponding to the singlet delta state monomolecular decay was observed. Using(18)[(3)O2], we observed the formation of (18)O-labeled (1)O2 ((18)[(1)O2]) by the chemical trapping of (18)[(1)O2]with the anthracene-9,10-diyldiethane-2,1-diyl disulfate disodium salt (EAS) and detected the corresponding (18)O-labeled EAS endoperoxide usingHPLC-MS/MS. The combined use of the thermolysis of a water-soluble naphthalene endoperoxide as a generator of (18)O labeled (1)O2 and the sensitivity of HPLC-MS/MS allowed the study of (1)O2reactivity toward biomolecules. Photoemission properties and chemical trapping clearly demonstrate that the production of hydroperoxide and excited carbonyls generates (18)[(1)O2], and points to the involvement of (1)O2 in physiological and pathophysiological mechanism. Supported by FAPESP (2012/12663-1), CAPES, INCT Redoxoma (FAPESP/CNPq/CAPES; 573530/2008-4), NAP Redoxoma (PRPUSP; 2011.1.9352.1.8), CEPID

  5. Protein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A Review

    Peiqiang Yu

    2007-01-01

    Full Text Available The utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of the whole protein was often vital to understanding its digestive behavior and nutritive value in animals. In this review, recently obtained information on protein molecular structural effects of heat processing was reviewed, in relation to protein characteristics affecting digestive behavior and nutrient utilization and availability. The emphasis of this review was on (1 using the newly advanced synchrotron technology (S-FTIR as a novel approach to reveal protein molecular chemistry affected by heat processing within intact plant tissues; (2 revealing the effects of heat processing on the profile changes of protein subfractions associated with digestive behaviors and kinetics manipulated by heat processing; (3 prediction of the changes of protein availability and supply after heat processing, using the advanced DVE/OEB and NRC-2001 models, and (4 obtaining information on optimal processing conditions of protein as intestinal protein source to achieve target values for potential high net absorbable protein in the small intestine. The information described in this article may give better insight in the mechanisms involved and the intrinsic protein molecular structural changes occurring upon processing.

  6. Final Report, "Molecular Design of Hydrocarbon Oxidation Catalytic Processes"

    Professor Francisco Zaera

    2007-08-09

    The main goal of this project had been to use model systems to correlate selectivities in partial oxidation catalysis with the presence of specific sites on the surface of the catalyst. Extensive work was performed this year on characterizing oxygen-treated nickel surfaces by chemical means. Specifically, the surface chemistry of ammonia coadsorbed with atomic oxygen on Ni(110) single-crystal surfaces was studied by temperature-programmed desorption (TPD) and X-ray photoelectron spectroscopy (XPS). It was determined that at intermediate oxygen coverages direct ammonia adsorption on nickel sites is suppressed, but a new high-temperature reaction regime is generated at 400 K where NHx surface fragments are rehydrogenated concurrently with the production of water and molecular hydrogen. The extensive isotope scrambling and hydrogen transfer seen from nitrogen- to oxygen-containing surface intermediates, and the optimum yields seen for this 400 K state at intermediate oxygen coverages, strongly suggest the direct interaction of the adsorbed ammonia with oxygen atoms at the end of the –Ni–O- rows that form upon reconstruction of the surface. Hydrogen transfer between ammonia and oxygen appears to take place directly via hydrogen bonding, and to be reversible but biased towards water formation. An equilibrium is reached between the produced water and the reacting surface oxygen and hydrogen. The strong influence of the OH surface groups on the thermal chemistry of the adsorbed ammonia was interpreted in terms of the adsorbing geometry of the OH groups on the surface, and of hydrogen bonding between adsorbed OH and NH3 species. In terms of alcohol reactivity, the adsorption of 2-iodoethanol, a precursor for the preparation of 2-hydroxyethyl and oxametallacycle surface species, was found to lead to two configurations involving either just the iodine atom or both iodine and hydroxyl ends of the molecule. A complex chemical behavior starts around 140 K with the

  7. Spatially Resolved Atomic and Molecular Spectroscopy in Microelectronics Processing Plasmas

    Hebner, G.A.

