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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. 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

  4. 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 Kashas 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 spinorbit 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) effect on the non-radiative decay. We further combined the non-adiabatic coupling and spinorbit coupling for the triplet state decay (phosphorescence) quantum efficiency. All the formalisms have been developed analytically, which have been applied to optical spectroscopy, aggregation-induced emission phenomena, and polymer photovoltaic property

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

    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

  6. 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.

  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. 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.

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

    Abdelmonem, A.; Ltzenkirchen, J.; Leisner, T.

    2015-08-01

    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. At Molecular level

    Cancer involves abnormal growth and growth depends on energy metabolism. The response of ATP levels and isocitrate dehydrogenase activity in CaNT tumours, after different sorts of ionising radiation, was investigated in order to shed some light on the complex relationships between energy metabolism, radiation damage and repair processes and their implication for cancer therapy. Male mice were inoculated with tumour cells and the subsequent tumours were irradiated with different photon energies. The levels of ATP in the CaNT tumours were measured 2.5 hours after receiving 10 Gy of the different photon energies: 100 kVp X-rays, 250 kVp X-rays, 60Co gamma-rays and 8 MeV X-rays. The resulting measured ATP concentrations with respect to unirradiated controls were 3.78 times with 100 kVp, 1.56 times greater with 250 kVp and 1.23 times greater with 1.17/1.33 MeV gammas. With 8 MeV radiation, the tumour ATP concentration remained unchanged to within the experimental uncertainty. ATP appeared to play an important role in repair mechanisms, including cellular repair following radiation damage. The increased reducing equivalents generated by this enzyme under injury conditions give protection against further damage due to peroxidative processes in membrane repair. Thus, the initial increase in energy metabolism after the dose of ionising radiation represents an adaptive defence mechanism against radiation damage. 14 refs., 3 figs., 2 tabs

  11. Dynamic cooperativity of molecular processes in active streaming, muscle contraction, and subcellular dynamics: the molecular mechanism of self-organization at the subcellular level.

    Shimizu, H

    1979-01-01

    Life phenomena are a kind of ordered dynamics appearing in macroscopic systems, living systems. Schrödinger has proposed a molecular mechanism for the organization of life phenomena, i.e., 'order-from-order' mechanism where ordered dynamics are composed of molecular dynamics having order as the ordered dynamics of a watch is caused by orderly movements of its mechanical elements. However, neither evidence supporting the 'order-from-order' mechanism has been found in living systems nor the reason why molecular dynamics acquire order instead of disorder has been elucidated for more than 30 years. The latter is quite anomalous from the point of views of thermodynamics, which is based on disordered behaviors of molecules. In this paper, we verify from studies of a streaming system reconstituted from rabbit skeletal F-actin and HMM that one life phenomenon, active streaming, is caused by the 'order-from-order' mechanism. This is also the case for muscle contraction. Moreover, it is probable that this mechanism generally works at the subcellular level, not only in biological motilities but also in life phenomena at biomembranes. We also clarify that dynamic cooperativity among molecule gives rise to order in molecular dynamics. Hence, dynamic cooperativity is the key mechanism for life phenomena caused by the 'order-from-order' principle at the subcellular level. To produce dynamic cooperativity it is necessary for component molecules or elements to have three states, i.e., inactive (stable) state 0, energized or energy storing (quasi-stable) state 1, and active (unstable) state 2. Each molecule performs elementary cycle 0 yields 1 yields 2 yields 0 repeatedly by using free energy at the molecular level. In a state far from thermodynamic equilibrium dynamic cooperativity is yielded in 2 yields 0 due to a kind of triggering action of neighboring elements and breaks thermodynamic detailed balance. In addition, dynamic cooperativity gives component molecules long-range interactions which depend on the structure of organelles or molecular assemblies. Dynamic cooperativity is able to decrease entropy production and will give a high efficiency in chemo-mechanical conversions. Great progress would be achieved in the understanding of the molecular mechanisms and thermodynamic principles of energy transformations in biological systems, if molecular dynamics during transformation could be directly observed. This is not only because physical changes accompanied by specific movements of macromolecules are essentially involved but also because such molecular movements play a substantial role in energy transformation. Entirely new ideas will be needed for this purpose although high voltage electron microscopy or X-ray diffraction, for instance, is now expected as to be one of the possible tools in the future. Fortunately even at present it is possible to obtain important information on molecular dynamics from biochemical and physiological data, if analyses are properly performed... PMID:161690

  12. Molecular Processes in Comets

    Dalgarno, A.

    1998-01-01

    The research focused on molecular hydrogen and its response to ultraviolet radiation, photoelectron impact excitation and X-ray radiation and on the interpretation of the ultraviolet spectra of the Jupiter dayglow and auroras. A systematic effort was made to obtain reliable rate coefficients for rovibrational energy transfer of H2, particularly in collisions with hydrogen atoms. We carried out elaborate quantum-mechanical calculations of the scattering of H and H2 on what had been characterized as a reliable potential energy surface of the H3 molecular system. These calculations took into account reactive channels and rate coefficients for ortho-para transitions were obtained. Quantal calculations are too complex to be applied to all the possible rovibrational transitions and we turned to a semi-classical method. With it we calculated rate coefficients for transitions, reactive and non-reactive, for all the rovibrational levels. We carried out the calculations for three of the available H3 potential energy surfaces. We discovered an unexpected sensitivity of the rate coefficients for the non-reactive channels to the potential energy surface. This discovery stimulated more thorough investigations of the potential energy surface elsewhere and to the construction of a new surface. We have used it in further semi-classical calculations in work that will shortly be 2 completed and which, together with new quantum-mechanical calculations should comprise a set of reliable rate coefficients that can be used in discussions of H2 on the Jovian planets. We carried out a detailed study of the Jovian ultraviolet dayglow. There has been a long-running argument about the dayglow on Jupiter. There are two sources of excitation: fluorescence and photoelectron impact excitation. It had been argued that a third source "the electron glow" was needed to bring theory and observation into agreement. We believe we have shown conclusively that the third source is unnecessary. We have achieved a close quantitative agreement between the predicted spectrum arising from fluorescence and photoelectrons and the measured spectrum. We also demonstrated a method by which the presence of HD could be established observationary. Similar calculations were carried out of the ultraviolet spectra of the Jovian auroras. We again found close agreement. Indeed, the agreement was so detailed we were able to derive the temperature of the atmosphere. We found, contrary to the standard model of the time, a high temperature between 400 K and 600 K and established the presence of a significant temperature gradient. A large temperature gradient was indeed found by direct sampling with the Jupiter probe.

  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. 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

  15. 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

  16. Higher Levels of Process Synchronisation

    Welch, Peter H.; Wood, David C.

    1997-01-01

    Four new synchronisation primitives (SEMAPHOREs, RESOURCEs, EVENTs and BUCKETs) were introduced in the KRoC 0.8beta release of occam for SPARC (SunOS/Solaris) and Alpha (OSF/1) UNIX workstations [1][2][3]. This paper reports on the rationale, application and implementation of two of these (SEMAPHOREs and EVENTs). Details on the other two may be found on the web [4]. The new primitives are designed to support higher-level mechanisms of SHARING between parallel processes and give us greater ...

  17. 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)

  18. 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.'

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

    Full text: Why do we need radiopharmacy, radiopharmacy, radiopharmacy training? In this post-genomic era, molecular imaging has gain tremendous interest not only amongst physicians but also from biologists, chemists, physicists, engineers, statisticians, pharmaceutical companies and even from governments. There is no doubt that nuclear medicine has been engaged in molecular medicine more than one decade ago. Positron emission tomography (PET) has reawaken interest in long forgotten radiopharmacy. Only major hospitals in the developed countries have invested in the development of dedicated radiopharmacy laboratory and training or recruitment of radiopharmacist. But PET has forced nuclear medicine to create a radiopharmacy unit and adopt radiopharmacy guidelines such as good radiopharmaceutical practice (GRPP) and good manufacturing practice (GMP). It is compounded by the fact that SPECT radiopharmaceutical chemistry has advanced significantly for both diagnostics and therapeutics, which calls for a high level of understanding on radiopharmaceutical chemistry and technical know-how. These factors eventually lead to introduction of tran ing program, courses and degree program. The most striking examples will be European Association of Nuclear Medicine (EANM) radiopharmacy courses and a series of IAEA activities on GRPP, GMP and technologist training programs. Various forms of training or education program can be formulated for various levels, starting from basic radiopharmacy course to PhD program, depending on the following factors; (1) National interest and policies on bio/medical sector; (2) Size of the nuclear medicine community in the respective country; (3) Institution interest and policies; and (4) Existing infrastructure and programs. Current Radiopharmacy Education in Singapore: In Singapore, all of the major nuclear medicine centers are supervised by radiopharmacists with PhD degree. All of the nuclear medicine technologists in the major centers have got 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, ultrasound, etc. Examples of practical applications. (author)

  20. 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 properties to produce an environmentally responsible, formaldehyde-free adhesive. It is also imperative to study the adhesion between protein and wood.

  1. 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

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. 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

    Bulienkov, N. A., E-mail: lmm@phyche.ac.ru [Russian Academy of Sciences, Frumkin Institute of Physical Chemistry and Electrochemistry (Russian Federation)

    2011-07-15

    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.

  13. 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.

  14. Molecular sieving silica membrane fabrication process

    Raman, N.K.; Brinker, C.J.

    1999-08-10

    A process is described for producing a molecular sieve silica membrane comprising depositing a hybrid organic-inorganic polymer comprising at least one organic constituent and at least one inorganic constituent on a porous substrate material and removing at least a portion of the at least one organic constituent of the hybrid organic-inorganic polymer, forming a porous film. 11 figs.

  15. Mass separation during molecular beam sampling process

    In a molecular beam sampling process, if the stagnation gas is a mixture, heavier species are concentrated onto the axis of the molecular beam, while lighter ones are diffused away from it. This phenomenon is generally called ''mass separation.'' Mass separation is caused mainly by three phenomena: (1) pressure diffusion, (2) Mach-number focusing and (3) skimmer interference. Pressure diffusion has already been analyzed by Sherman. In the present work, the mass separation for a binary mixture of Ar and He was experimentally measured by means of a molecular beam-mass filter system, and its kinetic analysis was carried out with regard to Mach-number focusing taking into consideration of the non-equilibrium of translational temperatures. The experimental results and the theoretical prediction agree well except in the cases of a shorter nozzle-skimmer distance, where skimmer interference is dominant, and in the cases of a higher Ar content. (author)

  16. 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...

  17. Higher-level motor processes.

    Rumiati, Raffaella Ida; Papeo, Liuba; Corradi-Dell'Acqua, Corrado

    2010-03-01

    Traditionally the motor system was thought of as a movement output device that, after brain damage, can impede patients from correctly planning and executing an action. In the last 20 years neuropsychological observations have contributed to the development of a new view that attributes higher-level functions to this system. Rapidly, this area of investigation has grown very popular, with motor representations being considered critical for action and object recognition, imagery and even language understanding. At present, we can distinguish between embodied and disembodied theories. The former predominantly are built on associations of deficits in these abilities whereas the latter rely on dissociations between deficits. Neuroimaging research has also showed that different action-related functions activate either overlapping or discrete regions, thus sustaining either association-based or dissociation-based models. Although no convincing theory is, to date, available to explain both sets of observations, cognitive neuroscientists have begun to explore this intermediate hypothesis space. Here we suggest that concepts like strategy and simulation seem promising in explaining how the cognitive system alternates between action-related functions. PMID:20392283

  18. 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

  19. 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)

  20. From supramolecular electrochemistry to molecular-level devices

    Supramolecular (multi-component) systems can perform complex functions which result from the cooperation of actions performed by suitably selected molecular components. Looking at supramolecular systems, from the viewpoint of the functions, shows that the concept of macroscopic device can be extended to molecular level. Nature exploits very complex molecular-level devices to substain life, and, in the last twenty years, the development of supramolecular chemistry has allowed the construction of simple molecular-level devices, that are of interest not only for basic research, but also for the growth of nanoscience and nanotechnology. Molecular-level devices operate via electronic and/or nuclear rearrangements, and like macroscopic devices, they need energy to operate and signals to communicate with the operator. Electrochemistry can provide the answer to this dual requirement, since electrons/holes, besides supplying the energy needed to make a devices work, can also be useful to 'read' the state of the system and thus to control and monitor the operation of the device. In this article, some examples of molecular-level devices investigated in our laboratory will be reviewed

  1. Processing AIRS Scientific Data Through Level 2

    Oliphant, Robert; Lee, Sung-Yung; Chahine, Moustafa; Susskind, Joel; arnet, Christopher; McMillin, Larry; Goldberg, Mitchell; Blaisdell, John; Rosenkranz, Philip; Strow, Larrabee

    2007-01-01

    The Atmospheric Infrared Spectrometer (AIRS) Science Processing System (SPS) is a collection of computer programs, denoted product generation executives (PGEs), for processing the readings of the AIRS suite of infrared and microwave instruments orbiting the Earth aboard NASA s Aqua spacecraft. AIRS SPS at an earlier stage of development was described in "Initial Processing of Infrared Spectral Data' (NPO-35243), NASA Tech Briefs, Vol. 28, No. 11 (November 2004), page 39. To recapitulate: Starting from level 0 (representing raw AIRS data), the PGEs and their data products are denoted by alphanumeric labels (1A, 1B, and 2) that signify the successive stages of processing. The cited prior article described processing through level 1B (the level-2 PGEs were not yet operational). The level-2 PGEs, which are now operational, receive packages of level-1B geolocated radiance data products and produce such geolocated geophysical atmospheric data products such as temperature and humidity profiles. The process of computing these geophysical data products is denoted "retrieval" and is quite complex. The main steps of the process are denoted microwave-only retrieval, cloud detection and cloud clearing, regression, full retrieval, and rapid transmittance algorithm.

  2. 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

  3. 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....

  4. 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).

  5. 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)

  6. Information storage at the molecular level - The design of a molecular shift register memory

    Beratan, David N.; Onuchic, Jose Nelson; Hopfield, J. J.

    1989-01-01

    The control of electron transfer rates is discussed and a molecular shift register memory at the molecular level is described. The memory elements are made up of molecules which can exist in either an oxidized or reduced state and the bits can be shifted between the cells with photoinduced electron transfer reactions. The device integrates designed molecules onto a VLSI substrate. A control structure to modify the flow of information along a shift register is indicated schematically.

  7. User-Level Process Migration Mechanism

    Dr. Narayan A. Joshi

    2013-02-01

    Full Text Available In networks of workstations, running processes lead to a situation, in which some of the nodes are highly loaded whereas other nodes mayremain lightly loaded or almost idle. It may lead to reduction in throughput and lot of computational power offered by the lightly loaded or the idle processors. This computational power goes unused while the jobs are striving for the availability of processor-cycles. The issue of efficient utilization of computing resources is noteworthy in the networked workstations such as local area networks as well; which can be tackled by spreading the running processes among the connected workstations by means of the mechanism such as process migration. The application of process migrationmechanism may consequent into the proficient utilization of the overall networked computing environment through the utilization of the lightly loaded workstations or the almost idle workstations. The paper discusses characteristics of many user level process migration mechanisms.

  8. 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...

  9. 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.

  10. 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.

  11. Binaural processing of modulated interaural level differences

    Thompson, Eric Robert; Dau, Torsten

    2008-01-01

    Two experiments are presented that measure the acuity of binaural processing of modulated interaural level differences ILDs using psychoacoustic methods. In both experiments, dynamic ILDs were created by imposing an interaurally antiphasic sinusoidal amplitude modulation AM signal on high...... frequency, broadly tuned, bandpass-shaped patterns were obtained. Simulations with an existing binaural model show that a low-pass filter to limit the binaural temporal resolution is not sufficient to predict the results of the experiments....

  12. A new vibrational level of the H2+ molecular ion

    A new vibrational level of the molecular ion H2+ with binding energy of 1.09 x 10-9 a.u. ? 30 neV below the first dissociation limit is predicted, using highly accurate numerical non-relativistic quantum calculations, which go beyond the Born-Oppenheimer approximation. It is the first-excited vibrational level v=1 of the 2p?u electronic state, antisymmetric with respect to the exchange of the two protons, with orbital angular momentum L=0. It manifests itself as a huge p - H scattering length of a = 750 5 Bohr radii. (authors)

  13. 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.

  14. How Effective Are Simulated Molecular-level Experiments for Teaching Diffusion and Osmosis?

    Meir, Eli; Perry, Judith; Stal, Derek; Maruca, Susan; Klopfer, Eric

    2005-01-01

    Diffusion and osmosis are central concepts in biology, both at the cellular and organ levels. They are presented several times throughout most introductory biology textbooks (e.g., Freeman, 2002), yet both processes are often difficult for students to understand (Odom, 1995; Zuckerman, 1994; Sanger et al., 2001; and results herein). Students have deep-rooted misconceptions about how diffusion and osmosis work, especially at the molecular level. We hypothesized that this might be in part due t...

  15. Molecular Doping Processes in Organic Semiconductors investigated by Photoelectron Spectroscopy

    Tietze, Max Lutz

    2014-01-01

    Molecular doping is a key technique for realizing high efficient organic light-emitting diodes (OLEDs) and photovoltaics (OPV). Furthermore, its most recent application in organic field-effect transistors (OFETs) marks a milestone on the roadmap towards flexible organic CMOS technology. However, in contrast to silicon based devices, the understanding of the fundamental processes of molecular doping is still controversially discussed. This work aims at the detailed analysis of the molecular do...

  16. The SILMO laser uranium enrichment molecular process

    Laser uranium enrichment is based on the different light absorption characteristics of the two uranium hexafluoride (U F6) molecules. The process principles are detailed and its application to plant-scale uranium enrichment with low temperature, high flow rate and scavenger issues is discussed. Infrared technology is now largely imposed for this process, enabling higher photodissociation performances. Laser issues are still under study

  17. 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-based techniques and is partially attributed to the ease in controlling composition and CZTS phase through this technique. Based on this platform, comprehensive characterization on CZTS devices is carried out including solar cells and transistors. Especially defects properties are exploited in Chapter 4 targeting to identify the limiting factors for further improvement on CZTS solar cells efficiency. Finally, molecular structures and precursor solution stability have been explored, potentially to provide a universal approach to process multinary compounds.

  18. 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)

  19. Low level processing of diode spectrometry results

    Systematic measurements in gamma spectrometry on slightly radioactive samples have led to study low levels existing in the spectra and to develop suitable processing methods. These methods and the advance that they represent in reading sensitivity are now applicable to all types of spectrum. The principles of this automatic reading are briefly summarized, leading to a description of the modifications which proved necessary to increase sensitivity. Three sample spectra are used to illustrate the arguments employed to achieve this result. The conclusions from the corresponding measurements provide a clearer understanding of the quality of the responses obtained during the initial reading. The application of these methods to systematic measurements is considered in the case of atmospheric aerosols. The owerall results obtained since 1969 are presented

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

    . 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...... 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...

  1. 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.

  2. A Property Based Approach for Simultaneous Process and Molecular Design

    Eljack, F.T.; Solvason, Charles Conrad; Chemmangattuvalappil, Nishanth; Eden, Mario R.

    2009-01-01

    In this work, property clustering techniques and group contribution methods are combined to enable simultaneous consideration of process performance requirements and molecular property constraints. Using this methodology, the process design problem is solved to identify the property targets corresponding to the desired process performance. A significant advantage of the developed methodology is that for problems that can be satisfactorily described by only three properties, the process and mo...

  3. An approach of molecular orbital calculations to process plasmas

    Remarkable progresses in the development of personal computers and molecular orbital methods have made it possible the calculation of complicated properties of molecules, which has been impossible so far. On the other hand, the plasma process such as reactive ion etching has been development while many plasma phenomena being unsolved. For the further development of the process, it is essential to make basic phenomena and problems in the plasma process clear. In the present article, an introduction to molecular orbital calculations is being presented for convenience of beginners in this field. (J.P.N.)

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

    Larade, Brian; Taylor, Jeremy Philip; Zheng, Q. R.; Mehrez, Hatem; Pomorski, Pawel; Guo, Hong

    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...... levels and main transmission features shift in energy corresponding to half the applied bias voltage. This is also consistent with our finding that the voltage drops by V-b/2 at each molecule/electrode contact....

  5. 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

  6. Molecular epidemiology biomarkers-Sample collection and processing considerations

    Biomarker studies require processing and storage of numerous biological samples with the goals of obtaining a large amount of information and minimizing future research costs. An efficient study design includes provisions for processing of the original samples, such as cryopreservation, DNA isolation, and preparation of specimens for exposure assessment. Use of standard, two-dimensional and nanobarcodes and customized electronic databases assure efficient management of large sample collections and tracking results of data analyses. Standard operating procedures and quality control plans help to protect sample quality and to assure validity of the biomarker data. Specific state, federal and international regulations are in place regarding research with human samples, governing areas including custody, safety of handling, and transport of human samples. Appropriate informed consent must be obtained from the study subjects prior to sample collection and confidentiality of results maintained. Finally, examples of three biorepositories of different scale (European Cancer Study, National Cancer Institute and School of Public Health Biorepository, University of California, Berkeley) are used to illustrate challenges faced by investigators and the ways to overcome them. New software and biorepository technologies are being developed by many companies that will help to bring biological banking to a new level required by molecular epidemiology of the 21st century

  7. 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)

  8. 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…

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. Interaction networks for identifying coupled molecular processes in microbial communities

    Bosse, Magnus; Heuwieser, Alexander; Heinzel, Andreas; Nancucheo, Ivan; Melo Barbosa Dall’Agnol, Hivana; Lukas, Arno; Tzotzos, George; Mayer, Bernd

    2015-01-01

    Background Microbial communities adapt to environmental conditions for optimizing metabolic flux. Such adaption may include cooperative mechanisms eventually resulting in phenotypic observables as emergent properties that cannot be attributed to an individual species alone. Understanding the molecular basis of cross-species cooperation adds to utilization of microbial communities in industrial applications including metal bioleaching and bioremediation processes. With significant advancements...