    1998-10-14

    Plasma processing of microelectronic materials is strongly dependent on the generation and control of neutral radial and ion species generated in a plasma. For example, process uniformity across a #er is drken by a combination of plasma charged particle and neutral uniformity. Due to extensive rexarch and engineering the current generation of commercial plasma reactors can generate very radially uniform ion distributions, usually better than ~ 2 perwnt as determined by ion saturation measurements. Due in part to the difficulty associated with determining the neutral radial distributions, control of the neutral radical uniformity is less well developed. This abstract will review our recent measurements of the spatial distribution of severaI important atomic and molecukw species in inductively coupled plasmas through C12 / BCIJ / Ar containing gas mixtures. Measured species include the ground state Cl and BC1 densities as well as the metastable argon density. The fbeus of this review will be on the experimental techniques and results. In addition to assisting in the development of a fbndarnental understanding of the important pkunna physics, these measurements have been used to benchmark multi dimensional plasma discharge codes.

  8. Quantum correlation dynamics in photosynthetic processes assisted by molecular vibrations

    During the long course of evolution, nature has learnt how to exploit quantum effects. In fact, recent experiments reveal the existence of quantum processes whose coherence extends over unexpectedly long time and space ranges. In particular, photosynthetic processes in light-harvesting complexes display a typical oscillatory dynamics ascribed to quantum coherence. Here, we consider the simple model where a dimer made of two chromophores is strongly coupled with a quasi-resonant vibrational mode. We observe the occurrence of wide oscillations of genuine quantum correlations, between electronic excitations and the environment, represented by vibrational bosonic modes. Such a quantum dynamics has been unveiled through the calculation of the negativity of entanglement and the discord, indicators widely used in quantum information for quantifying the resources needed to realize quantum technologies. We also discuss the possibility of approximating additional weakly-coupled off-resonant vibrational modes, simulating the disturbances induced by the rest of the environment, by a single vibrational mode. Within this approximation, one can show that the off-resonant bath behaves like a classical source of noise

  9. Quantum correlation dynamics in photosynthetic processes assisted by molecular vibrations

    Giorgi, G.L., E-mail: g.giorgi@inrim.it [INRIM, Strada delle Cacce 91, I-10135 Torino (Italy); Roncaglia, M. [INRIM, Strada delle Cacce 91, I-10135 Torino (Italy); Raffa, F.A. [Politecnico di Torino, Dipartimento di Scienza Applicata e Tecnologia, Corso Duca degli Abruzzi 24, I-10129 Torino (Italy); Genovese, M. [INRIM, Strada delle Cacce 91, I-10135 Torino (Italy)

    2015-10-15

    During the long course of evolution, nature has learnt how to exploit quantum effects. In fact, recent experiments reveal the existence of quantum processes whose coherence extends over unexpectedly long time and space ranges. In particular, photosynthetic processes in light-harvesting complexes display a typical oscillatory dynamics ascribed to quantum coherence. Here, we consider the simple model where a dimer made of two chromophores is strongly coupled with a quasi-resonant vibrational mode. We observe the occurrence of wide oscillations of genuine quantum correlations, between electronic excitations and the environment, represented by vibrational bosonic modes. Such a quantum dynamics has been unveiled through the calculation of the negativity of entanglement and the discord, indicators widely used in quantum information for quantifying the resources needed to realize quantum technologies. We also discuss the possibility of approximating additional weakly-coupled off-resonant vibrational modes, simulating the disturbances induced by the rest of the environment, by a single vibrational mode. Within this approximation, one can show that the off-resonant bath behaves like a classical source of noise.

  10. Effect of heparin and low-molecular weight heparin on serum potassium and sodium levels

    Girish M Bengalorkar

    2011-01-01

    Full Text Available Introduction: To study the effects of heparin and low-molecular weight heparin (LMWH on potassium and sodium levels in patients with cardiovascular diseases (CVDs and stroke. Materials and Methods : Sixty patients were recruited with 30 patients each receiving heparin and enoxaparin. Patients with CVD and stroke receiving heparin and LMWH were compared for their demographic profile and laboratory data, and this was analyzed by descriptive statistics. Risk factors associated with the development of hyperkalemia were analyzed using multiple logistic regression model. Results : There was an increase in potassium levels and decrease in sodium levels compared with baseline in both the groups. The difference between the groups with respect to sodium and potassium levels was not statistically significant. On analysis, the risk factors for development of hyperkalemia were baseline potassium levels, serum creatinine, and creatinine clearance. The change in sodium and potassium levels on the fifth day of therapy was increased with LMWH compared with heparin, although not statistically significant. Conclusions : The clinician should anticipate hyperkalemia especially in patients with renal impairment receiving these drugs.