  14. Molecular-beam Studies of Primary Photochemical Processes

    Lee, Y. T.

    1982-12-01

    Application of the method of molecular-beam photofragmentation translational spectroscopy to the investigation of primary photochemical processes of polyatomic molecules is described. Examples will be given to illustrate how information concerning the energetics, dynamics, and mechanism of dissociation processes can be obtained from the precise measurements of angular and velocity distributions of products in an experiment in which a well-defined beam of molecules is crossed with a laser.

  15. Modeling stochastic kinetics of molecular machines at multiple levels: from molecules to modules.

    Chowdhury, Debashish

    2013-06-01

    A molecular machine is either a single macromolecule or a macromolecular complex. In spite of the striking superficial similarities between these natural nanomachines and their man-made macroscopic counterparts, there are crucial differences. Molecular machines in a living cell operate stochastically in an isothermal environment far from thermodynamic equilibrium. In this mini-review we present a catalog of the molecular machines and an inventory of the essential toolbox for theoretically modeling these machines. The tool kits include 1), nonequilibrium statistical-physics techniques for modeling machines and machine-driven processes; and 2), statistical-inference methods for reverse engineering a functional machine from the empirical data. The cell is often likened to a microfactory in which the machineries are organized in modular fashion; each module consists of strongly coupled multiple machines, but different modules interact weakly with each other. This microfactory has its own automated supply chain and delivery system. Buoyed by the success achieved in modeling individual molecular machines, we advocate integration of these models in the near future to develop models of functional modules. A system-level description of the cell from the perspective of molecular machinery (the mechanome) is likely to emerge from further integrations that we envisage here. PMID:23746505

  16. Processing method of high level radioactive solution

    A reagent which acts on zirconium to form precipitates is added to zirconium contained in a solution of spent nuclear fuels or a high level radioactive solution generated along with reprocessing. As the reagent, phosphoric acid, molybdic acid, telluric acid or salts thereof, namely, phosphate, molybdate and tellurate can be used. In addition, if the addition of these reagents and heat treatment are joined, formation of precipitates can be promoted. According to this method, zirconium present in the high level radioactive solution in the form of fine precipitates, colloid or in a dissolved state can be converted to easily removable precipitates without losing safety or applying significant effects on co-existent elements. (T.M.)

  17. Solidification process for high level radioactive waste

    Purpose: To integrally solidify high level radioactive wastes with water-curable solidifying material thereby improve the heat- and radiation-resistance. Constitution: High level radioactive wastes are integrally solidified with water curable solidifying material comprising a mixture of alumina cements, aggregates, inorganic fluidizing materials and dispersing agent. Alumina cements are mainly composed of calcium aluminate and excellent in refractory property. Chamotte particles and baked bauxite particles are used as the aggregates, which can improve the strength of the solidification products. Fine alumina powder and fine silica powder of less than 10 ?m radius are used as the inorganic fluidizing materials and condensated phosphoric acid salt and polycarboxylic acid type polymeric surface active agent are used as the dispersing agents for improving the slidability between the particles. (Yoshino, Y.)

  18. Spectroscopic studies of the molecular imprinting self-assembly process.

    Svenson, J; Andersson, H S; Piletsky, S A; Nicholls, I A

    1998-01-01

    A method for the rapid estimation of the extent of complex formation in molecular imprinting prepolymerization mixtures is described. By the use of a UV spectroscopy titration procedure, apparent binding constants for such self-assembly processes have been obtained. This method was used for comparison of the interactions between a dipeptide template (N-acetyl-L-phenylalaninyl-L-tryptophanyl methyl ester) and the functional monomer methacrylic acid, and the monomer analogues acetic acid and trifluoroacetic acid. The importance of template-monomer association during the molecular imprinting prepolymerization phase is discussed with respect to the systems studied. PMID:10076812

  19. 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)

  20. Low-level nitrate waste process development

    Thermal and chemical methods for denitrification of nitrate wastes have been investigated. Experiments were conducted using a high temperature fluid wall reactor to determine its nitrate/nitrite destruction efficiency on simulated Rocky Flats Plant and Savannah River Plant waste streams. These streams included nitrate contaminated soils and feeds containing surrogate fission-products. Various additives were tested to enhance nitrate destruction, reduce NO/sub x/ off-gas generation, and produce an acceptable final waste form. In addition, testing was completed with actual Rocky Flats Plant nitrate wastes on an aqueous process consisting of formic and sulfuric acid reflux, followed by evaporation of the liquid to dryness. Experimental results are discussed and conclusions are presented on both the thermal and the aqueous processes. An update of an earlier survey on nitrate waste generation and inventories at DOE facilities is also provided

  1. Status of Safeguards and Separations Model Development at Plant and Molecular Levels

    de Almeida, Valmor F [ORNL; Hay, Benjamin [ORNL; DePaoli, David W [ORNL

    2009-10-01

    A primary goal of the Safeguards and Separations IPSC effort is the development of process modeling tools that allow dynamic simulations of separations plant operations under various configurations and conditions, and integration of relevant safeguards analyses. A requirement of the effort is to develop codes on modern, expandable architectures, with flexibility to explore and evaluate a wide range of process options. During FY09, efforts at ORNL have been focused on two priority tasks toward achieving the IPSC goal: (1) a top-down exploration of architecture - Subtask 1: Explore framework for code development and integration for plant-level simulation; and (2) a bottom-up fundamental modeling effort - Subtask 2: Development of molecular-level agent design code. Subtask 1 is important because definition and development of architecture is a key issue for the overall effort, as selection of an overall approach and code/data requirements is a necessary first step in the organization, design and development of separations and safeguards codes that will be incorporated. The agent design effort of Subtask 2 is a molecular-level modeling effort that has a direct impact on a near-term issue of the Separations and Waste Forms Campaign. A current focus of experimental efforts is the development of robust agents and processes for separation of Am/Cm. Development of enhanced agent-design codes will greatly accelerate discovery and experimental testing.

  2. 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)

  3. Angular distribution and spin polarization of molecular auger processes

    Lohmann, B.; Bonhoff, S.; Bonhoff, K.; Lehmann, J.; Blum, K.

    1997-02-01

    The general theory for angular distribution and spin polarization of molecular Auger electrons emitted from freely rotating diatomic molecules is discussed within the framework of a two-step model. Assuming electron impact ionization then, in contrast to a primary photoionization process, the number of independent parameters is no longer restricted by dipole selection rules. Different spin polarization states of the primary electron beam will be considered. The physical importance of a coherent excitation process is discussed within a simple example. Numerical results for the anisotropy parameters characterizing the dynamics of the Auger emission process are discussed for HF.

  4. 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)

  5. Molecular-Level Design of Heterogeneous Chiral Catalysis

    The following is a proposal to continue our multi-institutional research on heterogeneous chiral catalysis. Our team combines the use of surface-sensitive analytical techniques for the characterization of model systems with quantum and statistical mechanical calculations to interpret experimental data and guide the design of future research. Our investigation focuses on the interrelation among the three main mechanisms by which enantioselectivity can be bestowed to heterogeneous catalysts, namely: (1) by templating chirality via the adsorption of chiral supramolecular assemblies, (2) by using chiral modifiers capable of forming chiral complexes with the reactant and force enantioselective surface reactions, and (3) by forming naturally chiral surfaces using imprinting chiral agents. Individually, the members of our team are leaders in these various aspects of chiral catalysis, but the present program provides the vehicle to generate and exploit the synergies necessary to address the problem in a comprehensive manner. Our initial work has advanced the methodology needed for these studies, including an enantioselective titration procedure to identify surface chiral sites, infrared spectroscopy in situ at the interface between gases or liquids and solids to mimic realistic catalytic conditions, and DFT and Monte Carlo algorithms to simulate and understand chirality on surfaces. The next step, to be funded by the monies requested in this proposal, is to apply those methods to specific problems in chiral catalysis, including the identification of the requirements for the formation of supramolecular surface structures with enantioselective behavior, the search for better molecules to probe the chiral nature of the modified surfaces, the exploration of the transition from supramolecular to one-to-one chiral modification, the correlation of the adsorption characteristics of one-to-one chiral modifiers with their physical properties, in particular with their configuration, 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.

  6. Molecular-Level Design of Heterogeneous Chiral Catalysis

    Francisco Zaera

    2012-03-21

    The following is a proposal to continue our multi-institutional research on heterogeneous chiral catalysis. Our team combines the use of surface-sensitive analytical techniques for the characterization of model systems with quantum and statistical mechanical calculations to interpret experimental data and guide the design of future research. Our investigation focuses on the interrelation among the three main mechanisms by which enantioselectivity can be bestowed to heterogeneous catalysts, namely: (1) by templating chirality via the adsorption of chiral supramolecular assemblies, (2) by using chiral modifiers capable of forming chiral complexes with the reactant and force enantioselective surface reactions, and (3) by forming naturally chiral surfaces using imprinting chiral agents. Individually, the members of our team are leaders in these various aspects of chiral catalysis, but the present program provides the vehicle to generate and exploit the synergies necessary to address the problem in a comprehensive manner. Our initial work has advanced the methodology needed for these studies, including an enantioselective titration procedure to identify surface chiral sites, infrared spectroscopy in situ at the interface between gases or liquids and solids to mimic realistic catalytic conditions, and DFT and Monte Carlo algorithms to simulate and understand chirality on surfaces. The next step, to be funded by the monies requested in this proposal, is to apply those methods to specific problems in chiral catalysis, including the identification of the requirements for the formation of supramolecular surface structures with enantioselective behavior, the search for better molecules to probe the chiral nature of the modified surfaces, the exploration of the transition from supramolecular to one-to-one chiral modification, the correlation of the adsorption characteristics of one-to-one chiral modifiers with their physical properties, in particular with their configuration, 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.

  7. Electron impact atomic and molecular processes - theoretical and application highlights

    Electron impact atomic/molecular scattering is an established but ever growing field of multidisciplinary theoretical and experimental research. This is so because the impact processes are found to take place in a wide variety of natural and man-made systems. There has long since been a fundamental as well as applied interest in this area of atomic and molecular Physics. The key quantities employed in interpreting the impact phenomena are cross sections, differential as well as total, which exhibit the characteristics of the target and the collision energy. In this article, the author discussed some aspects of electron -atom and electron - molecule collisions, that result into elastic and various inelastic processes. Theoretical highlights along with a few results are presented here as a preliminary account

  8. 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.

  9. 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...

  10. 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...

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

    O'Brien, Cathal P.; Finn, Stephen P

    2014-01-01

    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 devi...

  12. Molecular link between BRCA1 protein levels and obesity

    NCI researchers have defined a possible molecular link between breast cancer risk and obesity. New study results show that a protein called C-terminal binding protein (CtBP) acts to control a gene linked to breast cancer risk in rapidly growing cells by m

  13. Evidence for atomic processes in molecular valence double ionization

    Complete molecular valence-electron spectra were measured for CO. Unexpectedly, discrete lines at low kinetic energies were found, superimposed on a continuous energy spectrum representing direct double-ionization processes. The appearance of these lines is discussed in the context of the formation of the C++O+ ion pair near its associated threshold at 38.4 eV. It is ascribed to valence-excited repulsive (CO+)* states, which dissociate to a large part rapidly into atomic fragments before electronic relaxation takes place. From our spectra, partial cross sections for the different processes leading to dissociative valence double ionization are derived

  14. 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.

  15. 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) modified by a variety of chiral templates. • Demonstrated enantioselective separation of racemic PO on chemically synthesized chiral gold nanoparticles. • Discovery of zwitterionic adsorption states of amino acids on Pd(111). • First structure determinations of adsorbed amino acids and identification of tetrameric chiral template structures. • Exploration of the enantiospecific interaction of PO and R-3-MCHO adsorption on chirally modified Cu(100), Cu(110) and Cu(111). One-to-One Interactions • Determination of cinchona orientation on Pt surfaces in situ at the solid-liquid interface using FT-IRAS. • Systematic study of the influence of solution properties on the adsorption of modified cinchonas alkaloids onto Pt surfaces. • Correlation of cinchona adsorption with catalytic activity, as affected by concentration, the nature of the solvent, and dissolved gases in the liquid phase. • Measurement of enantioselective chemisorption on 1-(1-naphthyl) ethylamine (NEA) modified Pt(111) and Pd(111) surfaces. • Imaging of chiral docking complexes between NEA and methyl pyruvate on Pd(111). Chiral Catalyst Synthesis • Anchoring of cinchona alkaloid to surfaces • Synthesis of chiral Au nanoparticles and demonstration of their enantiospecific interactions with R- and S-PO. • Elucidation of the driving forces for chiral imprinting of Cu(100) by L- and D-lysine to form Cu(3,1,17)R&S facets.

  16. Boolean and fuzzy logic implemented at the molecular level

    Gentili, Pier Luigi

    2007-07-01

    In this work, it is shown how to implement both hard and soft computing by means of two structurally related heterocyclic compounds: flindersine (FL) and 6(5H)-phenanthridinone (PH). Since FL and PH have a carbonyl group in their molecular skeletons, they exhibit Proximity Effects in their photophysics. In other words, they have an emission power that can be modulated through external inputs such as temperature ( T) and hydrogen-bonding donation (HBD) ability of solvents. This phenomenology can be exploited to implement both crisp and fuzzy logic. Fuzzy Logic Systems (FLSs) wherein the antecedents of the rules are connected through the AND operator, are built by both the Mamdani's and Sugeno's models. Finally, they are adopted as approximators of the proximity effect phenomenon and tested for their prediction capabilities. Moreover, FL as photochromic compound is also a multiply configurable crisp logic molecular element.

  17. 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.

  18. Molecular Level Studies of the Metal/Atmosphere Interface

    Weissenrieder, Jonas

    2003-01-01

    The chemistry andphysics involved at the metal/atmosphereinterface is interesting both from a fundamental and an appliedperspective. Since iron is the most important of all metalsthis interface is of particular interest. The objective withthis thesis is to obtain new information on a molecular levelof the iron/atmosphere interface with a special emphasis on theinitial atmospheric corrosion. The work presented herein combines a large variety ofdifferent analytical surface science techniques. B...

  19. 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

  20. 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...

  1. Molecular sieve sensors for selective detection at the nanogram level

    Zeolites have long been known for their molecular sieving properties based upon crystalline pore structures of molecular dimensions. The authors explore strategies to introduce molecular sieving functions into inorganic thin films and membranes which are of current interest for sensor coatings and gas-phase separations. The zeolite films offer high thermal stability (> 770 K) and chemical resistance. Surface acoustic wave devices can be operated as highly sensitive piezoelectric balances that respond to small fractions of single-crystal monolayer adsorption via frequency changes of an oscillator circuit. Since the response is nonselective, a number of organic and organometallic coatings on SAW devices have previously been explored to impart chemical selectivity. The SAW device (97 MHz, detection limit ca. 100 pg/cm2) used in the present study to measure selective adsorption of organic vapors (0.1% of saturation in nitrogen flow, 295 K) consists of a single-crystal quartz substrate with interdigital transducers which was coated with zeolite-silica thin films and mounted in a test chamber with gas inlet and outlet

  2. 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.

  3. Limitations and improvements upon the two-level approximation for molecular nonlinear optics

    Andrews, David L.; Bradshaw, David S.; Coles, Matt M.

    2011-03-01

    When parametric nonlinear processes are employed in the cause of efficient optical frequency conversion, the media involved are generally subjected to substantially off-resonant input radiation. As such, it is usually only electronic ground states of the conversion material that are significantly populated; higher levels are engaged only in the capacity of virtual states, and it is frequently assumed that just one such state dominates in determining the response. Calculating the nonlinear optical susceptibilities of molecules on this basis, excluding all but the ground and one excited state in a sum-over-states formulation, signifies the adoption of a two-level model, a technique that is widely deployed in the calculation and analysis of nonlinear optical properties. The two-level model offers tractable and physically simple representations of molecular response, including wavelength dependence; it is also the origin of the widely applied 'push-pull' approach to designing optically nonlinear chromophores. By contrast, direct ab initio calculations of optical susceptibility are commonly frustrated by a complete failure to determine such dispersion features. However, caution is required; the two-level model can deliver potentially misleading results if it is applied without regard to the criteria for its validity, especially when molecular excited states are significantly populated. On the basis of a precise, quantum electrodynamical basis for the theory, we explore in detail why there are grounds for questioning the general validity of two-level calculations in nonlinear optics; we assess the criteria for high frequency conversion efficiency and provide a new graphical method to assist in determining the applicability of a two-level model for hyperpolarizability calculations. Lastly, this paper also explores the applicability and detailed conditions for the two-level model for electronically excited molecules, identifying problematic results and providing tractable methods for improving the accuracy of calculations on real molecule-photon interactions.

  4. The influence of molecular weight in radiotracers of inflamators processes

    Four 99mTc-radiopharmaceuticals (RPs) were compared as a radiotracers of inflammatory process. The RPs were divided in two groups according to their molecular weights and nature. One group included the human IgG and the ior t3 MoAb (anti-CD3), another included the Ciprofloxacine and the DMSA. The RPs were studied by different quality controls, and a biodistribution study in an aseptic inflammatory model made by steril Carragenin. The results obtained in the reduction of the immunoglobulins with 2-mercaptoethanol and sodium metabisulphite demonstrated that both reducing agents were equivalent, because the radiochemical purity obtained were similar and independent of the immunoglobulins. The biodistribution demonstrated a higher incorporation for the radiopharmaceuticals of high molecular weight, and the highest values were obtained with the 2-mercaptoethanol

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

    O'Brien, Cathal P; Finn, Stephen P

    2014-01-01

    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. PMID:25988159

  6. 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.

  7. 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...

  8. 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...

  9. Two Molecular Information Processing Systems Based on Catalytic Nucleic Acids

    Stojanovic, Milan

    Mixtures of molecules are capable of powerful information processing [1]. This statement is in the following way self-evident: it is a hierarchically organized complex mixture of molecules that is formulating it to other similarly organized mixtures of molecules. By making such a statement I am not endorsing the extreme forms of reductionism; rather, I am making what I think is a small first step towards harnessing information processing prowess of molecules and, hopefully, overcoming some limitations of more traditional computing paradigms. There are different ideas on how to understand and use molecular information processing abilities and I will list some below. My list is far from inclusive, and delineations are far from clear-cut; whenever available, I will provide examples from our research efforts. I should stress, for a computer science audience that I am a chemist. Thus, my approach may have much different focus and mathematical rigor, then if it would be taken by a computer scientist.

  10. Ab-initio molecular treatment of the symmetric Mg2+-Mg charge transfer process

    Amami, M.; Moussa, A.; Zaidi, A.; Lahmar, S.; Bacchus-Montabonel, M. C.

    2016-02-01

    Potential energy curves of the MgMg2+ molecular system in the lowest electronic states as well as radial and rotational couplings between these states are obtained from ab-initio calculations at the CASSCF/MRCI level of theory using large basis sets. These data are used to investigate, via the semi-classical molecular close coupling method, the single symmetric charge transfer processes of Mg2+-Mg collisions in the [1.0-650] keV laboratory energy range. Total and partial cross sections for the expected capture channels are calculated and compared with the available experimental and theoretical results.

  11. 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 ...

  12. Molecular level water and solute transport in reverse osmosis membranes

    Lueptow, Richard M.; Shen, Meng; Keten, Sinan

    2015-11-01

    The water permeability and rejection characteristics of six solutes, methanol, ethanol, 2-propanol, urea, Na+, and Cl-, were studied for a polymeric reverse osmosis (RO) membrane using non-equilibrium molecular dynamics simulations. Results indicate that water flux increases with an increasing fraction of percolated free volume in the membrane polymer structure. Solute molecules display Brownian motion and hop from pore to pore as they pass through the membrane. The solute rejection depends on both the size of the solute molecule and the chemical interaction of the solute with water and the membrane. When the open spaces in the polymeric structure are such that solutes have to shed at least one water molecule from their solvation shell to pass through the membrane molecular structure, the water-solute pair interaction energy governs solute rejection. Organic solutes more easily shed water molecules than ions to more readily pass through the membrane. Hydrogen-bonding sites for molecules like urea also lead to a higher rejection. These findings underline the importance of the solute's solvation shell and solute-water-membrane chemistry in solute transport and rejection in RO membranes. Funded by the Institute for Sustainability and Energy at Northwestern with computing resources from XSEDE (NSF grant ACI-1053575).

  13. Eleven Levels of Spinous Process Fractures in Thoracolumbar Spine

    Kim, Whoan Jeang; Chi, Yong Joo; Park, Kyung Hoon; Choy, Won Sik

    2014-01-01

    Cases of over 5-level spinous process fractures are extremely rare. Thoracolumbar region of spine is superimposed on ribs; and as such additional studies such as computerized tomography are needed to diagnose fractures in this region. We report a case of 11 contiguous level thoracolumbar spinous process fractures, which has been treated conservatively.

  14. Molecular dynamics simulations of cluster fission and fusion processes

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

    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...

  15. 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...

  16. Simulation analysis of molecular laser isotope separation process for safeguards design

    In this report, firstly an approach to a satisfactory safeguards concept is studied and proposed, among other things, as such that a process model should be developed only on a basis of published theories and data and that the safeguards should be designed using this process model. Secondly, as the first step of this approach, the photon-molecular reaction dynamics for a uranium-235-selective excitation process which is one of the infrared multi-photon dissociation processes for uranium enrichment was computer-simulated using a mathematical model as follows: through the investigation of a selective excitation probability in each energy level and of the transition probability to quasi-continuum levels from the top discrete level, a sensitivity analysis was carried out on the important parameters for process operations such as the optimum relative intensities between the laser for selective excitation and the laser for dissociation, the laser pulse widths to be required, and the asynchronous multi-laser irradiation. As a result, the conditions to be satisfied by such operational parameters in the design of photon-excited selective process were made clear. Although the dissociation process in the quasi-continuum and in the true continuum levels must be investigated in order to have a complete picture of the uranium-235 separation process, the optimization of the photon-excited selective process which was analyzed in this report is the most important theme for the molecular laser uranium enrichment and the detailed analysis of the characteristics of such excitation process not only gives fundamental data for the design of enrichment process but also is necessary for analyzing the diversion possibilities of producing higher enrichment than declared for safeguards design. (author)

  17. 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...

  18. In-Line Detection and Measurement of Molecular Contamination in Semiconductor Process Solutions

    Wang, Jason; West, Michael; Han, Ye; McDonald, Robert C.; Yang, Wenjing; Ormond, Bob; Saini, Harmesh

    2005-09-01

    This paper discusses a fully automated metrology tool for detection and quantitative measurement of contamination, including cationic, anionic, metallic, organic, and molecular species present in semiconductor process solutions. The instrument is based on an electrospray ionization time-of-flight mass spectrometer (ESI-TOF/MS) platform. The tool can be used in diagnostic or analytical modes to understand process problems in addition to enabling routine metrology functions. Metrology functions include in-line contamination measurement with near real-time trend analysis. This paper discusses representative organic and molecular contamination measurement results in production process problem solving efforts. The examples include the analysis and identification of organic compounds in SC-1 pre-gate clean solution; urea, NMP (N-Methyl-2-pyrrolidone) and phosphoric acid contamination in UPW; and plasticizer and an organic sulfur-containing compound found in isopropyl alcohol (IPA). It is expected that these unique analytical and metrology capabilities will improve the understanding of the effect of organic and molecular contamination on device performance and yield. This will permit the development of quantitative correlations between contamination levels and process degradation. It is also expected that the ability to perform routine process chemistry metrology will lead to corresponding improvements in manufacturing process control and yield, the ability to avoid excursions and will improve the overall cost effectiveness of the semiconductor manufacturing process.

  19. 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...

  20. Molecular processes of transgenerational acclimation to a warming ocean

    Veilleux, Heather D.; Ryu, Taewoo; Donelson, Jennifer M.; van Herwerden, Lynne; Seridi, Loqmane; Ghosheh, Yanal; Berumen, Michael L.; Leggat, William; Ravasi, Timothy; Munday, Philip L.

    2015-12-01

    Some animals have the remarkable capacity to acclimate across generations to projected future climate change; 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.

  1. 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.

  2. Space Based Multi-level Process Flow and Logistics Analysis

    Zhou Qiu-Zhong

    2013-01-01

    Full Text Available In order to thoroughly promote the enterprise digital construction and meet the demand of production management, the space based multi-level process data organization model has been put forward. Firstly, according to the practical division situation of enterprise production space, the multi-level organization method of production space has been proposed. Then through analyzing the manufacturing process of the products in different space layers, the space based multi-level process flow idea has been presented. At the same time, the mathematical model and formalized expression of multi-level technological process have been established. Finally, the in-output material flow relationship between different levels process flow units has been analyzed and the source of input object as well as the disposition of the output object of various level process flow units has been put into detailed analysis. At the mean time, particular statistical sum and trace arithmetic are provided so as to profoundly illustrate the essence of manufacturing process in theory. As a result, the models proposed in this study are not only express the manufacturing process flow of the product in an intuitive and clear way, but also satisfy all types of demands of production management.

  3. The Building Blocks of Materials: Gathering Knowledge at the Molecular Level

    2003-01-01

    Two start-up positions were created within SD46 to pursue developments in the rapidly expanding areas of biomineralization and nano-technology. As envisioned by Dr. Sandor Lehoczy, the new laboratories to be developed must have the capacity to investigate not only processes associated with the self-assembly of molecules but also the examination of self-assembled structures. For these purposes, laboratories capable of performing the intended function, particularly light scattering spectroscopy and atomic force microscopy were created. What follows then are recent advances arising from the development of these new laboratories. With the implementation of the Atomic Force Microscopy Facility, examples of investigations that determine a correlation between the molecular structure of materials and their macroscopic physical properties are provided. In addition, examples of investigations with particular emphasis on the physical properties of protein crystals, at the molecular level, and subsequent macroscopic characteristics are as provided. Finally, progress in fabrication of technology at the nano-scale levels at the developmental stage is also presented.

  4. Kratzer potential for vibrational levels in molecular hydrogen

    Hooydonk, Guido van [Ghent Univ., Faculty of Sciences (Belgium)

    2009-12-15

    The vibrational part of the dihydrogen Hamiltonian obeys a quantized Sommerfeld-Kratzer potential, which takes into account internal H{sub 2} symmetries. All constants {omega}{sub e}, k{sub e}, and r{sub e} needed for the H{sub 2} vibrational system derive from hydrogen mass. Ionic Kratzer bond theory gives covalent bond energy within 0.08% and all levels within 0.02%, which is 30 times better than with a Dunham oscillator and as accurate as early ab initio quantum mechanics. (orig.)

  5. 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.

  6. 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

  7. 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.

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

    Tamascelli, Dario; Dambrosio, Francesco Saverio [Dipartimento di Fisica, Università degli Studi di Milano, via Celoria 16, 20133 Milano (Italy); Conte, Riccardo [Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322 (United States); Ceotto, Michele, E-mail: michele.ceotto@unimi.it [Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano (Italy)

    2014-05-07

    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.

  9. 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...

  10. 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

  11. Low-energy electron-collision processes in molecular chlorine

    The results of close-coupling calculations using the complex Kohn variational method are reported for a variety of low-energy electron-collision processes involving molecular chlorine. We report cross sections for elastic scattering and momentum transfer, as well as dissociative excitation of the five lowest electronically excited states (1,3?u, 1,3?g, 3?u+) which are formed by promoting an occupied valence electron into an antibonding (5?u) orbital. We also report cross sections for the excitation of the lowest bound optically allowed states in Cl2. The cross sections, especially at very low energies, are found to depend sensitively on both target polarization and a proper balance of correlation effects in the N- and (N+1)-electron systems. Comparison is made between the results of this study and the limited body of experimental results available for this system

  12. Electron-impact excitation levels of the rotational levels of molecular electron states in gas discharges

    The principles of rotational state excitation of molecules with a simultaneous electron transition under electron impact are investigated in gas discharge plasma conditions. The possibility of a substantial change (up to 5-6 ℎ or higher) in the angular momentum of the molecule in such a process is demonstrated. The relative transition probabilities with various changes in the rotation quantum numbers excited by electrons from the lowest rotational levels of the electron ground state were determined experimentally for hydrogen. The complete probability matrix is determined from these results incorporating the adiabatic approximation. The electron beam technique is used to investigate rotational excitation of H2 at various electron energies and it is demonstrated that the most efficient collisions occur between electrons of energies near the excitation threshold of the lectron state. These results establish the limits of applicability of the spectroscopic method of measuring gas temperature of a nonequilibrium plasma based on the relative intensities in the rotational structure of the electron spectra of molecules

  13. Ageing and photoageing of the skin: observations at the cellular and molecular level

    It is now well established that ageing occurs at the level of individual cells in the skin and other organ systems. Changes in cell behaviour, protein production and gene expression in response to standardized stimuli are readily observed in cultured cells derived from young vs old donors and from photoaged vs sun-protected body sites. Whether these changes are best viewed as a cause or a consequence of ageing cannot be determined at present. Nevertheless, available data now provide cellular and molecular correlates for the well-known differences in clinical responsiveness between newborn, adult and photoaged skin. From this basis, it will hopefully be possible to develop a more comprehensive understanding of cutaneous ageing processes. (Author)

  14. Radiation studies at the physical, molecular, cellular and macrocolony level

    Radiation effects in stationary yeast cells have been studied after irradiation with 30 MeV electrons, X-rays and alpha-particles. At the level of cfa alpha particles and X-rays cause more irreparable damage than 30 MeV electrons. The behaviour of an irradiated yeast cell population is studied by microscopic observation of single cells followed by computer analysis of the stored optical data. During the first four generations after irradiation the second cell division is the critical one for survival of the cells. The production of DNA dsbs in irradiated yeast cells is investigated by velocity sedimentation in a sucrose gradient. The average number of dsbs as a function of absorbed dose is determined by computer simulation of random breakage applied to the control DNA and by fitting these curves to the DNA profiles obtained from irradiated cells. It is shown that dsbs are exclusively produced by direct radiation effects. Changes in number of dsbs during liquid holding recovery are investigated and are compared with changes in cfa. The possible significance of certain energy deposition patterns of electrons, X-rays and alpha particles for the different radiation induced biological effects is estimated

  15. 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.

  16. 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

  17. 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

  18. Update of technologies for examining the stratum corneum at the molecular level.

    Norln, L

    2014-09-01

    Understanding the molecular organization of the stratum corneum is still an outstanding problem, despite being both fundamentally and clinically significant. There is a need to develop methodology that yields molecular-level resolution of the stratum corneum components in their native state, without introducing artefacts. We outline here the recent success of cryo-electron microscopy of vitreous sections (CEMOVIS) combined with electron microscopy simulation to elucidate the molecular organization of the stratum corneum in its near-native state. Furthermore, some emerging technologies for studying the physical properties and dynamic behaviour of native stratum corneum at the molecular level are briefly reviewed. These encompass multiphoton microscopy (MPM), polarization transfer solid-state nuclear magnetic resonance (PTssNMR) and PeakForce tapping-mode atomic force microscopy combined with frequency-modulation Kelvin probe force microscopy (KPFM). CEMOVIS combined with electron microscopy simulation allows for molecular structure determination in situ in native stratum corneum, while MPM allows probing of the stratum corneum local physicochemical properties such as fluorophore diffusion coefficients, water content and pH. PTssNMR allows for evaluation of the molecular mobility of stratum corneum keratin and lipid components, and PeakForce KPFM allows for analysis of the local nanomechanical properties of stratum corneum. These emerging techno-logies may contribute to a molecular-level understanding of stratum corneum structure and function in vivo. PMID:25234173

  19. Ochratoxin A: Molecular Interactions, Mechanisms of Toxicity and Prevention at the Molecular Level.

    Kőszegi, Tamás; Poór, Miklós

    2016-01-01

    Ochratoxin A (OTA) is a widely-spread mycotoxin all over the world causing major health risks. The focus of the present review is on the molecular and cellular interactions of OTA. In order to get better insight into the mechanism of its toxicity and on the several attempts made for prevention or attenuation of its toxic action, a detailed description is given on chemistry and toxicokinetics of this mycotoxin. The mode of action of OTA is not clearly understood yet, and seems to be very complex. Inhibition of protein synthesis and energy production, induction of oxidative stress, DNA adduct formation, as well as apoptosis/necrosis and cell cycle arrest are possibly involved in its toxic action. Since OTA binds very strongly to human and animal albumin, a major emphasis is done regarding OTA-albumin interaction. Displacement of OTA from albumin by drugs and by natural flavonoids are discussed in detail, hypothesizing their potentially beneficial effect in order to prevent or attenuate the OTA-induced toxic consequences. PMID:27092524

  20. 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...

  1. 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...

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

    Foti, Giuseppe; Vázquez, Héctor

    2016-03-01

    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.

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

    Foti, Giuseppe; Vzquez, Hctor

    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

  4. Dynamics of Molecular Motors with Finite Processivity on Heterogeneous Tracks

    Kafri, Y; Nelson, D R; Kafri, Yariv; Lubensky, David K.; Nelson, David R.

    2004-01-01

    The dynamics of molecular motors which occasionally detach from a heterogeneous track like DNA or RNA is considered. Motivated by recent single molecule experiments, we study a simple model for a motor moving along a disordered track using chemical energy while an external force opposes its motion. The motors also have finite processivity, i.e., they can leave the track with a position dependent rate. We show that the response of the system to disorder in the hopping off rate depends on the value of the external force. For most values of the external force, strong disorder causes the motors which survive for long times on the track to be localized at preferred positions. However, near the stall force, localization occurs for any amount of disorder. Existence of localized states near the top of the band implies a stretched exponential contribution to the decay of the survival probability. To obtain these results, we study the complex eigenvalue spectrum of the time evolution operator. A similar spectral analys...

  5. Evaluation of tocopherol recovery through simulation of molecular distillation process.

    Moraes, E B; Batistella, C B; Alvarez, M E Torres; Filho, Rubens Maciel; Maciel, M R Wolf

    2004-01-01

    DISMOL simulator was used to determine the best possible operating conditions to guide, in future studies, experimental works. This simulator needs several physical-chemical properties and often it is very difficult to determine them because of the complexity of the involved components. Their determinations must be made through correlations and/or predictions, in order to characterize the system and calculate it. The first try is to have simulation results of a system that later can be validated with experimental data. To implement, in the simulator, the necessary parameters of complex systems is a difficult task. In this work, we aimed to determe these properties in order to evaluate the tocopherol (vitamin E) recovery using a DISMOL simulator. The raw material used was the crude deodorizer distillate of soya oil. With this procedure, it is possible to determine the best operating conditions for experimental works and to evaluate the process in the separation of new systems, analyzing the profiles obtained from these simulations for the falling film molecular distillator. PMID:15054286

  6. 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

  7. Nanoarchitectonics for Dynamic Functional Materials from Atomic-/Molecular-Level Manipulation to Macroscopic Action.

    Ariga, Katsuhiko; Li, Junbai; Fei, Jinbo; Ji, Qingmin; Hill, Jonathan P

    2016-02-01

    Objects in all dimensions are subject to translational dynamism and dynamic mutual interactions, and the ability to exert control over these events is one of the keys to the synthesis of functional materials. For the development of materials with truly dynamic functionalities, a paradigm shift from "nanotechnology" to "nanoarchitectonics" is proposed, with the aim of design and preparation of functional materials through dynamic harmonization of atomic-/molecular-level manipulation and control, chemical nanofabrication, self-organization, and field-controlled organization. Here, various examples of dynamic functional materials are presented from the atom/molecular-level to macroscopic dimensions. These systems, including atomic switches, molecular machines, molecular shuttles, motional crystals, metal-organic frameworks, layered assemblies, gels, supramolecular assemblies of biomaterials, DNA origami, hollow silica capsules, and mesoporous materials, are described according to their various dynamic functions, which include short-term plasticity, long-term potentiation, molecular manipulation, switchable catalysis, self-healing properties, supramolecular chirality, morphological control, drug storage and release, light-harvesting, mechanochemical transduction, molecular tuning molecular recognition, hand-operated nanotechnology. PMID:26436552

  8. 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

  9. 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.

  10. 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 evaluate the influence of surface morphologies on the micro- and nanomechanical properties. Keeping nanotribological application in mind, a comparative AFM analysis were carried out and the influence of carbon content on the mechanical behaviour of such a coatings was evaluated. (author)

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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...

  16. 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)

  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 experimentally testable and has an intriguing implication for biological organization and evolution, as it amounts to "optimization without natural selection of replicators". Unlike the statistical-mechanical approaches to self-organization, the Cf principle does not encounter the problem of "tradeoff between stability and complexity" at the level of individual cell. Physically, the Cf is considered as a harmonic-like force of reaction, which keeps the state of the cell close to the ground state, defined here as a state where ...

  18. 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)

  19. 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

  20. Molecular and genetic diversity in the metastatic process of melanoma

    Harbst, Katja; Lauss, Martin; Cirenajwis, Helena; Winter, Christof; Howlin, Jillian; Törngren, Therese; Kvist, Anders; Nodin, Björn; Olsson, Eleonor; Häkkinen, Jari; Jirström, Karin; Staaf, Johan; Lundgren, Lotta; Olsson, Håkan; Ingvar, Christian

    2014-01-01

    Diversity between metastatic melanoma tumours in individual patients is known; however, the molecular and genetic differences remain unclear. To examine the molecular and genetic differences between metastatic tumours, we performed gene-expression profiling of 63 melanoma tumours obtained from 28 patients (two or three tumours/patient), followed by analysis of their mutational landscape, using targeted deep sequencing of 1697 cancer genes and DNA copy number analysis. Gene-expression signatur...

  1. Molecular processes that handle and mishandle dietary lipids

    Williams, Kevin Jon

    2008-01-01

    Overconsumption of lipid-rich diets, in conjunction with physical inactivity, disables and kills staggering numbers of people worldwide. Recent advances in our molecular understanding of cholesterol and triglyceride transport from the small intestine to the rest of the body provide a detailed picture of the fed/fasted and active/sedentary states. Key surprises include the unexpected nature of many pivotal molecular mediators, as well as their dysregulation but possible reversibility in ob...

  2. 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 were revealed by flow cytometry. The model would then be able to decipher qualitatively the molecular dynamics infolded in the regulation of cell behavior. To decipher the signaling pathway quantitatively, we employed a nanomechanical sensor at the bottom of the cell, quartz crystal microbalance with energy dissipation monitoring (QCM-D) to monitor the change at the basal area of the cell. This would provide the real time focal adhesion information and would be used in accordance with the AFM measurement data on the top of the cell to build a more complete mechanical profile during the antibody induced signaling process. We developed a model from a systematic control perspective that considers the signaling cascade at certain stimulation as the controller and the mechanical and structural interaction of the cell as the plant. We firstly derived the plant model based on QCM-D and AFM measurement processes. A signaling pathway model was built on a grey box approach where part of the pathway map was delineated in detail while others were condensed into a single reaction. The model parameters were obtained by extracting the mechanical response from the experiment. The model refinements were conducted by testing a series of inhibition mechanisms and comparing the simulation data with the experimental data. The model was then used to predict the existences of certain reactions that are qualitatively reported in the literature.

  3. 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

  4. Use of Rubber Process Analyzer for Characterizing the Molecular Weight Parameters of Natural Rubber

    Tianming Gao; Ruihong Xie; Linghong Zhang; Hongxing Gui; Maofang Huang

    2015-01-01

    The aim of this work is to introduce a simple and rapid method for characterizing the molecular weight parameters and other molecular structure parameters of natural rubber (NR) using a rubber process analyzer (RPA). In this work, NR of different molecular weights was prepared by milling. Molecular weight parameters were measured by gel permeation chromatography coupled with laser light scattering (GPC-LLS) for comparison with RPA results. It was verified that increasing of milling time leads...

  5. Low-level radioactive waste disposal process and apparatus

    The primary object of this invention is to provide an improved process and apparatus for disposing of low-level liquid radioactive wastes wherein the volume of the wastes can be reduced by a factor of at least ten to thereby minimize costs of storage and ultimate disposal of the wastes. The wastes will be in a form more suitable for storage, transit and burial while still conforming to safety codes. Another object of this invention is to provide a process of disposing of low-level liquid radioactive wastes wherein the wastes are reduced in volume to a mass of free-flowing, solid particles by calcining and the particles are packaged in the presence of a solidifying agent or the particles are compressed, sintered or fused to cause the wastes to be converted to a monolithic product capable of being readily and more safely stored or moved to a burial site. (auth)

  6. 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

  7. Wafer-Level Membrane-Transfer Process for Fabricating MEMS

    Yang, Eui-Hyeok; Wiberg, Dean

    2003-01-01

    A process for transferring an entire wafer-level micromachined silicon structure for mating with and bonding to another such structure has been devised. This process is intended especially for use in wafer-level integration of microelectromechanical systems (MEMS) that have been fabricated on dissimilar substrates. Unlike in some older membrane-transfer processes, there is no use of wax or epoxy during transfer. In this process, the substrate of a wafer-level structure to be transferred serves as a carrier, and is etched away once the transfer has been completed. Another important feature of this process is that two electrodes constitutes an electrostatic actuator array. An SOI wafer and a silicon wafer (see Figure 1) are used as the carrier and electrode wafers, respectively. After oxidation, both wafers are patterned and etched to define a corrugation profile and electrode array, respectively. The polysilicon layer is deposited on the SOI wafer. The carrier wafer is bonded to the electrode wafer by using evaporated indium bumps. The piston pressure of 4 kPa is applied at 156 C in a vacuum chamber to provide hermetic sealing. The substrate of the SOI wafer is etched in a 25 weight percent TMAH bath at 80 C. The exposed buried oxide is then removed by using 49 percent HF droplets after an oxygen plasma ashing. The SOI top silicon layer is etched away by using an SF6 plasma to define the corrugation profile, followed by the HF droplet etching of the remaining oxide. The SF6 plasma with a shadow mask selectively etches the polysilicon membrane, if the transferred membrane structure needs to be patterned. Electrostatic actuators with various electrode gaps have been fabricated by this transfer technique. The gap between the transferred membrane and electrode substrate is very uniform ( 0.1 m across a wafer diameter of 100 mm, provided by optimizing the bonding control). Figure 2 depicts the finished product.

  8. Modelling molecular networks: relationships between different formalisms and levels of details

    Soliman, Sylvain; Chaouiya, Claudine; Batt, Grégory; Fages, Francois; Remy, Élisabeth; Pommereau, Franck; Calzone, Laurence

    2010-01-01

    This document is the deliverable 1.3 of French ANR CALAMAR. It presents a study of different formalisms used for modelling and analyzing large molecular regulation networks, their formal links, in terms of mutual encodings and of abstractions, and the corresponding levels of detail captured.

  9. 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)

  10. 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.