  11. Molecular-Level Transformations of Lignin During Photo-Oxidation and Biodegradation

    Feng, X.; Hills, K.; Simpson, A. J.; Simpson, M. J.

    2009-05-01

    As the second most abundant component of terrestrial plant residues, lignin plays a key role in regulating plant litter decomposition, humic substance formation, and dissolved organic matter (OM) production from terrestrial sources. Biodegradation is the primary decomposition process of lignin on land. However, photo- oxidation of lignin-derived compounds has been reported in aquatic systems and is considered to play a vital role in arid and semiarid regions. With increasing ultraviolet (UV) radiation due to ozone depletion, it is important to understand the biogeochemical fate of lignin exposed to photo-oxidation in terrestrial environments. This study examines and compares the transformation of lignin in a three-month laboratory simulation of biodegradation and photo-oxidation using molecular-level techniques. Lignin-derived monomers extracted by copper oxidation were analyzed by gas chromatography/mass spectrometry (GC/MS) from the water-soluble and insoluble OM of 13C-labeled corn leaves. Biodegradation increased the solubility of lignin monomers in comparison to the control samples, and the acid-to-aldehyde (Ad/Al) ratios increased in both the water-soluble and insoluble OM, indicating a higher degree of side-chain lignin oxidation. Photo-oxidation did not produce a significant change on the solubility or Ad/Al ratios of lignin from corn leaves. However, the ratios of trans-to-cis isomers of both cinnamyl units (p-coumaric acid and ferulic acid) increased with photo-oxidation and decreased with biodegradation in the insoluble OM. We also investigated the role of photo-oxidation in lignin transformation in soils cropped with 13C-labeled corn. Interestingly, the organic carbon content increased significantly with time in the water-soluble OM from soil/corn residues under UV radiation. An increase in the concentration of lignin monomers and dimers and the Ad/Al ratios was also observed with photo-oxidation. Iso-branched fatty acids of microbial origin remained in

  12. Molecular MRI differentiation of VEGF receptor-2 levels in C6 and RG2 glioma models.

    He, Ting; Smith, Nataliya; Saunders, Debra; Pittman, Benjamin P; Lerner, Megan; Lightfoot, Stanley; Silasi-Mansat, Robert; Lupu, Florea; Towner, Rheal A

    2013-01-01

    Vascular endothelial growth factor receptor 2 (VEGFR2) is an important angiogenic marker over-expressed in gliomas. With the use of molecular magnetic resonance imaging (mMRI) differing levels of VEGFR2 can be characterized in vivo with in rodent gliomas varying in angiogenesis. VEGFR2 levels were assessed by intravenous administration of an anti-VEGFR2 probe (anti-VEGFR2-albumin-Gd (gadolinium)-DTPA (diethylene triamine penta acetic acid)-biotin) into C6 or RG2 glioma-bearing rats, and visualized with mMRI. A non-specific IgG was coupled to the albumin-Gd-DTPA-biotin construct as a contrast agent molecular weight control. VEGFR2 levels are heterogeneous in different regions of C6 gliomas, whereas VEGFR2 was more homogenous or evenly distributed in RG2 gliomas. RG2 gliomas have less VEGFR2 within tumor periphery and peri-necrotic (pmMRI results were confirmed with fluorescence staining and mean fluorescence intensity (MFI) quantification of the anti-VEGFR2 probe in excised glioma and brain tissues, as well as detection of VEGFR2 in C6 and RG2 gliomas and corresponding contalateral brain tissues. Ex vivo VEGFR2 levels were found to be significantly higher in C6 gliomas compared to RG2 tumors (p<0.001), which corresponded with in vivo detection using the VEGFR2 probe. Immunohistochemistry staining for HIF-1α (hypoxia inducible factor 1α), which is associated with angiogenesis, indicated higher levels in RG2 (p<0.01) compared to C6 gliomas. The data suggests that C6 gliomas have angiogenesis which is associated more with large blood vessels in tumor periphery and peri-necrotic regions, and less microvascular angiogenesis within the tumor interior, compared to RG2 gliomas. PMID:23901356