  11. 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

  12. 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

    Context. The filamentary structure of molecular clouds may set important constraints on the mass distribution of stars forming within them. It is therefore important to understand which physical mechanism dominates filamentary cloud fragmentation and core formation. Aims: Orion A is the nearest giant molecular cloud, and its so-called ∫-shaped filament is a very active star-forming region that is a good target for such a study. We have recently reported on the collapse and fragmentation properties of the northernmost part of this structure, located ~2.4 pc north of Orion KL - Orion Molecular Cloud (OMC) 3. As part of our project to study the ∫-shaped filament, we analyze the fragmentation properties of the northern OMC 1 filament (located ≲0.3 pc north of Orion KL). This filament is a dense structure previously identified by JCMT/SCUBA submillimeter continuum and VLA NH3 observations and was shown to have fragmented into clumps. Our aim is to search for cores and young protostars embedded within OMC 1n and to study how the filament is fragmenting to form them. Methods: We observed OMC 1North (hereafter OMC 1n) with the Submillimeter Array (SMA) at 1.3 mm and report on our analysis of the continuum data. Results: We discovered 24 new compact sources, ranging in mass from 0.1 to 2.3, in size from 400 to 1300 au, and in density from 2.6 × 107 to 2.8 × 106 cm-3. The masses of these sources are similar to those of the SMA protostars in OMC 3, but their typical sizes and densities are lower by a factor of ten. Only 8% of the new sources have infrared counterparts, but there are five associated CO molecular outflows. These sources are thus likely in the Class 0 evolutionary phase but it cannot be excluded that some of the sources might still be pre-stellar cores. The spatial analysis of the protostars shows that they are divided into small groups that coincide with previously identified JCMT/SCUBA 850 μm and VLA NH3 clumps, which are separated by a quasi-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

  13. 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

  14. 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

  15. Molecular processes that handle -- and mishandle -- dietary lipids.

    Williams, Kevin Jon

    2008-10-01

    Overconsumption of lipid-rich diets, in conjunction with physical inactivity, disables and kills staggering numbers of people worldwide. Recent advances in our molecular understanding of cholesterol and triglyceride transport from the small intestine to the rest of the body provide a detailed picture of the fed/fasted and active/sedentary states. Key surprises include the unexpected nature of many pivotal molecular mediators, as well as their dysregulation - but possible reversibility - in obesity, diabetes, inactivity, and related conditions. These mechanistic insights provide new opportunities to correct dyslipoproteinemia, accelerated atherosclerosis, insulin resistance, and other deadly sequelae of overnutrition and underexertion. PMID:18830418

  16. Understanding molecular weight reduction of starch during heating-shearing processes

    Einde, R.M., van den; Goot, A.J., van der; Boom, R.M.

    2003-01-01

    Recent understanding of the mechanisms underlying the changes in molecular weight of starch as a function of process parameters during thermomechanical treatment, for example extrusion, holds promise towards more effective optimization of thermomechanical processes according to the desired modification of molecular weight. This paper summarizes recent advances in theoretical understanding and experimental methods. Empirical observations from extruder experiments can be better understood on th...

  17. Elucidation of polymer induced DNA condensation. Visualisation at the single molecular level

    DNA condensation is a phenomenon that has stimulated interest from biologists, physicists, and polymer chemists for decades. At the cellular level, this process is key to the packing of DNA within the nuclear envelope, and the exposure of the appropriate nucleic acid sequences in order for transcription to occur, and proteins to be produced. The advent of gene therapy has led to an invigoration of this subject area. In order to successfully deliver to, and transfect target cells, many delivery vectors condense the therapeutic DNA into small compact particles. The nature of these particles have a considerable influence on the ultimate expression of the administered nucleic acid material. In addition, at its most fundamental, DNA itself is a classical polyelectrolyte polymer, the behaviour of which has applicability to other charged polymeric systems. There are two core interwound themes to this investigation; the visualisation of DNA condensate morphology at ultra-resolution, and the elucidation of the mechanisms of formation of these structures. The technique of atomic force microscopy is central to these investigations. Methodologies have been devised allowing the visualisation of the tertiary structure and conformational behaviour of individual DNA condensates in near in situ conditions. Condensation of the nucleic acid material has been induced by two classes of cation; small molecular cations, like those found within eukaryotic cells, and a range of cationic polymers. The cationic polymers investigated all have considerable potential as gene delivery vectors. The resultant DNA condensates have been assessed and contrasted in terms of their tertiary morphology, lateral dimensions, and structural volume. Assessments have also been made regarding the influence of the molecular architecture of the cationic moiety and the nature of the input nucleic acid material on the resultant DNA condensates. With regard to the elucidation of the mechanisms of DNA condensate formation, this question has been addressed in two ways. Firstly, in an attempt to form intermediates of the condensation process, DNA has been exposed to cationic moieties over a range of cationic charge to DNA nucleotide ratios. The morphologies of the resulting complexes have been analysed, and hypotheses have been constructed, regarding the mechanisms of DNA condensate formation. The second methodology adopted involved the visualisation of the formation of DNA condensates in real time. DNA-cation complexes have been visualised in a near in situ environment, allowing dynamic tertiary conformational change of individual DNA condensates to be observed. The investigations presented here are among the first to utilise atomic force microscopy, operating in an aqueous environment, to elucidate DNA condensate morphology and dynamic conformational change in real time, and to apply atomic force microscopy in the characterisation of potential gene delivery vectors. (author)

  18. 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

  19. 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 (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. 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

  1. SENTINEL-2 Level 1 Products and Image Processing Performances

    Baillarin, S. J.; Meygret, A.; Dechoz, C.; Petrucci, B.; Lacherade, S.; Tremas, T.; Isola, C.; Martimort, P.; Spoto, F.

    2012-07-01

    In partnership with the European Commission and in the frame of the Global Monitoring for Environment and Security (GMES) program, the European Space Agency (ESA) 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 satellites constellation deployed in polar sun-synchronous orbit. While ensuring data continuity of former SPOT and LANDSAT multi-spectral missions, Sentinel-2 will also offer wide improvements such as a unique combination of global coverage with a wide field of view (290 km), a high revisit (5 days with two satellites), a high resolution (10 m, 20 m and 60 m) and multi-spectral imagery (13 spectral bands in visible and shortwave infra-red domains). In this context, the Centre National d'Etudes Spatiales (CNES) supports ESA to define the system image products and to prototype the relevant image processing techniques. This paper offers, first, an overview of the Sentinel-2 system and then, introduces the image products delivered by the ground processing: the Level-0 and Level-1A are system products which correspond to respectively raw compressed and uncompressed data (limited to internal calibration purposes), the Level-1B is the first public product: it comprises radiometric corrections (dark signal, pixels response non uniformity, crosstalk, defective pixels, restoration, and binning for 60 m bands); and an enhanced physical geometric model appended to the product but not applied, the Level-1C provides ortho-rectified top of atmosphere reflectance with a sub-pixel multi-spectral and multi-date registration; a cloud and land/water mask is associated to the product. Note that the cloud mask also provides an indication about cirrus. The ground sampling distance of Level-1C product will be 10 m, 20 m or 60 m according to the band. The final Level-1C product is tiled following a pre-defined grid of 100x100 km2, based on UTM/WGS84 reference frame. The stringent image quality requirements are also described, in particular the geo-location accuracy for both absolute (better than 12.5 m) and multi-temporal (better than 0.3 pixels) cases. Then, the prototyped image processing techniques (both radiometric and geometric) will be addressed. The radiometric corrections will be first introduced. They consist mainly in dark signal and detector relative sensitivity correction, crosstalk correction and MTF restoration. Then, a special focus will be done on the geometric corrections. In particular the innovative method of automatic enhancement of the geometric physical model will be detailed. This method takes advantage of a Global Reference Image database, perfectly geo-referenced, to correct the physical geometric model of each image taken. The processing is based on an automatic image matching process which provides accurate ground control points between a given band of the image to refine and a reference image, allowing to dynamically calibrate the viewing model. The generation of the Global Reference Image database made of Sentinel-2 pre-calibrated mono-spectral images will be also addressed. In order to perform independent validation of the prototyping activity, an image simulator dedicated to Sentinel-2 has been set up. Thanks to this, a set of images have been simulated from various source images and combining different acquisition conditions and landscapes (mountains, deserts, cities ). Given disturbances have been also simulated so as to estimate the end to end performance of the processing chain. Finally, the radiometric and geometric performances obtained by the prototype will be presented. In particular, the geo-location performance of the level-1C products which widely fulfils the image quality requirements will be provided.

  2. Process Design Concepts for Stabilization of High Level Waste Calcine

    T. R. Thomas; A. K. Herbst

    2005-06-01

    The current baseline assumption is that packaging ¡§as is¡¨ and direct disposal of high level waste (HLW) calcine in a Monitored Geologic Repository will be allowed. The fall back position is to develop a stabilized waste form for the HLW calcine, that will meet repository waste acceptance criteria currently in place, in case regulatory initiatives are unsuccessful. A decision between direct disposal or a stabilization alternative is anticipated by June 2006. The purposes of this Engineering Design File (EDF) are to provide a pre-conceptual design on three low temperature processes under development for stabilization of high level waste calcine (i.e., the grout, hydroceramic grout, and iron phosphate ceramic processes) and to support a down selection among the three candidates. The key assumptions for the pre-conceptual design assessment are that a) a waste treatment plant would operate over eight years for 200 days a year, b) a design processing rate of 3.67 m3/day or 4670 kg/day of HLW calcine would be needed, and c) the performance of waste form would remove the HLW calcine from the hazardous waste category, and d) the waste form loadings would range from about 21-25 wt% calcine. The conclusions of this EDF study are that: (a) To date, the grout formulation appears to be the best candidate stabilizer among the three being tested for HLW calcine and appears to be the easiest to mix, pour, and cure. (b) Only minor differences would exist between the process steps of the grout and hydroceramic grout stabilization processes. If temperature control of the mixer at about 80„aC is required, it would add a major level of complexity to the iron phosphate stabilization process. (c) It is too early in the development program to determine which stabilizer will produce the minimum amount of stabilized waste form for the entire HLW inventory, but the volume is assumed to be within the range of 12,250 to 14,470 m3. (d) The stacked vessel height of the hot process vessels in the hydroceramic grout process (i.e., 21 m) appears to be about the same as that estimated by the Direct Cementitious Waste Process in 1998, for which a conceptual design was developed. Some of the conceptual design efforts in the 1998 study may be applicable to the stabilizer processes addressed in this EDF. (e) The gamma radiation fields near the process vessels handling HLW calcine would vary from a range of about 300-350 R/hr at a distance of 2.5 cm from the side of the vessels to a range of about 50-170 R/hr at a distance of 100 cm from the side of the vessels. The calculations were made for combined calcine, which was defined as the total HLW calcine inventory uniformly mixed. (f) The gamma radiation fields near the stabilized waste in canisters would range from about 25-170 R/hr at 2.5 cm from the side of the canister and 5-35 R/hr at 100 cm from the side of the canister, depending on the which bin set was the source of calcine.

  3. Melt-processing method for low level radioactive wastes

    When melting low level radioactive solid wastes for processing them, it is effective for stably capturing Cs as one of volatile nuclides in a molten material to increase concentration of SiO2 or the concentration of Al2O3 among ingredients of slug layers in the molten material. On the other hand, coal ash (including fly ash) contains a great amount of SiO2 and Al2O3. In the present invention, the coal ash is added when melting the low level radioactive wastes. In this case, the coal ash is taken into the slug layers of the molten materials to increase not only the SiO2 concentration but also Al2O3 concentration in the slug layers and lower the basicity. Accordingly, volatility of Cs is suppressed even if the melting point exceeds far beyond the boiling point of Cs, and Cs is captured effectively in the molten material. (T.M.)

  4. Identification of mycobacteria in peat moss processing plants : application of molecular biology approaches

    Cayer, M.P.; Veillette, M.; Pageau, P.; Cormier, Y.; Duchaine, C.; Meriaux, A. [Laval Univ., Quebec City, PQ (Canada). Inst. Universitaire de pneumologie et de cardiologie; Veillette, M.; Meriaux, A.; Cormier, Y. [Laval Univ., Quebec City, PQ (Canada). Dept. of Biology and Microbiology; Hamelin, R.; Bergeron, M.J. [Natural Resources Canada, Sainte-Foy, PQ (Canada). Canadian Forest Service

    2007-01-15

    Health concerns regarding environmental mycobacteria has led to the development of exposure assessment methods for the evaluation of certain workplaces where the presence of these agents is suspected. Hypersensitivity pneumonitis (HP) has been described in peat moss workers who are regularly exposed to significant levels of bioaerosols in peat moss processing plants. Although mycobacteria have been cultured from peat moss, plant workers exposure to mycobacterial bioaerosols has never been studied. This article presented the results of a study that evaluated the presence of mycobacteria in air samples from peat moss processing plants using molecular biology approaches (cloning-sequencing and polymerase chain reaction (PCR)) and the workers exposure using immunoglobin G (IgG) complexes to mycobacteria. It also compared species detected in air samples and in peat moss. Two peat moss processing plants were chosen among 14 previously studied and a total of 49 clones were sequenced. Real-time PCR was also performed on the same air samples to evaluate the airborne concentration of mycobacteria and estimate exposure levels. The article discussed the materials and methods used in the study, the results of the study, and subsequent discussion of the results. It was concluded that peat moss processing plants workers are exposed to mycobacteria in addition to other biological agents. It was suggested that further studies are needed to confirm the specificity of the mycobacterial IgG. 34 refs., 2 tabs., 1 fig.

  5. Coupled processes in NRC high-level waste research

    The author discusses NRC research effort in support of evaluating license applications for disposal of nuclear waste and for promulgating regulations and issuing guidance documents on nuclear waste management. In order to do this they fund research activities at a number of laboratories, academic institutions, and commercial organizations. One of our research efforts is the coupled processes study. This paper discusses interest in coupled processes and describes the target areas of research efforts over the next few years. The specific research activities relate to the performance objectives of NRC's high-level waste (HLW) regulation and the U.S. Environmental Protection Agency (EPA) HLW standard. The general objective of the research program is to ensure the NRC has a sufficient independent technical base to make sound regulatory decisions

  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 metal and the organic monolayer can be fully decoupled from the work-function modification induced by the SAM. (author)

  8. 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

  9. Oak Ridge Y-12 Plant Emergency Action Level (EAL) Process

    Bailiff, E.G.; Bolling, J.D.

    2000-08-01

    This report establishes requirements and standard methods for the development and maintenance of the Emergency Action Level (EAL) Process used by all lead and event contractors for emergency planning and preparedness. The EAL process ensures a technically defensible approach to emergency categorization/classification in accordance with DOE Order 151.1. The instructions provided in this document include methods and requirements for the development and approval of the EAL process. EALs are developed to cover events inside and outside the Y-12 Plant and to allow the Emergency Response Organization (ERO) to classify or reclassify events promptly based on specific indicators. This report is divided into the following 11 subsections: (1) EAL Process, (2) Categorization/Classification System for Operational Emergencies, (3) Development of EALs, (4) Barrier Analysis for EALs, (5) Symptom-Based and Event-Based EALs, (6) Other Considerations, (7) Integration of EALs with Normal and Off-Normal Operations, (8) EAL Manual, (9) Testing EALs for Completeness, (10) Training and Implementation of EALs, and (11) Configuration Management.

  10. Molecular and genetic diversity in the metastatic process of melanoma.

    Harbst, Katja; Lauss, Martin; Cirenajwis, Helena; Winter, Christof; Howlin, Jillian; Törngren, Therese; Kvist, Anders; Nodin, Björn; Olsson, Eleonor; Häkkinen, Jari; Jirström, Karin; Staaf, Johan; Lundgren, Lotta; Olsson, Håkan; Ingvar, Christian; Gruvberger-Saal, Sofia K; Saal, Lao H; Jönsson, Göran

    2014-05-01

    Diversity between metastatic melanoma tumours in individual patients is known; however, the molecular and genetic differences remain unclear. To examine the molecular and genetic differences between metastatic tumours, we performed gene-expression profiling of 63 melanoma tumours obtained from 28 patients (two or three tumours/patient), followed by analysis of their mutational landscape, using targeted deep sequencing of 1697 cancer genes and DNA copy number analysis. Gene-expression signatures revealed discordant phenotypes between tumour lesions within a patient in 50% of the cases. In 18 of 22 patients (where matched normal tissue was available), we found that the multiple lesions within a patient were genetically divergent, with one or more melanoma tumours harbouring 'private' somatic mutations. In one case, the distant subcutaneous metastasis of one patient occurring 3 months after an earlier regional lymph node metastasis had acquired 37 new coding sequence mutations, including mutations in PTEN and CDH1. However, BRAF and NRAS mutations, when present in the first metastasis, were always preserved in subsequent metastases. The patterns of nucleotide substitutions found in this study indicate an influence of UV radiation but possibly also DNA alkylating agents. Our results clearly demonstrate that metastatic melanoma is a molecularly highly heterogeneous disease that continues to progress throughout its clinical course. The private aberrations observed on a background of shared aberrations within a patient provide evidence of continued evolution of individual tumours following divergence from a common parental clone, and might have implications for personalized medicine strategies in melanoma treatment. PMID:24399611

  11. 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 conditions, is rather small, of about 1 kGy, that makes the use of electron beam processing very economically attractive in this type of application. Thus, if all auxiliary systems are made and suitable adapted, the estimation of processing rate is 3600 kg/h. The acrylamide - acrylic acid copolymers are used in the range of 4 to 8 g per 1 m3 of wastewater. A vegetable oil plant which processes 100 000 ton/year of sunflower produces about 1 260 000 m3/year wastewater. The necessary amount of polyelectrolytes is 315-630 kg/year. This value can by ensured by our technology in a very short time, from 315 s to 630 s. (authors)

  12. Molecular cytogenetics in an assessment of DNA damage and repair processes

    Mutagenesis is one of the simplest and most effective methods for inducing plant variability. The mechanisms, which evoke variability, are chromosomal aberrations, arising from DNA double strand breaks (DSB). The frequency of chromosomal aberrations is correlated with the level of DNA damage and effectivity of cell repair system. Chromosomal aberrations can be detected using simple cytogenetic methods, however to assess the direct DNA damage and the effectivity of repair processes during recovery time after mutagenic treatment. in nucleus molecular methods are required. Comet assay and TUNEL test were successfully adapted and accepted for the detection of DNA fragmentation in mutagenesis. TUNEL test, based on labelling the 3'OH ends of DNA with fluorochrome - conjugated dUTP by terminal deoxynucleotidyl transferase (TdT) allows to distinguish the nuclei with DNA fragmentation. Another method - comet assay, based on the migration of damaged DNA fragments in electric field and forming an image similar to comet, is used for analysis of the level of DNA damage in single nucleus. Fluorescent in situ hybridization (FISH), provides new tools for the identification of individual chromosomes/chromosome arms participating in formation of the aberration. An advantage of FISH is possibility to understand the composition of the micronuclei thus improving an existing micronucleus test. An application of region-specific DNA probes (telomere and centromere) as well as rDNA as probes enables the analysis of the break points in the chromosomes leading to micronuclei. The application of the molecular cytogenetic methods will be presented as the analysis of the level of DNA damage and effectivity of repair processes in Hordeum vulgare cells (2n=14) after mutagenic treatment with γ-rays, MH, and MNU in different postincubation times. FISH with rDNA and centromeric/telomeric DNA as probes, to evaluate chromosome aberrations in barley cells caused by these mutagens will show the differences between action of these mutagens. (author)

  13. 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

  14. Process technology for vitrification of high level waste

    Vitrification as a process for the management of high level liquid waste (HLLW) has been accepted worldwide including India. Vitrification process based on borosilicate matrices has evolved in India right from employing metallic melters in early eighties to currently deployed ceramic melters. Induction of cold crucible melters are also on the anvil for vitrification of HLLW from advanced fuel cycles. The vitrification technology is a challenge in view of remote operation under molten corrosive glass environment and intense radiations. Successful operation of the vitrification plants and induction of new generation melters is a vital step for our successful implementation of reprocessing and recycle programme. Right from melter feeding, processing, product draining, canister welding and product withdrawal call for a robust technology with remote operations and high operator skills. High corrosion potential of molten glass on material of construction of the melter throws ample challenge to engineer the entire system. Mastering the technology of vitrification is a challenge and the experiences gained from the design and operations of the existing vitrification plants are a big achievement in itself

  15. 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. Discussion will start with an examination of how scanning probe techniques are being used to characterize the TiO2(110) surface in ways that are relevant to photocatalysis. We will then discuss specific classes of photochemical reaction on TiO2(110) for which SPM has proven indispensible in providing unique molecular-level insights, and conclude with discussion of future areas in which SPM studies may prove valuable to photocatalysis on TiO2. This work was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. I.L. was partially supported by a Pacific Northwest National Laboratory (PNNL) Chemical Imaging Initiative project. PNNL is a multiprogram national laboratory operated for DOE by Battelle.

  16. Biological processes, properties and molecular wiring diagrams of candidate low-penetrance breast cancer susceptibility genes

    Moreno Víctor

    2008-12-01

    Full Text Available Abstract Background Recent advances in whole-genome association studies (WGASs for human cancer risk are beginning to provide the part lists of low-penetrance susceptibility genes. However, statistical analysis in these studies is complicated by the vast number of genetic variants examined and the weak effects observed, as a result of which constraints must be incorporated into the study design and analytical approach. In this scenario, biological attributes beyond the adjusted statistics generally receive little attention and, more importantly, the fundamental biological characteristics of low-penetrance susceptibility genes have yet to be determined. Methods We applied an integrative approach for identifying candidate low-penetrance breast cancer susceptibility genes, their characteristics and molecular networks through the analysis of diverse sources of biological evidence. Results First, examination of the distribution of Gene Ontology terms in ordered WGAS results identified asymmetrical distribution of Cell Communication and Cell Death processes linked to risk. Second, analysis of 11 different types of molecular or functional relationships in genomic and proteomic data sets defined the "omic" properties of candidate genes: i/ differential expression in tumors relative to normal tissue; ii/ somatic genomic copy number changes correlating with gene expression levels; iii/ differentially expressed across age at diagnosis; and iv/ expression changes after BRCA1 perturbation. Finally, network modeling of the effects of variants on germline gene expression showed higher connectivity than expected by chance between novel candidates and with known susceptibility genes, which supports functional relationships and provides mechanistic hypotheses of risk. Conclusion This study proposes that cell communication and cell death are major biological processes perturbed in risk of breast cancer conferred by low-penetrance variants, and defines the common omic properties, molecular interactions and possible functional effects of candidate genes and proteins.

  17. Highly accurate calculation of the energy levels of the H2+ molecular ion

    In this paper we present a new numerical method for the calculation of energy levels of the non-relativistic molecular ion H2+, which is 'exact', i.e. beyond the Born-Oppenheimer approximation. It relies on the choice of a suitable basis using the dynamical symmetries of the system, in which the Hamiltonian is a sparse banded matrix. The numerical diagonalization of the Hamiltonian produces well converged energy levels, with a typical accuracy of 10-12, and also highly accurate wavefunctions. (author)

  18. A new vibrational level of the H{sub 2}{sup +} molecular ion

    Carbonell, J.; Lazauskas, R. [Institut des Sciences Nucleaires, 38 - Grenoble (France); Delande, D.; Hilico, L.; Kilic, S. [Laboratoire Kastler Brossel, 75 - Paris (France); Kilic, S. [Universite d' Evry Val d' Essonne, 91 - Evry (France)

    2003-11-01

    A new vibrational level of the molecular ion H{sub 2}{sup +} with binding energy of 1.09 x 10{sup -9} a.u. {approx} 30 neV below the first dissociation limit is predicted, using highly accurate numerical non-relativistic quantum calculations, which go beyond the Born-Oppenheimer approximation. It is the first-excited vibrational level v=1 of the 2p{sigma}{sub u} electronic state, antisymmetric with respect to the exchange of the two protons, with orbital angular momentum L=0. It manifests itself as a huge p - H scattering length of a = 750 {+-} 5 Bohr radii. (authors)

  19. Phase behaviour of macromolecular liquid crystalline materials. Computational studies at the molecular level

    Molecular simulations provide an increasingly useful insight into the static and dynamic characteristics of materials. In this thesis molecular simulations of macro-molecular liquid crystalline materials are reported. The first liquid crystalline material that has been investigated is a side chain liquid crystal polymer (SCLCP). In this study semi-atomistic molecular dynamics simulations have been conducted at a range of temperatures and an aligning potential has been applied to mimic the effect of a magnetic field. In cooling the SCLCP from an isotropic melt, microphase separation was observed yielding a domain structure. The application of a magnetic field to this structure aligns the domains producing a stable smectic mesophase. This is the first study in which mesophases have been observed using an off-lattice model of a SCLCP. The second material that has been investigated is a dendrimer with terminal mesogenic functionalization. Here, a multi-scale approach has been taken with Monte Carlo studies of a single dendrimer molecule in the gas phase at the atomistic level, semi-atomistic molecular dynamics of a single molecule in liquid crystalline solvents and a coarse-grained molecular dynamics study of the dendrimer in the bulk. The coarse-grained model has been developed and parameterized using the results of the atomistic and semi-atomistic work. The single molecule studies showed that the liquid crystalline dendrimer was able to change its structure by conformational changes in the flexible chains that link the mesogenic groups to the core. Structural change was seen under the application of a mean field ordering potential in the gas phase, and in the presence of liquid crystalline solvents. No liquid crystalline phases were observed for the bulk phase studies of the coarse-grained model. However, when the length of the mesogenic units was increased there was some evidence for microphase separation in these systems. (author)

  20. 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

  1. Elementary processes, transport and kinetics of molecular plasmas

    State to state vibrational resolved electron molecule cross sections for the triplet-triplet transitions in molecular hydrogen have been calculated by using the impact parameter method. The construction of a data base for dissociative attachment of ro-vibrational states of H2 and its isotopes is in progress. A classical approach has been used for calculating the ionization cross sections for N2 and O2 in different vibrational states. Cross sections and rate coefficients for the system H-H2(?,j), calculated by the quasiclassical trajectory method, have been improved by using a new and more accurate potential energy surface. Transport cross sections of electronically excited states of atomic hydrogen have been derived by using semiclassical approaches. The data have been used to calculate the transport coefficients (viscosity, thermal conductivity, electrical conductivity) of thermal plasmas in a wide range of temperatures and pressures. The results, which show the strong influence of excited states on the transport coefficients of atomic plasmas, have been completed last year and published this year. Transport cross sections of electronically excited nitrogen and oxygen atoms have been also derived. We have implemented kinetic codes to describe the kinetics of molecular plasmas (mainly hydrogen) in different non-equilibrium conditions. These codes include quasi-homogeneous plasma models including a radiative-collisional model for atomic and molecular hydrogen; PIC-MCC (Particle In Cell with Monte-Carlo Collisions) for describing parallel plate hydrogen plasma reactors; 1D Euler code coupled with the kinetics of partially ionized gases to describe high enthalpy flows through nozzles of different geometries; DSMC (Direct Simulation with Monte Carlo collisions) model for describing shock wave propagation; zero dimensional code to reproduce the plasma kinetics in multipole magnetic plasmas. The codes have been applied to reproduce different experimental situations. In particular the first model has been used to rationalize the experimental CARS measurements of the vibrational and rotational temperatures in RF discharges obtained in our laboratory, while the PIC-MCC code has been used to reproduce different experimental quantities obtained in other laboratories

  2. Tectonic processes modelling for high-level radioactive waste disposal

    The possibility of using deep geological formations to dispose of high-level radioactive waste (HLW) is a subject raising heated debate among scientists. In Russia, the idea of constructing HLW repository in the Niznekansky granitoid massif (NKM) in Krasnoyarsk area is widely discussed. To solve this problem we are elaborating a technology associated with time – space stability prediction of the geological environment, which is subject to geodynamic processes evolutionary effects. It is based on the prediction of isolation properties stability in a structural tectonic block of the Earth’s crust for a given time. The danger is in the possibility that the selected structural block may be broken by new tectonic faults or movements on a passive fault may be activated and thus underground water may penetrate to HLW containers

  3. 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

    The ubiquitous abundance of pyrolysed, highly aromatic organic matter, called "Black Carbon" (BC), in all environmental compartments became increasingly important in different fields of research beyond intensive investigated atmospheric aerosol due to climatic relevance. Its predominant high resistance to abiotic and biotic degradation resulted in turnover times from less than a century to several millennia. This recalcitrance led to the enrichment of BC in soils, accounting for 1-6% (European forest soils) to 60% (Chernozems) of total soil organic matter (SOM). Hence, soil BC acts an important sink in the global carbon cycle. In contrast, consequences for the nitrogen cycle up to date are rather inconsistently discussed. Soil related dissolved organic matter (DOM) is a major controlling factor in soil formation, an important pathway of organic matter transport and one of the largest active carbon reservoirs on earth, if considering oceans and other bodies of water. The aim of this study was to evaluate the effects of artificially simulated wildfire by thermal treatment on the molecular composition of water extractable soil organic matter (DOM). Soils from two outdoor lysimeters with different management history were investigated. Soil samples, non-heated and heated up to 350°C were analyzed for elemental composition (carbon, nitrogen and sulfur) and for bulk molecular composition by Pyrolysis-Field Ionization Mass Spectrometry (Py-FIMS) and synchrotron-based X-ray Absorption Near-Edge Spectroscopy (XANES) at the C- and N K-edges. DOM-samples obtained by hot water extraction, desalting and concentration by solid phase extraction were subsequently analyzed by flow injection analysis in a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FTICR-MS), equipped with an ESI source and a 7 T supra-conducting magnet (LTQ-FT Ultra, ThermoFisher Scientific). This technique is the key technique for the analysis of complex samples due to its outstanding mass 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.

  4. Atmospheric processes on ice nanoparticles in molecular beams

    Frnk, Michal; Poterya, Viktoriya

    2014-02-01

    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 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.

  5. Atmospheric processes on ice nanoparticles in molecular beams

    MichalFrnk

    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 waternitric 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. Deformation processes in polycrystalline Zr by molecular dynamics simulations

    Lu, Zizhe; Noordhoek, Mark J.; Chernatynskiy, Aleksandr; Sinnott, Susan B.; Phillpot, Simon R.

    2015-07-01

    Molecular dynamics simulation is used to characterize the deformation behavior of polycrystalline Zr. The predictions of two different potentials, an embedded atom method potential and a charge optimized many body potential are compared. The experimentally observed prismatic dislocations, pyramidal dislocations and twinning behaviors are produced in the simulations of [ 1 1 2 bar 0 ] and [0 0 0 1] textured structures and in fully 3D structure simulations. The relationship between the generalized stacking fault energy and the mechanical properties is discussed. In particular we find that the different shapes of the generalized stacking-fault energy curve for the two different interatomic descriptions of Zr have a significant effect on the deformation mechanisms. The deformation behavior of Zr is compared with analogous simulations of deformation of polycrystalline Mg.

  7. Impact of Altimeter Data Processing on Sea Level Studies

    Clara Lázaro

    2006-03-01

    Full Text Available This study addresses the impact of satellite altimetry data processing on sea levelstudies at regional scale, with emphasis on the influence of various geophysical correctionsand satellite orbit on the structure of the derived interannual signal and sea level trend. Thework focuses on the analysis of TOPEX data for a period of over twelve years, for threeregions in the North Atlantic: Tropical (0o≤φ≤25o, Sub-Tropical (25o≤φ≤50o and Sub-Arctic (50o≤φ≤65o. For this analysis corrected sea level anomalies with respect to a meansea surface model have been derived from the GDR-Ms provided by AVISO by applyingvarious state-of-the-art models for the geophysical corrections. Results show that sea leveltrend determined from TOPEX altimetry is dependent on the adopted models for the majorgeophysical corrections. The main effects come from the sea state bias (SSB, and from theapplication or not of the inverse barometer (IB correction. After an appropriate modellingof the TOPEX A/B bias, the two analysed SSB models induce small variations in sea leveltrend, from 0.0 to 0.2 mm/yr, with a small latitude dependence. The difference in sea leveltrend determined by a non IB-corrected series and an IB-corrected one has a strong regionaldependence with large differences in the shape of the interannual signals and in the derivedlinear trends. The use of two different drift models for the TOPEX Microwave Radiometer(TMR has a small but non negligible effect on the North Atlantic sea level trend of about0.1 mm/yr. The interannual signals of sea level time series derived with the NASA and theCNES orbits respectively, show a small departure in the middle of the series, which has noimpact on the derived sea level trend. These results strike the need for a continuousimprovement in the modelling of the various effects that influence the altimetermeasurement.

  8. 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

  9. All-Atom Molecular-Level Analysis of the Ballistic-Impact-Induced Densification and Devitrification of Fused Silica

    Grujicic, M.; Snipes, J. S.; Ramaswami, S.; Yavari, R.; Barsoum, R. S.

    2015-08-01

    All-atom molecular-level computations are carried out to infer the dynamic response and material microstructure/topology changes of fused silica subjected to ballistic impact by a hard projectile. The analysis was focused on the investigation of specific aspects of the dynamic response and of the microstructural changes such as the deformation of highly sheared and densified regions and the conversion of amorphous fused silica to SiO2 crystalline allotropic modifications (in particular, α-quartz and stishovite). The microstructural changes in question were determined by carrying out a post-processing atom-coordination procedure. This procedure suggested the formation of stishovite (and perhaps α-quartz) within fused silica during ballistic impact. To rationalize the findings obtained, the all-atom molecular-level computational analysis is complemented by a series of quantum-mechanics density functional theory (DFT) computations. The latter computations enable determination of the relative potential energies of the fused silica, α-quartz, and stishovite under ambient pressure (i.e., under their natural densities) as well as under imposed (as high as 50 GPa) pressures (i.e., under higher densities) and shear strains. In addition, the transition states associated with various fused-silica devitrification processes were identified. The results obtained are found to be in good agreement with their respective experimental counterparts.

  10. 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.

  11. 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

  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.; Gu, L.; Zheng, D. N.; Wang, W. H.

    2016-01-01

    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. 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.

  14. 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

  15. Ellipticity dependence of plateau structures in atomic and molecular processes in a strong laser field

    In this paper, we present a quantum-mechanical theory in order to describe laser-induced and laser-assisted atomic and molecular processes with an emphasis on an elliptically polarized strong laser field. The features of the high-energy regions of spectra and their cutoffs are analyzed in detail for different values of ellipticity, laser intensities and various atomic and molecular species. Our theoretical study is focused on the ellipticity dependence of the plateau structures that appear in the energy spectra of atomic and molecular processes in strong laser fields. (paper)

  16. The molecular basis of low activity levels of coagulation factor VII: a Brazilian cohort.

    Rabelo, F Y; Jardim, L L; Landau, M B; Gadelha, T; Corra, M F B; Pereira, I F M; Rezende, S M

    2015-09-01

    Inherited factor VII (FVII) deficiency is the most common among the rare bleeding disorders. It is transmitted as an autosomal recessive inheritance, due to mutations in the FVII gene (F7). Molecular studies of FVII deficiency are rare in non-Caucasian populations. The aim of the study was to evaluate the molecular basis behind low levels of FVII activity (FVII:C) levelsin a cohort of Brazilian patients. A total of 34 patients with low FVII levels were clinically evaluated and submitted to laboratory tests, among these, prothrombin time and FVII:C, with different thromboplastins. All exons and intron/exon boundaries of F7 were amplified and sequenced. A total of 14 genetic alterations were identified, of which six were described previously, c.1091G>A, c.1151C>T, c.-323_-313insCCTATATCCT, c.285G>A, c.525C>T, c.1238G>A and eight (54.0%) and eight were new, c.128G>A, c.252C>T, c.348G>A, c.417G>A, c.426G>A, c.745_747delGTG, c.843G>A and c.805+52C>T. In addition to the mutation c.1091G>A, known as FVII Padua, the mutation c.1151C>T also presented discrepant FVII:C levels when tested with human and rabbit brain thromboplastin. There was no association between phenotype and genotype. Most of the identified genetic alterations found were polymorphisms. Low levels of FVII:C in this population were mostly related to polymorphisms in F7 and associated with a mild clinical phenotype. Mutation c.1151C>T was associated with discrepant levels of FVII:C using different thromboplastins, such as reported with FVII Padua. PMID:25828579

  17. Molecular Surveillance of Viral Processes Using Silicon Nitride Membranes

    Kelly, Deborah F; McDonald, Sarah M.; Madeline J. Dukes; Allison O. McKell; Boudreaux, Crystal E; Tanner, Justin R.; Brian L. Gilmore

    2013-01-01

    Here we present new applications for silicon nitride (SiN) membranes to evaluate biological processes. We determined that 50-nanometer thin films of SiN produced from silicon wafers were sufficiently durable to bind active rotavirus assemblies. A direct comparison of SiN microchips with conventional carbon support films indicated that SiN performs equivalent to the traditional substrate to prepare samples for Electron Microscopy (EM) imaging. Likewise, SiN films coated with Ni-NTA affinity la...

  18. Patterns and Processes of Molecular Evolution in Rickettsia

    Amiri, Haleh

    2002-01-01

    Species of the genus Rickettsia are obligate intracellular parasites of the a-proteobacterial subdivision. It has been suggested that obligate intracellular bacteria have evolved from free-living bacteria with much larger genome sizes. Transitions to intracellular growth habitats are normally associated with radical genomic alterations, particularly genome rearrangements and gene losses. This thesis presents a comparative study of evolutionary processes such as gene rearrangements, deletions ...

  19. Quantum molecular collision studies for processes of astrophysical interest

    Denis alpizar, Otoniel

    2014-01-01

    Tha analysis of the physico-chemical conditons taking place in the interstellar medium (ISM) requires to know the inclastic rate coefficents of the detected interstellar molecules in collisions with the moste common colliders int the ISM. We have comuted the four dimensional potential energy surfaces, and the bound levels for the CS-H2, HCN-H2, HCN-He and C3 -He complexes. For the collisions of Cs with H2, we also determined the rst inelastic cross section and rate coefficeients

  20. 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)

  1. MOLOCH computer code for molecular-dynamics simulation of processes in condensed matter

    Derbenev I.V.

    2011-01-01

    Full Text Available Theoretical and experimental investigation into properties of condensed matter is one of the mainstreams in RFNC-VNIITF scientific activity. The method of molecular dynamics (MD is an innovative method of theoretical materials science. Modern supercomputers allow the direct simulation of collective effects in multibillion atom sample, making it possible to model physical processes on the atomistic level, including material response to dynamic load, radiation damage, influence of defects and alloying additions upon material mechanical properties, or aging of actinides. During past ten years, the computer code MOLOCH has been developed at RFNC-VNIITF. It is a parallel code suitable for massive parallel computing. Modern programming techniques were used to make the code almost 100% efficient. Practically all instruments required for modelling were implemented in the code: a potential builder for different materials, simulation of physical processes in arbitrary 3D geometry, and calculated data processing. A set of tests was developed to analyse algorithms efficiency. It can be used to compare codes with different MD implementation between each other.

  2. 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 production of small amounts of ethylene and water, most likely via the concerted decomposition or disproportionation of the adsorbed molecular species. The bulk of the 2-iodoethanol decomposes at about 150 K via an initial carbon-iodine scission to form –O(H)CH2CH2– (~80%) and 2-hydroxyethyl (~20%) intermediates. Two competing reactions are involved with the subsequent conversion of the 2-hydroxyethyl species around 160 K, a reductive elimination with surface hydrogen to yield ethanol, and a β-H elimination to surface vinyl alcohol. The –O(H)CH2CH2–, on the other hand, dehydrogenates to a –OCH2CH2– oxametallacycle species about the same temperature. Both 2-hydroxyethyl and oxametallacycle species tautomerize to acetaldehyde, around 210 K and above 250 K, respectively, and some of that acetaldehyde desorbs while the rest decomposes to hydrogen and carbon monoxide. We contend that a better understanding of the surface chemistry of oxygen-containing surfaces can lead to better selectivities in catalysis. This is arguably the most important issue in the field of catalysis in the near future, and one that impacts several technologies of interest to DOE such as the manufacturing of speciality chemicals and the control and removal of pollutants. Additional work was performed on the characterization of the chemistry of methyl and methylene adsorbed species on oxygen-treated nickel surfaces. Complex chemistry was observed involving not only hydrogenation and dehydrogenation steps, but also C-C couplings and methylene insertions to produce heavier hydrocarbons, and oxygen insertion reactions that yield oxygenates. Finally, a dual titration technique employing xenon and a chemically sensitive probe was developed to identify minority catalytic sites on oxide surfaces. In the case of oxygen-treated Ni(110) single crystals, it was found that both hydrogen transfer with adsorbed water or ammonia and certain hydrocarbon hydrogenation reactions take place at the end of the –Ni–O rows that form in this system. Carbon and nitrogen oxides, on the other hand, display no preference for adsorption on those sites.

  3. Assessment of community level physiological profiles and molecular diversity of soil bacteria under different cropping systems

    DAS, Biswapriya; CHAKRABARTI, Kalyan

    2013-01-01

    Community level physiological profiles (CLPP) and molecular diversity of bacteria in soil under rice–rice (RR), rice-fallow (RF), rice-wheat (RW), legume (LG), mango orchard (MO), and grass land (GL) cropping systems occurring in South West Bengal, India (22°22'N latitude and 86°26'E longitude) were studied. The soils were mostly acidic (pH 5.4 to 6.85). The GL soil recorded the highest organic carbon (20.23 g kg-1) and total nitrogen (1.96 g kg-1). The RF soil was the mos...

  4. 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.

  5. 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

  6. 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.

  7. 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 a similar concentration in the water-soluble OM from the UV-radiated and control soils, indicating little microbial contribution to the observed increase in water-soluble carbon. These observations suggest that photo-oxidation may increase the solubility of soil organic matter (SOM) through the oxidation of lignin-derived compounds. Mechanisms of lignin oxidation (demethylation or side-chain oxidation) and molecular size distribution changes of the water-soluble and NaOH-soluble OM during photo-oxidation and biodegradation will also be examined using solution-state nuclear magnetic resonance (NMR) spectroscopy. Collectively, our experiment demonstrates that while biodegradation predominates in the decomposition of lignin in plant litter, photo- oxidation may play an important part in destabilizing lignin-derived compounds in the soil.

  8. 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

  9. A Molecular-Level View of the Physical Stability of Amorphous Solid Dispersions

    Yuan, Xiaoda

    Many pharmaceutical compounds being developed in recent years are poorly soluble in water. This has led to insufficient oral bioavailability of many compounds in vitro. The amorphous formulation is one of the promising techniques to increase the oral bioavailability of these poorly water-soluble compounds. However, an amorphous drug substance is inherently unstable because it is a high energy form. In order to increase the physical stability, the amorphous drug is often formulated with a suitable polymer to form an amorphous solid dispersion. Previous research has suggested that the formation of an intimately mixed drug-polymer mixture contributes to the stabilization of the amorphous drug compound. The goal of this research is to better understand the role of miscibility, molecular interactions and mobility on the physical stability of amorphous solid dispersions. Methods were developed to detect different degrees of miscibility on nanometer scale and to quantify the extent of hydrogen-bonding interactions between the drug and the polymer. Miscibility, hydrogen-bonding interactions and molecular mobility were correlated with physical stability during a six-month period using three model systems. Overall, this research provides molecular-level insights into many factors that govern the physical stability of amorphous solid dispersions which can lead to a more effective design of stable amorphous formulations.