  13. Study on the mechanism of action between dimethyl phthalate and herring sperm DNA at molecular level.

    Chi, Zhenxing; Wang, Donglin; You, Hong

    2016-08-01

    Dimethyl phthalate (DMP), a typical phthalic acid ester, is widespread in the environment and causes extensive concern due to its adverse effects on human health. To understand the genotoxicity of DMP at molecular level, the toxic interaction of DMP with herring sperm (hs) deoxyribonucleic acid (DNA; hs-DNA) was investigated in vitro under simulated physiological conditions using multi-spectroscopic techniques and a molecular modeling method. The results of Ultraviolet-Visible absorption spectroscopy, fluorescence emission spectroscopy, and circular dichroism spectra indicated that DMP interacts with hs-DNA in a groove-binding mode that changes the double helical structure of DNA. The binding constant and the number of binding sites calculated from the fluorescence quenching data were 565.718 L mol(-1) and 0.7872, respectively. A molecular modeling study revealed that DMP tends to bind with DNA in the A-T-rich regions of minor groove and that hydrogen bonding and van der Waals forces play main roles in the interaction. This research can help to elucidate the mechanism of DMP toxicity in vivo. PMID:27166703

  14. Short-Term Dynamics of North Sea Bacterioplankton-Dissolved Organic Matter Coherence on Molecular Level.

    Lucas, Judith; Koester, Irina; Wichels, Antje; Niggemann, Jutta; Dittmar, Thorsten; Callies, Ulrich; Wiltshire, Karen H; Gerdts, Gunnar

    2016-01-01

    Remineralization and transformation of dissolved organic matter (DOM) by marine microbes shape the DOM composition and thus, have large impact on global carbon and nutrient cycling. However, information on bacterioplankton-DOM interactions on a molecular level is limited. We examined the variation of bacterial community composition (BCC) at Helgoland Roads (North Sea) in relation to variation of molecular DOM composition and various environmental parameters on short-time scales. Surface water samples were taken daily over a period of 20 days. Bacterial community and molecular DOM composition were assessed via 16S rRNA gene tag sequencing and ultrahigh resolution Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS), respectively. Environmental conditions were driven by a coastal water influx during the first half of the sampling period and the onset of a summer phytoplankton bloom toward the end of the sampling period. These phenomena led to a distinct grouping of bacterial communities and DOM composition which was particularly influenced by total dissolved nitrogen (TDN) concentration, temperature, and salinity, as revealed by distance-based linear regression analyses. Bacterioplankton-DOM interaction was demonstrated in strong correlations between specific bacterial taxa and particular DOM molecules, thus, suggesting potential specialization on particular substrates. We propose that a combination of high resolution techniques, as used in this study, may provide substantial information on substrate generalists and specialists and thus, contribute to prediction of BCC variation. PMID:27014241

  15. Short-term dynamics of North Sea bacterioplankton-dissolved organic matter coherence on molecular level

    Judith eLucas

    2016-03-01

    Full Text Available Remineralisation and transformation of dissolved organic matter (DOM by marine microbes shape the DOM composition and thus, have large impact on global carbon and nutrient cycling. However, information on bacterioplankton-DOM interactions on a molecular level is limited. We examined the variation of bacterial community composition at Helgoland Roads (North Sea in relation to variation of molecular DOM composition and various environmental parameters on short-time scales. Surface water samples were taken daily over a period of twenty days. Bacterial community and molecular DOM composition were assessed via 16S rRNA gene tag sequencing and ultrahigh resolution Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS, respectively. Environmental conditions were driven by a coastal water influx during the first half of the sampling period and the onset of a summer phytoplankton bloom towards the end of the sampling period. These phenomena led to a distinct grouping of bacterial communities and DOM composition which was particularly influenced by total dissolved nitrogen concentration, temperature and salinity, as revealed by distance-based linear regression analyses. Bacterioplankton-DOM interaction was demonstrated in strong correlations between specific bacterial taxa and particular DOM molecules, thus, suggesting potential specialization on particular substrates. We propose that a combination of high resolution techniques, as used in this study, may provide substantial information on substrate generalists and specialists and thus, contribute to prediction of bacterial community composition variation.