  10. 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

  11. 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

  12. Unravelling Protein-DNA Interactions at Molecular Level: A DFT and NCI Study.

    Gonzlez, J; Baos, I; Len, I; Contreras-Garca, J; Cocinero, E J; Lesarri, A; Fernndez, J A; Milln, J

    2016-02-01

    Histone-DNA interactions were probed computationally at a molecular level, by characterizing the bimolecular clusters constituted by selected amino acid derivatives with polar (asparagine and glutamine), nonpolar (alanine, valine, and isoleucine), and charged (arginine) side chains and methylated pyrimidinic (1-methylcytosine and 1-methylthymine) and puric (9-methyladenine and 9-methylguanine) DNA bases. The computational approach combined different methodologies: a molecular mechanics (MMFFs forced field) conformational search and structural and vibrational density-functional calculations (M06-2X with double and triple-? Pople's basis sets). To dissect the interactions, intermolecular forces were analyzed with the Non-Covalent Interactions (NCI) analysis. The results for the 24 different clusters studied show a noticeable correlation between the calculated binding energies and the propensities for protein-DNA base interactions found in the literature. Such correlation holded even for the interaction of the selected amino acid derivatives with Watson and Crick pairs. Therefore, the balance between hydrogen bonds and van der Waals interactions (specially stacking) in the control of the final shape of the investigated amino acid-DNA base pairs seems to be well reproduced in dispersion-corrected DFT molecular models, reinforcing the idea that the specificity between the amino acids and the DNA bases play an important role in the regulation of DNA. PMID:26765058

  13. First-principle simulations of molecular processes at semiconductor surfaces

    The authors present an overview of basic adsorption and dynamical processes at semiconductor surfaces, studied by first-principle simulations. They have considered prototypical semiconductor surfaces such as GaAs(110), which is the cleavage plane of GaAs, and Si(100), which is the most common orientation for silicon from epitaxial growth. The authors present an adsorption path and the stable configurations of a Cl2 molecule on GaAs(110), as well as the equilibrium state for complete and partial monolayer adsorption of H on the same surface. They also show the dynamical evolution of Si2 dimers on the Si(100) face: they alternate their buckling in a correlated way producing different reconstructions

  14. Rovibrational coupling in molecular nitrogen at high temperature: An atomic-level study

    This article contains an atomic-level numerical investigation of rovibrational relaxation in molecular nitrogen at high temperature (>4000 K), neglecting dissociation. We conduct our study with the use of pure Molecular Dynamics (MD) and Classical Trajectory Calculations (CTC) Direct Simulation Monte Carlo (DSMC), verified to produce statistically identical results at the conditions of interest here. MD and CTC DSMC solely rely on the specification of a potential energy surface: in this work, the site-site Ling-Rigby potential. Additionally, dissociation is prevented by modeling the N–N bond either as a harmonic or an anharmonic spring. The selected molecular model was shown to (i) recover the shear viscosity (obtained from equilibrium pure MD Green-Kubo calculations) of molecular nitrogen over a wide range of temperatures, up to dissociation; (ii) predict well the near-equilibrium rotational relaxation behavior of N2; (iii) reproduce vibrational relaxation times in excellent accordance with the Millikan-White correlation and previous semi-classical trajectory calculations in the low temperature range, i.e., between 4000 K and 10 000 K. By simulating isothermal relaxations in a periodic box, we found that the traditional two-temperature model assumptions become invalid at high temperatures (>10 000 K), due to a significant coupling between rotational and vibrational modes for bound states. This led us to add a modification to both the Jeans and the Landau-Teller equations to include a coupling term, essentially described by an additional relaxation time for internal energy equilibration. The degree of anharmonicity of the N2 bond determines the strength of the rovibrational coupling. Although neglecting N2 dissociation only provides a partial description of a nitrogen system at very high temperatures, high-energy trends for bound-bound transitions are essential to understand nonequilibrium gas flows, with possible implications on rovibration/chemistry interaction at the onset of N2 dissociation

  15. Proton NMR for Measuring Quantum Level Crossing in the Magnetic Molecular Ring Fe10

    The proton nuclear spin-lattice relaxation rate 1/T1 has been measured as a function of temperature and magnetic field (up to 15thinspthinspT) in the molecular magnetic ring Fe10( OCH3)20(O2CCH2 Cl)10 (Fe10). Striking enhancement of 1/T1 is observed around magnetic field values corresponding to a crossing between the ground state and the excited states of the molecule. We propose that this is due to a cross-relaxation effect between the nuclear Zeeman reservoir and the reservoir of the Zeeman levels of the molecule. This effect provides a powerful tool to investigate quantum dynamical phenomena at level crossing. copyright 1999 The American Physical Society

  16. Proton NMR for Measuring Quantum Level Crossing in the Magnetic Molecular Ring Fe10

    Julien, M.; Jang, Z.H.; Borsa, F. [Department of Physics and Astronomy, Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States); Julien, M.; Lascialfari, A.; Borsa, F. [Dipartimento di Fisica A. Volta e Unita INFM di Pavia, Via Bassi 6, 27100 Pavia (Italy); Horvatic, M. [Grenoble High Magnetic Field Laboratory, CNRS and MPI-FKF, BP 166, 38042 Grenoble Cedex 9 (France); Caneschi, A.; Gatteschi, D. [Department of Chemistry, University of Firenze, Via Maragliano 77, 50144 Firenze (Italy)

    1999-07-01

    The proton nuclear spin-lattice relaxation rate 1/T{sub 1} has been measured as a function of temperature and magnetic field (up to 15thinspthinspT) in the molecular magnetic ring Fe{sub 10}( OCH{sub 3}){sub 20}(O{sub 2}CCH{sub 2} Cl){sub 10} (Fe10). Striking enhancement of 1/T{sub 1} is observed around magnetic field values corresponding to a crossing between the ground state and the excited states of the molecule. We propose that this is due to a cross-relaxation effect between the nuclear Zeeman reservoir and the reservoir of the Zeeman levels of the molecule. This effect provides a powerful tool to investigate quantum dynamical phenomena at level crossing. {copyright} {ital 1999} {ital The American Physical Society}

  17. Implications of the admixture process in skin color molecular assessment.

    Cerqueira, Caio Cesar Silva de; Hünemeier, Tábita; Gomez-Valdés, Jorge; Ramallo, Virgínia; Volasko-Krause, Carla Daiana; Barbosa, Ana Angélica Leal; Vargas-Pinilla, Pedro; Dornelles, Rodrigo Ciconet; Longo, Danaê; Rothhammer, Francisco; Bedoya, Gabriel; Canizales-Quinteros, Samuel; Acuña-Alonzo, Victor; Gallo, Carla; Poletti, Giovanni; González-José, Rolando; Salzano, Francisco Mauro; Callegari-Jacques, Sídia Maria; Schuler-Faccini, Lavínia; Ruiz-Linares, Andrés; Cátira Bortolini, Maria

    2014-01-01

    The understanding of the complex genotype-phenotype architecture of human pigmentation has clear implications for the evolutionary history of humans, as well as for medical and forensic practices. Although dozens of genes have previously been associated with human skin color, knowledge about this trait remains incomplete. In particular, studies focusing on populations outside the European-North American axis are rare, and, until now, admixed populations have seldom been considered. The present study was designed to help fill this gap. Our objective was to evaluate possible associations of 18 single nucleotide polymorphisms (SNPs), located within nine genes, and one pseudogene with the Melanin Index (MI) in two admixed Brazilian populations (Gaucho, N = 352; Baiano, N = 148) with different histories of geographic and ethnic colonization. Of the total sample, four markers were found to be significantly associated with skin color, but only two (SLC24A5 rs1426654, and SLC45A2 rs16891982) were consistently associated with MI in both samples (Gaucho and Baiano). Therefore, only these 2 SNPs should be preliminarily considered to have forensic significance because they consistently showed the association independently of the admixture level of the populations studied. We do not discard that the other two markers (HERC2 rs1129038 and TYR rs1126809) might be also relevant to admixed samples, but additional studies are necessary to confirm the real importance of these markers for skin pigmentation. Finally, our study shows associations of some SNPs with MI in a modern Brazilian admixed sample, with possible applications in forensic genetics. Some classical genetic markers in Euro-North American populations are not associated with MI in our sample. Our results point out the relevance of considering population differences in selecting an appropriate set of SNPs as phenotype predictors in forensic practice. PMID:24809478

  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. Reconstructing the free-energy landscape associated to molecular motors processivity

    Alamilla, J Lopez

    2012-01-01

    We propose a biochemical model providing the kinetic and energetic descriptions of the processivity dynamics of kinesin and dinein molecular motors. Our approach is a modified version of a well known model describing kinesin dynamics and considers the presence of a competitive inhibition reaction by ADP. We first reconstruct a continuous free-energy landscape of the cycle catalyst process that allows us to calculate the number of steps given by a single molecular motor. Then, we calculate an analytical expression associated to the translational velocity and the stopping time of the molecular motor in terms of time and ATP concentration. An energetic interpretation of motor processivity is discussed in quantitative form by using experimental data. We also predict a time duration of collective processes that agrees with experimental reports.

  20. Property Integration - A New Approach for Simultaneous Solution of Process and Molecular Design Problems

    The objective of this paper is to introduce the new concept of property integration. It is based on tracking and integrating properties throughout the process. This is made possible by exploiting the unique features at the interface of process and molecular design. Recently developed clustering...

  1. Proceedings of the DAE-BRNS theme meeting on application of molecular modeling in separation processes

    This conference deals with molecular modelling which encompasses all theoretical methods and computational techniques to model or mimic the behaviour of molecules. This is used as important tool to design and simulate extractants for solvent extraction processes, stationary phases for chromatographic separation processes, polymeric network for membranes and highly selective precipitants. Papers relevant to INIS are indexed separately

  2. The defense waste processing facility: the final processing step for defense high-level waste disposal

    The policy of the U.S. Department of Energy is to pursue an aggressive and credible waste management program that advocates final disposal of government generated (defense) high-level nuclear wastes in a manner consistent with environmental, health, and safety responsibilities and requirements. The Defense Waste Processing Facility (DWPF) is an essential component of the Department's program. It is the first project undertaken in the United States to immobilize government generated high-level nuclear wastes for geologic disposal. The DWPF will be built at the Department's Savannah River Plant near Aiken, South Carolina. When construction is complete in 1989, the DWPF will begin processing the high-level waste at the Savannah River Plant into a borosilicate glass form, a highly insoluble and non-dispersable product, in easily handled canisters. The immobilized waste will be stored on site followed by transportation to and disposal in a Federal repository. The focus of this paper is on the DWPF. The paper discusses issues which justify the project, summarizes its technical attributes, analyzes relevant environmental and insitutional factors, describes the management approach followed in transforming technical and other concepts into concrete and steel, and concludes with observations about the future role of the facility

  3. 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...

  4. Ions colliding with molecules and molecular clusters : fragmentation and growth processes

    Chen, Tao

    2015-01-01

    Inthis work we will discuss fragmentation and molecular growth processes in collisions of Polycyclic Aromatic Hydrocarbon (PAH) molecules, fullerenes, or their clusters with atoms or atomic ions. Simple collision models as well as molecular structure calculations are used to aid the interpretations of the present and other experimental results. Fragmentation features at center-of-mass collision energies around 10 keV are dominated by interactions between the fast ion/atom and the electron cl...

  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 Chlorophyll and of the lipid. A connection between lipid and Chlorophyll oxidation in irradiated liposomes was observed. The fluorescence and polarization spectra were used in obtaining the transition temperature for different liposome solutions. The temperature of lipid phase transition, as monitored by fluorescence of Chla in liposomes, is not affected by MW exposure. All MW exposure effects observed on liposomes (either observed by monitoring Chla or lipids) seem to be mediated by water. Excitation of water (strong MW absorber) facilitates the hydration of polar head groups of lipids, providing the necessary physical change of lipids and thus explaining the effect of MW on SUV. (authors)

  6. 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...

  7. Radiative and nonradiative rates and deep levels in zinc selenide grown by molecular-beam epitaxy

    Allen, J. W.; Reid, D. T.; Sibbett, W.; Sleat, W.; Zheng, Jia-Zhen; Hommel, D.; Jobst, B.

    1995-08-01

    A series of chlorine-doped epitaxial layers of ZnSe have been grown by molecular-beam epitaxy. Measurements have been made of the relative intensity of the blue photoluminescence at room temperature, of the decay time of this emission, and of the concentrations of deep levels determined by photocapacitance techniques. A GaAs buffer layer improves the light emission and decreases the deep-level concentrations. Over the uncompensated donor concentration range 2×1016 to 3×1018 cm-3 the photoluminescence intensity, decay rate, and deep-level concentrations only vary by one order of magnitude. The results are consistent with the room-temperature blue emission resulting in recombination of a free hole with electrons on relatively isolated donors, this radiative recombination competing with a strong nonradiative Hall-Shockley-Read recombination via deep levels in the lower half of the energy gap. The significance of these results for the making of light-emitting diodes and lasers is discussed.

  8. TRUEX process applied to radioactive Idaho Chemical Processing Plant high-level waste calcine

    Equal volume batch contact experiments were performed with dissolved, radioactive high-level waste (HLW) calcine and the TRansUranic EXtraction (TRUEX) process solvent. Extraction, scrub, and strip distribution coefficients (D) were obtained for the transuranic (TRU) elements in order to evaluate the efficiency of the TRUEX process in treating this waste. The extraction, scrub, and strip behavior of other elements, such as chromium, zirconium, and technetium, was also observed. A TRU alpha decontamination factor of >10,000 was achieved; after three extraction batch contacts TRU alpha activity was reduced from 1,420 nCi/g to 0.02 nCi/g. Dilute nitric acid was used to scrub extracted acid, zirconium, and iron from the solvent prior to stripping. Dilute 1-hydroxyethane, 1-1, diphosphonic acid (HEDPA) was used as a gross TRU stripping reagent to recover the extracted TRUs. Data from these batch contact experiments were used to develop a counter-current flowsheet for TRU removal using the Generic TRUEX Model (GTM). Process improvements and optimizations of the flowsheet have been evaluated using a non-radioactive dissolved calcine simulant spiked with tracers to obtain additional distribution coefficient data. These data were used in the GTM to refine the flowsheet. The flowsheet was then evaluated using a counter-current 5.5 cm centrifugal contactor pilot plant with a non-radioactive dissolved calcine simulant. The experiments involving radioactive waste provided crucial data for developing a baseline TRUEX process flowsheet which can effectively separate TRU components from ICPP high-level waste

  9. Managing and Organizing Concurrent Processes According to the CMM Levels

    David, Michael; Idelmerfaa, Zahra; Richard, Jacques

    2005-01-01

    Abstract Research for reduced lead time and cost in concurrent process development (CPD) becomes crucial in new work organizations. Today, the concurrent processes involve more and more activities and work groups which must be efficiently coordinated. In this article, the authors propose a framework for structuring concurrent activities in order to improve the global performance (lead time, workload, risks,...

  10. Memory Scanning, Introversion-Extraversion, and Levels of Processing.

    Eysenck, Michael W.; Eysenck, M. Christine

    1979-01-01

    Investigated was the hypothesis that high arousal increases processing of physical characteristics and reduces processing of semantic characteristics. While introverts and extroverts had equivalent scanning rates for physical features, introverts were significantly slower in searching for semantic features of category membership, indicating…

  11. 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

  12. New alternatives for processing low and medium level liquid wastes

    After a brief presentation of the actual scheme for low-level and intermediate-level radioactive liquid waste treatment in the new reprocessing plant of ''La Hague'', the new trends in ResdArch and Development studies are presented. In a first step, the total amount of low-level and intermediate-level wastes could be concentrated by distillation, with disposal of condensates. Concentrates, prior to conditioning, could be treated by chemical precipitation or by mineral ion exchangers. The saline solution, then free of α and βγ major radionuclides could be immobilized in bitumen and sent for disposal in surface storage conditions. The solid residual fraction, sludges or saturated ion exchangdRs, could be converted to oxides and sintered for deep geological disposal

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. Short-term molecular-level effects of silver nanoparticle exposure on the earthworm, Eisenia fetida

    Short-term changes in levels of expression of nine stress response genes and oxidative damage of proteins were examined in Eisenia fetida exposed to polyvinylpyrrolidone (PVP) coated Ag nanoparticles (Ag-NP) and AgNO3 in natural soils. The responses varied significantly among days with the highest number of significant changes occurring on day three. Similarity in gene expression patterns between Ag-NPs and AgNO3 and significant relationships of expression of CAT and HSP70 with Ag soil concentration suggest similarity in toxicity mechanisms of Ag ions and NPs. Significant increases in the levels of protein carbonyls on day three of the exposure to both ions and Ag-NPs indicate that both treatments induced oxidative stress. Our results suggest that Ag ions drive short term toxicity of Ag-NPs in E. fetida. However, given that 3 and Ag nanoparticles were similar. ► Expression of CAT and HSP70 were correlated with Ag soil concentration. ► Increase in protein carbonyls by ions and nanoparticles on day three. ► The results suggest that short-term toxicity is driven by Ag ions. - Similarity in molecular-level responses between silver nanoparticles (Ag-NPs) and ions suggests that ions are primarily responsible for short-term toxicity of Ag-NPs to Eisenia fetida.

  18. Determination of chloride at picogram levels by molecular fluorescence in a graphite furnace.

    Anwar, J; Anzano, J M; Petrucci, G; Winefordner, J D

    1991-10-01

    Chloride was determined at nanogram levels by adding excess of indium to the sample introduced into a graphite furnace and measuring the laser induced molecular fluorescence of indium chloride. The diatomic molecules of indium chloride were excited by a pulsed dye laser at 267 nm and fluorescence was measured at 359 nm. The effects of various parameters including amount of indium added, furnace thermal conditions and presence of concomitants were also studied. A linear calibration in the range of 0.025-1.25 ng and a detection limit of 17 pg of chloride were obtained under optimum conditions. The analytical usefulness of the method was checked by determining the chloride content in National Institute of Standards and Technology, Standard Reference Materials 1571a and 1571b Orchard Leaves. PMID:1801600

  19. Predicting Protein-Protein Interactions from the Molecular to the Proteome Level.

    Keskin, Ozlem; Tuncbag, Nurcan; Gursoy, Attila

    2016-04-27

    Identification of protein-protein interactions (PPIs) is at the center of molecular biology considering the unquestionable role of proteins in cells. Combinatorial interactions result in a repertoire of multiple functions; hence, knowledge of PPI and binding regions naturally serve to functional proteomics and drug discovery. Given experimental limitations to find all interactions in a proteome, computational prediction/modeling of protein interactions is a prerequisite to proceed on the way to complete interactions at the proteome level. This review aims to provide a background on PPIs and their types. Computational methods for PPI predictions can use a variety of biological data including sequence-, evolution-, expression-, and structure-based data. Physical and statistical modeling are commonly used to integrate these data and infer PPI predictions. We review and list the state-of-the-art methods, servers, databases, and tools for protein-protein interaction prediction. PMID:27074302

  20. Observation of a level crossing in a molecular nanomagnet using implanted muons

    We have observed an electronic energy level crossing in a molecular nanomagnet (MNM) using muon spin relaxation. This effect, not observed previously despite several muon studies of MNM systems, provides further evidence that the spin relaxation of the implanted muon is sensitive to the dynamics of the electronic spin. Our measurements on a broken ring MNM [H2NtBuisPr][Cr8CdF9(O2CC(CH3)3)18], which contains eight Cr ions, show clear evidence for the S=0→S=1 transition that takes place at Bc = 2.3 T. The crossing is observed as a resonance-like dip in the average positron asymmetry and also in the muon spin relaxation rate, which shows a sharp increase in magnitude at the transition and a peak centred within the S = 1 regime. (fast track communication)

  1. RNA-Seq and molecular docking reveal multi-level pesticide resistance in the bed bug

    Mamidala Praveen

    2012-01-01

    Full Text Available Abstract Background Bed bugs (Cimex lectularius are hematophagous nocturnal parasites of humans that have attained high impact status due to their worldwide resurgence. The sudden and rampant resurgence of C. lectularius has been attributed to numerous factors including frequent international travel, narrower pest management practices, and insecticide resistance. Results We performed a next-generation RNA sequencing (RNA-Seq experiment to find differentially expressed genes between pesticide-resistant (PR and pesticide-susceptible (PS strains of C. lectularius. A reference transcriptome database of 51,492 expressed sequence tags (ESTs was created by combining the databases derived from de novo assembled mRNA-Seq tags (30,404 ESTs and our previous 454 pyrosequenced database (21,088 ESTs. The two-way GLMseq analysis revealed ~15,000 highly significant differentially expressed ESTs between the PR and PS strains. Among the top 5,000 differentially expressed ESTs, 109 putative defense genes (cuticular proteins, cytochrome P450s, antioxidant genes, ABC transporters, glutathione S-transferases, carboxylesterases and acetyl cholinesterase involved in penetration resistance and metabolic resistance were identified. Tissue and development-specific expression of P450 CYP3 clan members showed high mRNA levels in the cuticle, Malpighian tubules, and midgut; and in early instar nymphs, respectively. Lastly, molecular modeling and docking of a candidate cytochrome P450 (CYP397A1V2 revealed the flexibility of the deduced protein to metabolize a broad range of insecticide substrates including DDT, deltamethrin, permethrin, and imidacloprid. Conclusions We developed significant molecular resources for C. lectularius putatively involved in metabolic resistance as well as those participating in other modes of insecticide resistance. RNA-Seq profiles of PR strains combined with tissue-specific profiles and molecular docking revealed multi-level insecticide resistance in C. lectularius. Future research that is targeted towards RNA interference (RNAi on the identified metabolic targets such as cytochrome P450s and cuticular proteins could lay the foundation for a better understanding of the genetic basis of insecticide resistance in C. lectularius.

  2. Information Flow Analysis of Level 4 Payload Processing Operations

    Danz, Mary E.

    1991-01-01

    The Level 4 Mission Sequence Test (MST) was studied to develop strategies and recommendations to facilitate information flow. Recommendations developed as a result of this study include revised format of the Test and Assembly Procedure (TAP) document and a conceptualized software based system to assist in the management of information flow during the MST.

  3. Mean level signal crossing rate for an arbitrary stochastic process

    Yura, Harold T.; Hanson, Steen Grüner

    2010-01-01

    The issue of the mean signal level crossing rate for various probability density functions with primary relevance for optics is discussed based on a new analytical method. This method relies on a unique transformation that transforms the probability distribution under investigation into a normal ...

  4. Yakima tribal perspectives on high level selection process

    When Congress went through the arduous process of fashioning a comprehensive plan for resolution of the nation's long-standing nuclear waste problem, it explicitly recognized that past federal efforts in this area had been inadequate. Congress also recognized that the primary reasons for the failure of earlier federal efforts was failure on the part of the federal government to seriously deal with very real technical questions about the geologic adequacy of prospective repository sites, and failure to address the concerns of state, tribal, and local governments in the repository selection and development process

  5. Processing of inflected nouns and levels of cognitive sensitivity

    Kostić Aleksandar Đ.

    2002-01-01

    Full Text Available In a series of experiments with lexical decision task it was demonstrated that processing of inflected Serbian noun forms is determined by the amount of information (bits carried by those forms. The amount of information is derived from form's probability and number of syntactic functions/meanings carried by a form. Form's probability, on the other hand, is specified within gender paradigm (e. g. what is the probability of suffix x to be attached to a feminine noun? by summing up probabilities of cases shared by a given inflected form. Within a paradigm of feminine nouns, however, there are number of subparadigms that differ in case distribution of their inflected forms and, by the same token, in distribution of the amount of information distribution. Previous studies have shown that the amount of information derived from probabilities of inflected forms derived from the dominant paradigm account for almost all processing variability. In this study we investigate whether processing of inflected forms from the non-dominant paradigm is affected by its probability distribution or by probability distribution of the dominant paradigm. The outcome of the experiment indicated that processing latencies to inflected forms are determined by probabilities derived from the dominant subparadigm.

  6. Ultraviolet-excited High Rotational Level Molecular Hydrogen in Interstellar Clouds: Models and Observational Results

    Lee, Dae-Hee; Pak, Soojong; van Dishoeck, Ewine F.

    We have calculated 2448 interstellar cloud models to investigate the formation and destruction of high rotational level H2 according to the combinations of five physical conditions: the input UV intensity, the H2 column density, cloud temperature, total density, and the H2 formation rate efficiency. The models include the populations of all the accessible states of H2 with the rotational quantum number J Dishoeck 1987). The high rotational levels J = 4 and J = 5 are both populated by direct formation into these levels of newly created molecules, and by pumping from J = 0 and J = 1, respectively. The model results show that N(4)/N(0) and N(5)/N(1) are proportional to the incident UV intensity, as predicted by Jura (1975), and are linearly decreased with the logarithm of molecular fraction, log f. Also, recent observational results are discussed with reference to the calculated models. Twenty-four high resolution spectra of H2 in the LMC and SMC (Tumlinson et al. 2002), and three translucent clouds (Sonnentrucker et al. 2002; Sonnentrucker et al. 2003; Rachford et al. 2001), observed by FUSE, provide an appropriate data set to examine the models. We have surveyed 54 early-type stars in the Galactic disk and halo with the Berkeley Extreme and Far-Ultraviolet Spectrometer (BEFS), part of the ORFEUS telescope, to obtain interstellar H2 absorption spectra for this research. The observed high rotational H2 level line ratios are well followed in the models, so that we can estimate the densities of the clouds from the models.

  7. Interference asymmetry of molecular frame photoelectron angular istributions in bichromatic UV ionization processes

    Yuan, Kai-Jun; Bandrauk, André D.

    2016-03-01

    We investigate molecular photoionization by ultrafast bichromatic linearly polarized UV laser pulses at frequencies 2{ω }1={ω }2 perpendicular to the internuclear axis R involving π orbital excitation. Results from numerical solutions of time dependent Schrödinger equations for aligned {{{H}}}2+ show that molecular frame photoelectron angular distributions (MFPADs) exhibit signatures of asymmetry perpendicular to the molecular symmetry axis, arising from interference of coherent electron wave packets created by respectively one {ω }2 and two-photon 2{ω }1 absorption. A resonant excitation process between the ground 1s{σ }{{g}} state and the excited 2p{π }{{u}} state is triggered by the {ω }1 pulse. The asymmetry of MFPADs varies periodically with pulse intensity I 0 and duration T, which we attribute to coherent resonant Rabi oscillations in electronic state population. A perturbative model is adopted to qualitatively describe and analyze these effects in both resonant and nonresonant photoionization processes.

  8. Belowground Carbon Cycling Processes at the Molecular Scale: An EMSL Science Theme Advisory Panel Workshop

    Hess, Nancy J.; Brown, Gordon E.; Plata, Charity

    2014-02-21

    As part of the Belowground Carbon Cycling Processes at the Molecular Scale workshop, an EMSL Science Theme Advisory Panel meeting held in February 2013, attendees discussed critical biogeochemical processes that regulate carbon cycling in soil. The meeting attendees determined that as a national scientific user facility, EMSL can provide the tools and expertise needed to elucidate the molecular foundation that underlies mechanistic descriptions of biogeochemical processes that control carbon allocation and fluxes at the terrestrial/atmospheric interface in landscape and regional climate models. Consequently, the workshop's goal was to identify the science gaps that hinder either development of mechanistic description of critical processes or their accurate representation in climate models. In part, this report offers recommendations for future EMSL activities in this research area. The workshop was co-chaired by Dr. Nancy Hess (EMSL) and Dr. Gordon Brown (Stanford University).

  9. Determination of cadmium at ultra-trace levels by CPE-molecular fluorescence combined methodology

    A highly sensitive micelle-mediated extraction methodology for the preconcentration and determination of trace levels of cadmium by molecular fluorescence has been developed. Metal was complexed with o-phenanthroline (o-phen) and eosin (eo) at pH 7.6 in buffer Tris medium and quantitatively extracted into a small volume of surfactant-rich phase of PONPE 7.5 after centrifugating. The chemical variables affecting cloud point extraction (CPE) were evaluated and optimized. The RSD for six replicates of cadmium determinations at 0.84 μg L-1 level was 1.17%. The linearity range using the preconcentration system was between 2.79 x 10-3 μg L-1 and 2.81 μg L-1 with a correlation coefficient of 0.99. Under the optimal conditions, it obtained a LOD of 8.38 x 10-4 μg L-1 and LOQ of 2.79 x 10-3 μg L-1. The method presented good sensitivity and selectivity and was applied to the determination of trace amounts of cadmium in commercially bottled mineral water, tap water and water well samples with satisfactory results. The proposed method is an innovative application of CPE-luminescence to metal analysis comparable in sensitivity and accuracy with atomic spectroscopies.

  10. Determination of cadmium at ultra-trace levels by CPE-molecular fluorescence combined methodology

    Talio, Maria Carolina [Instituto de Quimica de San Luis (INQUISAL-CONICET), Chacabuco y Pedernera, 5700 San Luis (Argentina); Luconi, Marta O. [Area de Quimica Analitica, Facultad de Quimica, Bioquimica y Farmacia, Universidad Nacional de San Luis, San Luis (Argentina); Masi, Adriana N. [Area de Bromatologia- Ensayo y Valoracion de Medicamentos, Facultad de Quimica, Bioquimica y Farmacia, Universidad Nacional de San Luis, San Luis (Argentina); Instituto de Quimica de San Luis (INQUISAL-CONICET), Chacabuco y Pedernera, 5700 San Luis (Argentina); Fernandez, Liliana P., E-mail: lfernand@unsl.edu.ar [Area de Quimica Analitica, Facultad de Quimica, Bioquimica y Farmacia, Universidad Nacional de San Luis, San Luis (Argentina); Instituto de Quimica de San Luis (INQUISAL-CONICET), Chacabuco y Pedernera, 5700 San Luis (Argentina)

    2009-10-15

    A highly sensitive micelle-mediated extraction methodology for the preconcentration and determination of trace levels of cadmium by molecular fluorescence has been developed. Metal was complexed with o-phenanthroline (o-phen) and eosin (eo) at pH 7.6 in buffer Tris medium and quantitatively extracted into a small volume of surfactant-rich phase of PONPE 7.5 after centrifugating. The chemical variables affecting cloud point extraction (CPE) were evaluated and optimized. The RSD for six replicates of cadmium determinations at 0.84 {mu}g L{sup -1} level was 1.17%. The linearity range using the preconcentration system was between 2.79 x 10{sup -3} {mu}g L{sup -1} and 2.81 {mu}g L{sup -1} with a correlation coefficient of 0.99. Under the optimal conditions, it obtained a LOD of 8.38 x 10{sup -4} {mu}g L{sup -1} and LOQ of 2.79 x 10{sup -3} {mu}g L{sup -1}. The method presented good sensitivity and selectivity and was applied to the determination of trace amounts of cadmium in commercially bottled mineral water, tap water and water well samples with satisfactory results. The proposed method is an innovative application of CPE-luminescence to metal analysis comparable in sensitivity and accuracy with atomic spectroscopies.

  11. Advances in low-level color image processing

    Smolka, Bogdan

    2014-01-01

    Color perception plays an important role in object recognition and scene understanding both for humans and intelligent vision systems. Recent advances in digital color imaging and computer hardware technology have led to an explosion in the use of color images in a variety of applications including medical imaging, content-based image retrieval, biometrics, watermarking, digital inpainting, remote sensing, visual quality inspection, among many others. As a result, automated processing and analysis of color images has become an active area of research, to which the large number of publications of the past two decades bears witness. The multivariate nature of color image data presents new challenges for researchers and practitioners as the numerous methods developed for single channel images are often not directly applicable to multichannel  ones. The goal of this volume is to summarize the state-of-the-art in the early stages of the color image processing pipeline.

  12. Level 1 remedial investigation work plan, 300 Area Process Ponds

    1987-06-01

    This report discusses the objectives of the site characterization for the 300 Area Process Ponds which are to identify and quantify contamination at the ponds and to estimate their potential impact on human health and the environment. The results of the site characterization will be used to identify any future actions related to contamination at the site and to identify any additional data requirements needed to support selection of a remedial action. 9 refs., 12 figs., 8 tabs.

  13. Comparison of the plant requirements, process performance and waste arisings for potential processes for the partitioning of high level waste

    Conceptual overall processes have been compared for six partitioning technologies for high level waste (HLW) integrating them with the PUREX process and with the downstream processes required to convert the products into forms suitable for transmutation or other purposes. Based on the process flowsheets, a semi-quantitative assessment ha been made of the relative investment in plant necessary for each process. An assessment is also made of the secondary wastes and by-products resulting from each process

  14. IAEA technical meeting on 'Technical aspects of atomic and molecular data processing and exchange'. Summary report

    The proceedings of the IAEA Advisory Group Meeting on 'Technical Aspects of Atomic and Molecular Data Processing and Exchange' (17th Meeting of A+M Data Centres and ALADDIN Network), held on 6-7 October, 2003 in Vienna, Austria are briefly described. The meeting conclusions and recommendations on the priorities in A+M data compilation and evaluation, and on the technical aspects of data processing, exchange, and distribution are also presented. (author)

  15. Corrosion and failure processes in high-level waste tanks

    A large amount of radioactive waste has been stored safely at the Savannah River and Hanford sites over the past 46 years. The aim of this report is to review the experimental corrosion studies at Savannah River and Hanford with the intention of identifying the types and rates of corrosion encountered and indicate how these data contribute to tank failure predictions. The compositions of the High-Level Wastes, mild steels used in the construction of the waste tanks and degradation-modes particularly stress corrosion cracking and pitting are discussed. Current concerns at the Hanford Site are highlighted

  16. Vitrification processing method and device for high level liquid waste

    A freeze-drying device is assembled to the midway of a line which connects a liquid waste tank and a melter in order to remove water. A freezing facility and a vacuum facility are connected to a drying box. With such a constitution, water is removed before supplying the high level liquid wastes to the melter, and the solid material removed with water is charged into the melter, and a vitrification material is formed. Accordingly, scattering of nuclides generated upon removing water can be reduced, and there is no need to dispose complicated equipments in the melter, thereby simplifying installation. (T.M.)

  17. Corrosion and failure processes in high-level waste tanks

    Mahidhara, R.K.; Elleman, T.S.; Murty, K.L. [North Carolina State Univ., Raleigh, NC (United States)

    1992-11-01

    A large amount of radioactive waste has been stored safely at the Savannah River and Hanford sites over the past 46 years. The aim of this report is to review the experimental corrosion studies at Savannah River and Hanford with the intention of identifying the types and rates of corrosion encountered and indicate how these data contribute to tank failure predictions. The compositions of the High-Level Wastes, mild steels used in the construction of the waste tanks and degradation-modes particularly stress corrosion cracking and pitting are discussed. Current concerns at the Hanford Site are highlighted.

  18. Technetium removal processes for soluble defense high-level waste

    Two methods for removing technetium from soluble defense high-level waste are described. In the first method, technetium is precipitated as tetraphenylphosphonium pertechnetate and separated from the decontaminated solution using sintered metal crossflow filters. In the second method, pertechnetate is removed from solution using a strong base anion exchange resin and then eluted from the resin with nitric acid. The nitric acid is recovered by sorption of the pertechnetate on a weak base ion exchange resin. The pertechnetate is eluted from the weak base resin with NaOH and recovered by precipitation as the sulfide or oxide. 7 refs., 3 figs

  19. A simplified molecular method for distinguishing among species and ploidy levels in European water frogs (Pelophylax).

    Hauswaldt, J Susanne; Her, Manuela; Ogielska, Maria; Christiansen, Ditte G; Dziewulska-Szwajkowska, Daria; Czernicka, El?bieta; Vences, Miguel

    2012-09-01

    Western Palearctic water frogs in the genus Pelophylax are a set of morphologically similar anuran species that form hybridogenetic complexes. Fully reliable identification of species and especially of hybrid ploidy depends on karyological and molecular methods. In central Europe, native water frog populations consist of the Pelophylax esculentus complex, that is, P.lessonae (LL), P.ridibundus (RR) and the hybrid form P.esculentus that can have different karyotypes (RL, LLR and RRL). We developed existing molecular methods further and propose a simple PCR method based on size-differences in the length of the serum albumin intron-1 and the RanaCR1, a non-LTR retrotransposon of the chicken repeat (CR) family. This PCR yields taxon-specific banding patterns that can easily be screened by standard agarose gel electrophoresis and correctly identify species in all of the 160 samples that had been identified to karyotype with other methods. To distinguish ploidy levels in LR, LLR and RRL specimens, we used the ratio of the peak heights of the larger (ridibundus specific) to the smaller (lessonae specific) bands of fluorescently labelled PCR products resolved on a capillary DNA sequencer and obtained a correct assignment of the karyotype in 93% of cases. Our new method will cut down time and expenses drastically for a reliable identification of water frogs of the P.esculentus complex and potentially for identification of other hybridogenetic complexes and/or taxa, and it even serves as a good indicator of the ploidy status of hybrid individuals. PMID:22716763

  20. The LHCb Data Acquisition and High Level Trigger Processing Architecture

    Frank, M.; Gaspar, C.; Jost, B.; Neufeld, N.

    2015-12-01

    The LHCb experiment at the LHC accelerator at CERN collects collisions of particle bunches at 40 MHz. After a first level of hardware trigger with an output rate of 1 MHz, the physically interesting collisions are selected by running dedicated trigger algorithms in the High Level Trigger (HLT) computing farm. This farm consists of up to roughly 25000 CPU cores in roughly 1750 physical nodes each equipped with up to 4 TB local storage space. This work describes the LHCb online system with an emphasis on the developments implemented during the current long shutdown (LS1). We will elaborate the architecture to treble the available CPU power of the HLT farm and the technicalities to determine and verify precise calibration and alignment constants which are fed to the HLT event selection procedure. We will describe how the constants are fed into a two stage HLT event selection facility using extensively the local disk buffering capabilities on the worker nodes. With the installed disk buffers, the CPU resources can be used during periods of up to ten days without beams. These periods in the past accounted to more than 70% of the total time.

  1. The LHCb Data Acquisition and High Level Trigger Processing Architecture

    Frank, M; Jost, B; Neufeld, N

    2015-01-01

    The LHCb experiment at the LHC accelerator at CERN collects collisions of particle bunches at 40 MHz. After a first level of hardware trigger with an output rate of 1 MHz, the physically interesting collisions are selected by running dedicated trigger algorithms in the High Level Trigger (HLT) computing farm. This farm consists of up to roughly 25000 CPU cores in roughly 1750 physical nodes each equipped with up to 4 TB local storage space. This work describes the LHCb online system with an emphasis on the developments implemented during the current long shutdown (LS1). We will elaborate the architecture to treble the available CPU power of the HLT farm and the technicalities to determine and verify precise calibration and alignment constants which are fed to the HLT event selection procedure. We will describe how the constants are fed into a two stage HLT event selection facility using extensively the local disk buffering capabilities on the worker nodes. With the installed disk buffers, the CPU resources ca...

  2. Atomic-level stress and induced growth of wurtzite zinc oxide using molecular dynamics simulation

    Molecular dynamics is used to simulate the film growth process of zinc oxide (ZnO) deposited on a ZnO substrate. In the work, the Buckingham-type interatomic potential is modelled to describe the interaction of Zn-O atoms. The effects of incident energy and substrate temperature on the layer coverage function, radial distribution function and residual stress are investigated. Results show that the crystal growth of the deposition film is a symmetric wurtzite lattice along the [0?0?0?1] direction due to charge transformation. Epitaxial-like growth only occurs at very low incident energies, while the intermixing process could start from an incident energy of 3 eV. The average stress of the Zn layer is a compressive stress that is close to zero. However, the average mean biaxial stress and the normal stress of the O layer are -4.49 GPa and -3.07 GPa, respectively. The simulation results are compared with experimental results available in the literature. (paper)

  3. Exposure to low pH induces molecular level changes in the marine worm, Platynereis dumerilii.

    Wäge, Janine; Lerebours, Adelaide; Hardege, Jörg D; Rotchell, Jeanette M

    2016-02-01

    Fossil fuel emissions and changes in net land use lead to an increase in atmospheric CO2 concentration and a subsequent decrease of ocean pH. Noticeable effects on organisms' calcification rate, shell structure and energy metabolism have been reported in the literature. To date, little is known about the molecular mechanisms altered under low pH exposure, especially in non-calcifying organisms. We used a suppression subtractive hybridisation (SSH) approach to characterise differentially expressed genes isolated from Platynereis dumerilii, a non-calcifying marine polychaeta species, kept at normal and low pH conditions. Several gene sequences have been identified as differentially regulated. These are involved in processes previously considered as indicators of environment change, such as energy metabolism (NADH dehydrogenase, 2-oxoglutarate dehydrogenase, cytochrome c oxidase and ATP synthase subunit F), while others are involved in cytoskeleton function (paramyosin and calponin) and immune defence (fucolectin-1 and paneth cell-specific alpha-defensin) processes. This is the first study of differential gene expression in a non-calcifying, marine polychaete exposed to low pH seawater conditions and suggests that mechanisms of impact may include additional pathways not previously identified as impacted by low pH in other species. PMID:26476878

  4. On reproduction in red algae: further research needed at the molecular level.

    García-Jiménez, Pilar; Robaina, Rafael R

    2015-01-01

    Multicellular red algae (Rhodophyta) have some of the most complex life cycles known in living organisms. Economically valuable seaweeds, such as phycocolloid producers, have a triphasic (gametophyte, carposporophyte, and tetrasporophyte) life cycle, not to mention the intricate alternation of generations in the edible "sushi-alga" nori. It is a well-known fact that reproductive processes are controlled by one or more abiotic factor(s), including day length, light quality, temperature, and nutrients. Likewise, endogenous chemical factors such as plant growth regulators have been reported to affect reproductive events in some red seaweeds. Still, in the genomic era and given the high throughput techniques at our disposal, our knowledge about the endogenous molecular machinery lags far behind that of higher plants. Any potential effective control of the reproductive process will entail revisiting most of these results and facts to answer basic biological questions as yet unresolved. Recent results have shed light on the involvement of several genes in red alga reproductive events. In addition, a working species characterized by a simple filamentous architecture, easy cultivation, and accessible genomes may also facilitate our task. PMID:25755663

  5. [Implementation on the operating level of the nursing process].

    Villalobos, N A

    1999-01-01

    The development of the nursing care attention process guided through the PDCA. (plan, do, check, act), provides a continuous improvement of our actual context. The meaning of PDCA is translated as VIDA for: view, implementation, discernment, at just. For its application it takes in view the change theory of Kurt Lewin. This paper provides the results of the Implementation stage using different approaches as technical care, education, administration and research. These strategies show that people did not express their feelings, beliefs and their own expectations and autonomy in nursing care. They even do not develop their citizenship, right of living and being able to grow. PMID:10734939

  6. Stochastic dynamics of small ensembles of non-processive molecular motors: The parallel cluster model

    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 the fraction of bound motors under load and thus to firm attachment even for small ensembles. This adaptation to load results in a concave force-velocity relation described by a Hill relation. For external load provided by a linear spring, myosin II ensembles dynamically adjust themselves towards an isometric state with constant average position and load. The dynamics of the ensembles is now determined mainly by the distribution of motors over the different kinds of bound states. For increasing stiffness of the external spring, there is a sharp transition beyond which myosin II can no longer perform the power stroke. Slow unbinding from the pre-power-stroke state protects the ensembles against detachment

  7. Stochastic dynamics of small ensembles of non-processive molecular motors: The parallel cluster model

    Erdmann, Thorsten; Albert, Philipp J.; Schwarz, Ulrich S. [BioQuant, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany and Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120 Heidelberg (Germany)

    2013-11-07

    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 the fraction of bound motors under load and thus to firm attachment even for small ensembles. This adaptation to load results in a concave force-velocity relation described by a Hill relation. For external load provided by a linear spring, myosin II ensembles dynamically adjust themselves towards an isometric state with constant average position and load. The dynamics of the ensembles is now determined mainly by the distribution of motors over the different kinds of bound states. For increasing stiffness of the external spring, there is a sharp transition beyond which myosin II can no longer perform the power stroke. Slow unbinding from the pre-power-stroke state protects the ensembles against detachment.

  8. Stochastic dynamics of small ensembles of non-processive molecular motors: The parallel cluster model

    Erdmann, Thorsten; Albert, Philipp J.; Schwarz, Ulrich S.

    2013-11-01

    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 the fraction of bound motors under load and thus to firm attachment even for small ensembles. This adaptation to load results in a concave force-velocity relation described by a Hill relation. For external load provided by a linear spring, myosin II ensembles dynamically adjust themselves towards an isometric state with constant average position and load. The dynamics of the ensembles is now determined mainly by the distribution of motors over the different kinds of bound states. For increasing stiffness of the external spring, there is a sharp transition beyond which myosin II can no longer perform the power stroke. Slow unbinding from the pre-power-stroke state protects the ensembles against detachment.