  16. Understanding the role of London dispersion forces in molecular surface processes

    Cooper, Valentino R.

    2012-02-01

    The interactions and dynamics of molecules at surfaces and within pores are essential to many chemical processes, ranging from molecular storage to catalysis and self-assembly. A molecular level understanding of molecule-surface interactions is crucial for tuning surface/pore selectivity and reactivity. While it is clear that strong chemisorption bonds facilitate these interactions, the role of weaker van der Waals (vdW) forces, which include London dispersion and π-π stacking interactions, are often unknown or overlooked. Recent advances in density functional theory (DFT) have now made it possible to reliably account for London dispersion interactions. In this paper, I will discuss the use of one such technique, the Rutgers-Chalmers vdW non-local correlation functional,ootnotetextM. Dion, H. Rydberg, E. Schr"oder, B. I. Lundqvist and D. C. Langreth, Phys. Rev. Lett., 92, 246401 (2004)^,ootnotetextT. Thonhauser, V. R. Cooper, S. Li, A. Puzder, P. Hyldgaard, and David C. Langreth, Phys. Rev. B, 76, 125112 (2007) to demonstrate how the inclusion of London dispersion forces is critical for a truly first principles understanding of processes sensitive to molecule-surface interactions, such as the loading of H2 within porous materials and the chemisorption of organic molecules at surfaces. These works highlight the fundamental importance of London dispersion interactions in the broader context of chemical physics. This work was supported by the Department of Energy, BES, Materials Sciences and Engineering Division.ootnotetextCollaborators: Guo Li, Isaac Tamblyn, Yungok Ihm, Jun-Hyung Cho, Shixuan Du, Jeffrey B. Neaton, Hong-Jun Gao, Zhenyu Zhang, James R. Morris

  17. Quantum information processing at the cellular level. Euclidean approach

    Ogryzko, Vasily

    2009-01-01

    Application of quantum principles to living cells requires a new approximation of the full quantum mechanical description of intracellular dynamics. We discuss what principal elements any such good approximation should contain. As one such element, the notion of "Catalytic force" Cf is introduced. Cf is the effect of the molecular target of catalysis on the catalytic microenvironment that adjusts the microenvironment towards a state that facilitates the catalytic act. This phenomenon is exper...

  18. Core level regulatory network of osteoblast as molecular mechanism for osteoporosis and treatment

    Zhu, Xiaomei; Li, Jun; Liang, Yuhong; Liu, Tao; Zhu, Yanxia; Zhang, Bingbing; Tan, Shuang; Guo, Huajie; Guan, Shuguang; Ao, Ping; Zhou, Guangqian

    2016-01-01

    To develop and evaluate the long-term prophylactic treatment for chronic diseases such as osteoporosis requires a clear view of mechanism at the molecular and systems level. While molecular signaling pathway studies for osteoporosis are extensive, a unifying mechanism is missing. In this work, we provide experimental and systems-biology evidences that a tightly connected top-level regulatory network may exist, which governs the normal and osteoporotic phenotypes of osteoblast. Specifically, we constructed a hub-like interaction network from well-documented cross-talks among estrogens, glucocorticoids, retinoic acids, peroxisome proliferator-activated receptor, vitamin D receptor and calcium-signaling pathways. The network was verified with transmission electron microscopy and gene expression profiling for bone tissues of ovariectomized (OVX) rats before and after strontium gluconate (GluSr) treatment. Based on both the network structure and the experimental data, the dynamical modeling predicts calcium and glucocorticoids signaling pathways as targets for GluSr treatment. Modeling results further reveal that in the context of missing estrogen signaling, the GluSr treated state may be an outcome that is closest to the healthy state. PMID:26783964

  19. Manipulating the proton transfer process in molecular complexes: synthesis and spectroscopic studies.

    Panja, Sumit Kumar; Dwivedi, Nidhi; Saha, Satyen

    2016-08-01

    The proton transfer process in carefully designed molecular complexes has been investigated directly in the solid and solution phase. SCXRD studies have been employed to investigate the N-H-O bonding interaction sites of the molecular complexes, with additional experimental support from FTIR and Raman spectroscopic studies, to gain information on the relative position of hydrogen in between the N and O centers. Further, the proton transfer process in solution is studied using UV-Visible spectroscopy through monitoring the intramolecular charge transfer (ICT) process in these molecular complexes, which is primarily governed by the number of electron withdrawing groups (nitro groups) on proton donor moieties (NP, DNP and TNP). It is found that the magnitude of the ICT process depends on the extent of proton transfer, which on the other hand depends on the relative stabilities of the constituent species (phenolate species). A correlation is observed between an increase in the number of nitro groups and an increase in the melting point of the molecular complexes, indicating the enhancement of ionic character due to the proton transfer process. The aliphatic H-bonding is identified and monitored using (1)H-NMR spectroscopy, which reveals that the identity of molecular complexes in solution interestingly depends on the extent of proton transfer, in addition to the nature of the solvents. The aliphatic C-H-O H-bonding interaction between the oxygen atom of the nitro group and the alkyl hydrogen in piperidinium was also found to play a significant role in strengthening the primary interaction involving a hydrogen transfer process. The conductivity of the molecular complexes increases with an increase in the number of nitro groups, indicating the enhancement in ionic character of the molecular complexes. PMID:27424765

  20. The hows and whys of face processing: Level of construal influences the holistic processing of human faces.

    Wyer, Natalie A; Hollins, Timothy J; Pahl, Sabine

    2015-12-01

    Face recognition and identification are optimized by holistic processing. Various visual-spatial manipulations appear to have transfer effects on holistic face processing. The present experiment tests the effects of a semantic manipulation--of construal level--on holistic processing as measured by composite congruency effects. Participants completed two blocks of trials. The first served as a baseline, whereas the second included a manipulation of construal level. High-level construal resulted in stronger congruency effects, indicative of greater holistic processing (relative to baseline and to low-level construal). These results have implications for conceptualizations of both construal level and holistic processing. PMID:26436426

  1. Computational methods to study the structure and dynamics of biomolecules and biomolecular processes from bioinformatics to molecular quantum mechanics

    2014-01-01

    Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over t...

  2. Is photon angular momentum important in molecular collision processes occurring in a laser field

    Devries, P. L.; George, T. F.

    1978-01-01

    The importance of the rigorous treatment of photon angular momentum in molecular-collision processes occurring in the presence of intense radiation is investigated. An alternate approximate treatment, which essentially neglects the angular momentum coupling between the photon and the molecular degrees of freedom by averaging over the angular dependence of the interaction matrix elements, is presented and applied to a model calculation. The degeneracy-averaged results of this calculation compare remarkably well with the results of a rigorous calculation, from which we conclude (with reservation) that the explicit consideration of photoangular momentum coupling in molecular-collision problems is unnecessary.

  3. Molecular and collisional processes during three photon ionisation transitions in caesium and rubidium vapours

    Interesting molecular and collisional processes are evident during three photon ionisation transitions in caesium and rubidium vapours. In particular, for caesium vapour broad hybrid resonances (molecular plus atomic transitions) have been identified. In rubidium vapour three photon ionisation s-nd, s-ns transitions as well as forbidden s-np have been observed with the s-s transitions being more prominent than theory predicts. These observations have been explained in terms of collisional ionisation. (author)

  4. Stochastic dynamics of small ensembles of non-processive molecular motors: the parallel cluster model

    Erdmann, Thorsten; Schwarz, Ulrich S

    2013-01-01

    Non-processive molecular motors have to work together in ensembles in order to generate appreciable levels of force or movement. In skeletal muscle, for example, hundreds of myosin II molecules cooperate in thick filaments. In non-muscle cells, by contrast, small groups with few tens of non-muscle myosin II motors contribute to essential cellular processes such as transport, shape changes or mechanosensing. Here we introduce a detailed and analytically tractable model for this important situation. Using a three-state crossbridge model for the myosin II motor cycle and exploiting the assumptions of fast power stroke kinetics and equal load sharing between motors in equivalent states, we reduce the stochastic reaction network to a one-step master equation for the binding and unbinding dynamics (parallel cluster model) and derive the rules for ensemble movement. We find that for constant external load, ensemble dynamics is strongly shaped by the catch bond character of myosin II, which leads to an increase of th...

  5. Studies on liposomes with Chlorophyll for monitoring the electromagnetic influence at molecular level

    The liposomes with Chlorophyll are excellent model membranes and could be successfully used to study the electromagnetic influence at molecular level. The strong visible absorption and fluorescence of Chlorophyll allow its use as sensor for the interactions at molecular level and as a fluorescence marker; it reflects certain aspects of the supramolecular structure of the lipid phase: fluidity, lipid and liposomes aggregation. The objective of our work was to evidence athermal effect of low level, pulsed microwave (MW) fields on liposomes and to evidence the possible mechanism of interaction at molecular level. Unilamellar liposomes were obtained from multilamellar vesicles by the hand-shaken method and sonication for 30 minutes. The multilamellar vesicles were prepared using Chla /lipid films with specific molar ratio (lipid/Chla 1/10 and 1/100) and different lipids (Dipalmitoyl phosphatidylcholine, Dimirystoyl Phosphatidylcholine and Dioleoyl Phosphatidylcholine-Sigma). The films were dispersed in buffer solutions of different pH (6.2 - 7.6). The Chlorophyll was freshly extracted from spinach leaves and separated by the chromatographic method. Portions of liposome suspension (0.6 ml) were inserted into Teflon cuvettes. The samples were irradiated in series, for periods of 5-30 minutes. The exposure system was: MW generator + adapted load (shortened rectangular waveguide) + Teflon cuvette filled with sample liquid. The effect of MW irradiation is not observable on multilamellar vesicles, but only on small unilamellar vesicles. The MW effect is athermal, verified by conventional heating in the same range of temperatures and results in enlarging the size of vesicles. The enlarging effect of MW is opposed to the effect of ultrasounds exposure. It is not clear if effects due to MW are proportional with exposure duration; it seems that this mostly depends on the type of lipid in vesicles. The UV and VIS spectra were recorded to observe the oxidation state of the

  6. Proposed methods for treating high-level pyrochemical process wastes

    This survey illustrates the large variety and number of possible techniques available for treating pyrochemical wastes; there are undoubtedly other process types and many variations. The choice of a suitable process is complicated by the uncertainty as to what will be an acceptable waste form in the future for both TRU and non-TRU wastes

  7. A study on melting process of perylene using molecular dynamics simulation

    M Peyvasteh

    2014-11-01

    Full Text Available Melting process of perylene is investigated using molecular dynamics simulation. Some of thermodynamic properties such as potential energy and transition order parameter are calculated as a function of temperature in the range of 500 K-600 K. These calculations are performed by two different methods in NPT and NVT ensembles. The selected interaction potential is Re-squared and the simulations are performed by LAMMPS (a classic molecular dynamics code. The results show that NPT ensemble is more appropraite for the study of melting process than NVT ensemble and shows a good agreement with experimental melting temperature.

  8. Bibliography of atomic and molecular processes. Volume 1, 1978-1981

    This annotated bibliography lists 10,676 works on atomic and molecular processes reported in publications dated 1978-1981. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the county of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

  9. Bibliography of atomic and molecular processes. Volume 1, 1978-1981

    Barnett, C.F.; Crandall, D.H.; Farmer, B.J. (comps.)

    1982-10-01

    This annotated bibliography lists 10,676 works on atomic and molecular processes reported in publications dated 1978-1981. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the county of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  10. Low-level radioactive waste processing at nuclear power plants

    This survey was limited to systems and materials used to process waste liquids contaminated with radionuclides. Since the chemical and radiological character of collected liquids may change dramatically, the survey describes waste and cleanup process streams encountered during normal outage or power production conditions. Influents containing specific organic compounds, salts, or solids common to local sources, and the special techniques developed to remove or concentrate these materials are not detailed in this report. The names and phone numbers of the individuals responsible for investigating and solving these problems, however, provides easy access to data which will save time and expense when facing abnormal processing, purchasing, or engineering challenges. The Liquid Radwaste Source Book contains information collected from 31 of 36 BWR's as well as contact information from all licensed commercial units. Since some sites share common radwaste processing facilities, not all units are represented by individual data sheets