  9. Molecular-level variation affects population growth in a butterfly metapopulation.

    Hanski, Ilkka; Saccheri, Ilik

    2006-05-01

    The dynamics of natural populations are thought to be dominated by demographic and environmental processes with little influence of intraspecific genetic variation and natural selection, apart from inbreeding depression possibly reducing population growth in small populations. Here we analyse hundreds of well-characterised local populations in a large metapopulation of the Glanville fritillary butterfly (Melitaea cinxia), which persists in a balance between stochastic local extinctions and recolonisations in a network of 4,000 discrete habitat patches. We show that the allelic composition of the glycolytic enzyme phosphoglucose isomerase (Pgi) has a significant effect on the growth of local populations, consistent with previously reported effects of allelic variation on flight metabolic performance and fecundity in the Glanville fritillary and Colias butterflies. The strength and the sign of the molecular effect on population growth are sensitive to the ecological context (the area and spatial connectivity of the habitat patches), which affects genotype-specific gene flow and the influence of migration on the dynamics of local populations. The biological significance of the results for Pgi is underscored by lack of any association between population growth and allelic variation at six other loci typed in the same material. In demonstrating, to our knowledge for the first time, that molecular variation in a candidate gene affects population growth, this study challenges the perception that differential performance of individual genotypes, leading to differential fitness, is irrelevant to population dynamics. These results also demonstrate that the spatial configuration of habitat and spatial dynamics of populations contribute to maintenance of Pgi polymorphism in this species. PMID:16620151

  10. MIPAS Level 1B algorithms overview: operational processing and characterization

    A. Kleinert

    2007-01-01

    Full Text Available This paper gives an overview of the MIPAS Level 1B (L1B processor whose main objective is to calibrate atmospheric measurements radiometrically, spectrally and geo-located. It presents also the results of instrument characterization done on ground and during the first years in-flight. An accurate calibration is mandatory for high quality atmospheric retrievals. MIPAS has shown very good performance and stability. The noise equivalent spectral radiance ranges from 3 to 50 nW/(cm2 sr cm?1 and is well within the requirements over nearly the whole spetral range. The systematic radiometric error is estimated to be within 1 or 2% in most situations.

  11. High level radioactive waste vitrification process equipment component testing

    Remote operability and maintainability of vitrification equipment were assessed under shielded-cell conditions. The equipment tested will be applied to immobilize high-level and transuranic liquid waste slurries that resulted from plutonium production for defense weapons. Equipment tested included: a turntable for handling waste canisters under the melter; a removable discharge cone in the melter overflow section; a thermocouple jumper that extends into a shielded cell; remote instrument and electrical connectors; remote, mechanical, and heat transfer aspects of the melter glass overflow section; a reamer to clean out plugged nozzles in the melter top; a closed circuit camera to view the melter interior; and a device to retrieve samples of the glass product. A test was also conducted to evaluate liquid metals for use in a liquid metal sealing system

  12. Processing highly tritiated water desorbed from molecular sieve bed using PERMCAT

    Highlights: ► HTW processed with PERMCAT. ► Processing of highly tritiated water (HTW). ► Molecular sieve bed with HTW adsorbed. - Abstract: Tritium handling facilities use molecular sieve beds (MSB) to collect and recover tritiated water. After reaching the capacity limit of the MSB, the water is desorbed and decontaminated in a water detritiation system (WDS). In the case of highly tritiated water (HTW) absorbed into a MSB, an inherent safe option for processing is necessary due to the HTW specific properties. Ideally, HTW should be processed immediately in a continuous mode. With this in consideration, the water desorption process from a zeolite bed was developed and optimized in a dedicated non active facility. The results of this experiments were applied into the regeneration of a MSB previously loaded with HTW containing an activity of 1.9 × 1014 Bq kg−1. The water was desorbed, by step increasing the temperature bed and fed by helium carrier gas into the PERMCAT for detritiation and tritium recovery. The processed water was collected in a dry MSB downstream of the PERMCAT. These initial studies successfully demonstrate the viability of the process. The obtained results of the preliminary study and the subsequent tests with tritium, will provide useful information for the design of tritium processes relying on MSB, such as the water processing foreseen for the test blanket modules in ITER.

  13. Supramolecular and heterosupramolecar chemistry in controlled release and molecular recognition processes

    Agostini, Alessandro

    2013-01-01

    La presente tesis doctoral titulada ¿Supramolecular and heterosupramolecular chemistry in controlled release and molecular recognition processes¿ está centrada en los dos aspectos principales de la química supramolecular que han experimentado un gran auge en los últimos años: el reconocimiento molecular y los procesos de liberación controlada. En particular la primera parte de la tesis se focaliza en el diseño y síntesis de moléculas orgánicas que pueden ser empleados cómo...

  14. 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

    2013-01-01

    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 eve...

  15. Accelerated molecular dynamics simulations with the AMOEBA polarizable force field on graphics processing units

    Lindert, S; Bucher, D; Eastman, P; Pande, V.; McCammon, JA

    2013-01-01

    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 eve...

  16. Anthropogenic and Climate Influences on Biogeochemical Dynamics and Molecular-Level Speciation of Soil Sulfur

    Solomon, D.; Lehmann, J; Kinyangi, J; Pell, A; Theis , J; Riha , S; Ngoze, S; Amelung, W; du Preez, C; et. al.

    2009-01-01

    The soil environment is a primary component of the global biogeochemical sulfur (S) cycle, acting as a source and sink of various S species and mediating oxidation state changes. However, ecological significance of the various S forms and the impacts of human intervention and climate on the amount and structural composition of these compounds are still poorly understood. We investigated the long-term influences of anthropogenically mediated transitions from natural to managed ecosystems on molecular-level speciation, biogeochemical dynamics, and the apparent temperature sensitivity of S moieties in temperate, subtropical, and tropical environments with mean annual temperature (MAT) ranging from 5C to 21C, using elemental analysis and X-ray absorption near-edge structure (XANES) spectroscopy. Land-use and land-cover changes led to the depletion of total soil S in all three ecoregions over a period of up to 103 years. The largest decline occurred from tropical forest agroecosystems (67% Kakamega and 76% Nandi, Kenya), compared to losses from temperate (36% at Lethbridge, Canada, and 40% at Pendleton, USA) and subtropical (48% at South Africa) grassland agroecosystems. The total S losses correlated significantly with MAT. Anthropogenic interventions profoundly altered the molecular-level composition and resulted in an apparent shift in oxidation states of organic S from native ecosystems composed primarily of S moieties in intermediate and highly reduced oxidation states toward managed agroecosystems dominated by organic S rich in strongly oxidized functionalities. The most prominent change occurred in thiols and sulfides, the proportion of which decreased by 46% (Lethbridge) and 57% (Pendleton) in temperate agroecosystems, by 46% in subtropical agroecosystems, and by 79% (Nandi) and 81% (Kakamega) in tropical agroecosystems. The proportion of organic S directly linked to O increased by 81%, 168%, 40%, 92%, and 85%, respectively. Among the various organic S functionalities, thiols and sulfides seem to have higher apparent temperature sensitivity, and thus these organic S moieties may become prone to losses due to land-use changes, even from the cooler regions of the world if MAT of these regions rise in the future.

  17. Wafer level warpage characterization of 3D interconnect processing wafers

    Chang, Po-Yi; Ku, Yi-Sha

    2012-03-01

    We present a new metrology system based on a fringe reflection method for warpage characterizations during wafer thinning and temporary bonding processes. A set of periodic fringe patterns is projected onto the measuring wafer and the reflected fringe images are captured by a CCD camera. The fringe patterns are deformed due to the slope variation of the wafer surface. We demonstrate the use of phase-shit algorithms, the wafer surface slope variation and quantitative 3D surface profile even tiny dimples and dents on a wafer can be reconstructed. The experimental results show the warpages of the bonded wafer are below 20 μm after thinning down to the nominal thickness of 75 μm and 50 μm. The measurement precision is better than 2 um.

  18. Constant current charging process of MV-level Marx generator

    A 4 MV pre-triggered Marx generator charged with series resistor has been designed. For better output property, higher charging efficiency and lower voltage difference between stages, the study conducted the analytic solution of its constant current charging (CCC) process. The results show that the voltage differences between different stages of capacitors are in direct proportion to charging resistance, capacitance and charging speed, but are independent of time; the charging efficiency improves with time, but is independent of charging speed. This solution is universally applicable. The simulation of CCC for the Marx generator was done with PSpice, and the results agree with the analytic solution. Compared to constant voltage charging (CVC) with 10 k? charging resistors, 400 nF capacitors and 10 kV/s charging speed, the charging efficiency of CCC is 90%, double that of CVC and the charging time is only one third. (authors)

  19. Ferroelectric molecular field-switch based on double proton transfer process: Static and dynamical simulations.

    Rode, Michał F; Jankowska, Joanna; Sobolewski, Andrzej L

    2016-04-01

    In this work, we present a reversible ferroelectric molecular switch controlled by an external electric field. The studied (2Z)-1-(6-((Z)-2-hydroxy-2-phenylvinyl)pyridin-3-yl)-2-(pyridin-2(1H)-ylidene)ethanone (DSA) molecule is polarized by two uniaxial intramolecular hydrogen bonds. Two protons can be transferred along hydrogen bonds upon an electric field applied along the main molecular axis. The process results in reversion of the dipole moment of the system. Static ab initio and on-the-fly dynamical simulations of the DSA molecule placed in an external electric field give insight into the mechanism of the double proton transfer (DPT) in the system and allow for estimation of the time scale of this process. The results indicate that with increasing strength of the electric field, the step-wise mechanism of DPT changes into the downhill barrierless process in which the synchronous and asynchronous DPTs compete with each other. PMID:27059566

  20. Vibrational spectral emission of fractional-principal-quantum-energy-level hydrogen molecular ion

    Mills, R.L.; Ray, P. [BlackLight Power, Inc., Cranbury, NJ (United States)

    2002-05-01

    From a solution of a Schroedinger-type wave equation with a nonradiative boundary condition based on Maxwell's equations, Mills solves the hydrogen atom, the hydrogen molecular ion, the hydrogen molecule and predicts corresponding species having fractional principal quantum numbers. Atomic hydrogen may undergo a catalytic reaction with certain atomized elements and ions which singly or multiply ionize at integer multiples of the potential energy of atomic hydrogen, m27.2 eV wherein m is an integer. The reaction involves a nonradiative energy transfer to form a hydrogen atom H(1/p) that is lower in energy than unreacted atomic hydrogen that corresponds to a fractional principal quantum number (n=1/p=1/integer replaces the well known parameter n=integer in the Rydberg equation for hydrogen excited states). One such atomic catalytic system involves argon ions. The reaction Ar{sup +} to Ar{sup 2+} has a net enthalpy of reaction of 27.63 eV, which is equivalent to m=1. Thus, it may serve as a catalyst to form H(1/2). Also, the second ionization energy of helium is 54.4 eV; thus, the ionization reaction of He{sup +} to He{sup 2+} has net enthalpy of reaction of 54.4 eV which is equivalent to 2x27.2 eV. The products of the catalysis reaction H(1/3) may further serve as catalysts to form H(1/4) and H(1/2). H(1/p) may react with a proton to form an excited state molecular ion H{sub 2}{sup *}(1/p){sup +} that has a bond energy and vibrational levels that are p{sup 2} times those of the molecular ion comprising uncatalyzed atomic hydrogen where p is an integer. Thus, the excited state spectrum of H{sub 2}{sup *}[n=1/4:n{sup *}=2]{sup +} was predicted to comprise rotationally broadened vibrational transitions at 1.185 eV increments to the dissociation limit of H{sub 2}[n=1/4]{sup +}. E{sub D}=42.88 eV (28.92 nm). Extreme ultraviolet spectroscopy was recorded on microwave discharges of argon or helium with 10% hydrogen in the range 10-65 nm. Novel emission lines assigned to vibrational transitions of H{sub 2}{sup *}[n=1/4:n{sup *}=2]{sup +} were observed in this range with energies of v1.185 eV, v=17-38 that terminated at about 28.9 nm. In addition, fractional molecular hydrogen rotational transitions were assigned to previously unidentified lines in the Solar coronal spectrum that matched theoretical predictions to five figures. (author)

  1. Large-scale network-level processes during entrainment.

    Lithari, Chrysa; Sánchez-García, Carolina; Ruhnau, Philipp; Weisz, Nathan

    2016-03-15

    Visual rhythmic stimulation evokes a robust power increase exactly at the stimulation frequency, the so-called steady-state response (SSR). Localization of visual SSRs normally shows a very focal modulation of power in visual cortex and led to the treatment and interpretation of SSRs as a local phenomenon. Given the brain network dynamics, we hypothesized that SSRs have additional large-scale effects on the brain functional network that can be revealed by means of graph theory. We used rhythmic visual stimulation at a range of frequencies (4-30Hz), recorded MEG and investigated source level connectivity across the whole brain. Using graph theoretical measures we observed a frequency-unspecific reduction of global density in the alpha band "disconnecting" visual cortex from the rest of the network. Also, a frequency-specific increase of connectivity between occipital cortex and precuneus was found at the stimulation frequency that exhibited the highest resonance (30Hz). In conclusion, we showed that SSRs dynamically re-organized the brain functional network. These large-scale effects should be taken into account not only when attempting to explain the nature of SSRs, but also when used in various experimental designs. PMID:26835557

  2. MULTI LEVEL SEMANTIC EXTRACTION FOR CRICKET VIDEO BY TEXT PROCESSING

    Dr. SUNITHA ABBURU

    2010-10-01

    Full Text Available Semantic video analysis, indexing and retrieval are necessary for effective utilization of video repositories. The semantics can be extracted from the semantic carriers such as voice and video text. Super imposed text is the proper source to extract semantics of the video which will increase the efficiency of retrieval system. This paper proposes a semiautomatic method to generate annotation for cricket videos and an automated tool- DLER, to extract the semantics of cricket video. The DLER tool provides a fast and robust approach for text Detection, Localization, Extraction, and Reorganization in video frames, which is flexible and customer friendly. The DLER integrates all the pre-processing steps and the OCR steps in to a single unit. The annotator can pick the ROI, increase or decrease the threshold, contrast, brightness or inverse the image based on the typeof the broadcasted video. The tool has been implemented and tested with cricket video and the results of the experiments are promising. Finally conclusion and future work has been discussed.

  3. Polarized emission from stretched PPV films viewed at the molecular level.

    Ramos, Rodrigo; Siqueira, Melissa F; Cazati, Thiago; Faria, Roberto M; Caldas, Marilia J

    2015-08-28

    We present a study on the photoluminescence (PL) of thin films of poly-(p-phenylene vinylene) (PPV), non-stretched and uniaxially stretched. The experimental study was carried out using linear polarized light as the excitation beam, oriented either parallel or perpendicular to the stretch axis (S). The results showed that when the excitation light source has polarization perpendicularly oriented to the stretch direction, the emitted PL presents maximum intensity in the orientation S, and a minimum in the direction orthogonal to S. In order to understand this interesting phenomenon, we employ theoretical simulations at the atomistic level. We use classical molecular dynamics to simulate amorphous PPV films, non-stretched and stretched, from which we find a tendency of overall alignment of PV units to S, and of local clustering in herring-bone and π-stacking partial symmetries. Our study of optical activity of these kinds of clusters, performed through a quantum semi-empirical method, allows us to explain this polarization conversion behavior, and indicates the possibility of using underivatized PPV as the active layer for polarized electroluminescent devices. PMID:26198411

  4. Shark tales: a molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes).

    Vlez-Zuazo, Ximena; Agnarsson, Ingi

    2011-02-01

    Sharks are a diverse and ecologically important group, including some of the ocean's largest predatory animals. Sharks are also commercially important, with many species suffering overexploitation and facing extinction. However, despite a long evolutionary history, commercial, and conservation importance, phylogenetic relationships within the sharks are poorly understood. To date, most studies have either focused on smaller clades within sharks, or sampled taxa sparsely across the group. A more detailed species-level phylogeny will offer further insights into shark taxonomy, provide a tool for comparative analyses, as well as facilitating phylogenetic estimates of conservation priorities. We used four mitochondrial and one nuclear gene to investigate the phylogenetic relationships of 229 species (all eight Orders and 31 families) of sharks, more than quadrupling the number of taxon sampled in any prior study. The resulting Bayesian phylogenetic hypothesis agrees with prior studies on the major relationships of the sharks phylogeny; however, on those relationships that have proven more controversial, it differs in several aspects from the most recent molecular studies. The phylogeny supports the division of sharks into two major groups, the Galeomorphii and Squalimorphii, rejecting the hypnosqualean hypothesis that places batoids within sharks. Within the squalimorphs the orders Hexanchiformes, Squatiniformes, Squaliformes, and Pristiophoriformes are broadly monophyletic, with minor exceptions apparently due to missing data. Similarly, within Galeomorphs, the orders Heterodontiformes, Lamniformes, Carcharhiniformes, and Orectolobiformes are broadly monophyletic, with a couple of species 'misplaced'. In contrast, many of the currently recognized shark families are not monophyletic according to our results. Our phylogeny offers some of the first clarification of the relationships among families of the order Squaliformes, a group that has thus far received relatively little phylogenetic attention. Our results suggest that the genus Echinorhinus is not a squaliform, but rather related to the saw sharks, a hypothesis that might be supported by both groups sharing 'spiny' snouts. In sum, our results offer the most detailed species-level phylogeny of sharks to date and a tool for comparative analyses. PMID:21129490

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

    Kuznetsov, A.M.; Ulstrup, Jens

    2002-01-01

    be weak, corresponding to the fully diabatic limit. The rectification process then reduces to a sequence of vibrationally relaxed single-electron transfer steps. In the limits where the interactions are strong, denoted as the partially and fully adiabatic limits, the character of the rectification...... reduces to a three-level transition similar to STM of large redox molecules. Recent data for rectification in hexadecyl-quinolinium tricyanodimethanide monolayers by Metzger and co-workers [J. Am. Chem. Soc. 119, 10455 (1997); Acc. Chem. Res. 32, 950 (1999)], are discussed in terms of the reported views...

  6. Process evaluation of an open architecture real-time molecular laboratory platform.

    Felder, Robin A; Jackson, Keith D; Walter, Adam M

    2014-10-01

    The needs of molecular diagnostic laboratories that perform both Food and Drug Administration-cleared as well as laboratory-developed tests are usually not met on a single analytical platform. Furthermore, little information is available about the direct impact of molecular automation on labor costs and efficiency in clinical laboratories. We performed a process impact analysis from time and motion studies of a novel molecular diagnostic robotic system designed to automate sample preparation, extraction, and analysis. All 27 preanalytical tasks were quantified for the amount of time spent preparing 24 specimens for analysis. These steps were completed in 899 s (14 min, 59 s) followed by 7887 s (131 min, 27 s) of instrument operation independent of operator control (walk-away time). Postanalytical results evaluation required 1 min per specimen. The instrument automatically extracted the nucleic acid from the specimen, added the eluted DNA to the amplification reagents, and performed the analysis. Only 12% of the total instrument operations required relatively unskilled human labor. Thus, the availability of automated molecular diagnostic instruments will facilitate the expansion of molecular testing in the clinical laboratory because they reduce operator costs with respect to time and complexity of the tasks they are asked to perform. PMID:24811476

  7. An overview of atomic and molecular processes in critical velocity ionization

    Alfven's critical ionization velocity (CIV) is a multistep process involving plasma physics and plasma chemistry. The authors present an overview of the time development of some atomic and molecular processes in CIV. In the pre-onset stage, metastable states play an important role: They provide an energy pooling mechanism allowing low energy electrons to participate in the ionization processes; they may explain the low energy threshold as well as the fast time scale in the onset of CIV. For a sustaining CIV to occur, Townsend's criterion has to be satisfied. The kinetic energies of the neutrals are transformed to plasma wave energies via beam-plasma instabilities, and the plasma waves that heat the electrons result in a tail formation. Excitation of neutrals with subsequent radiation is an important energy loss mechanism. Finite beam size also limits the instability growth rate. In the propagation of CIV, ion-molecule reactions and molecular dissociative recombination are important. Ion-molecule reactions change the temporal chemical composition in a CIV process and help explain some results in CIV experiments. Molecular dissociative recombination reduces the plasma density, lowers the effective neutral mass, and loses energy via excitation and radiation; it tends to quench the propagation of CIV. Depending on various parameters, oscillatory behavior of CIV may occur

  8. Download Process in Distributed Systems, Flow-level vs. Packet-level Simulation Analysis

    Dandoush, Abdulhalim; Jean-Marie, Alain

    2009-01-01

    Parallelism in the download process of large files is an efficient mechanism for distributed systems. In such systems, some peers (clients) exploit the power of parallelism to download blocks of data stored in a distributed way over some other peers (servers). Determining response times in parallel downloading with capacity constraints on both the client downloads and server uploads necessitates understanding the instantaneous shares of the bandwidths of each client/server is devoted to each ...

  9. Download Process in Distributed Systems, Flow-level Algorithm vs. Packet-level Simulation Model

    Dandoush, Abdulhalim; Jean-Marie, Alain

    2009-01-01

    Parallelism in the download process of large files is an efficient mechanism for distributed systems. In such systems, some peers (clients) exploit the power of parallelism to download blocks of data stored in a distributed way over some other peers (servers). Determining response times in parallel downloading with capacity constraints on both the client downloads and server uploads necessitates understanding the instantaneous shares of the bandwidths of each client/server is devoted to each ...

  10. Symmetry Breaking in NMR Spectroscopy: The Elucidation of Hidden Molecular Rearrangement Processes

    Michael J. McGlinchey

    2014-08-01

    Full Text Available Variable-temperature NMR spectroscopy is probably the most convenient and sensitive technique to monitor changes in molecular structure in solution. Rearrangements that are rapid on the NMR time-scale exhibit simplified spectra, whereby non-equivalent nuclear environments yield time-averaged resonances. At lower temperatures, when the rate of exchange is sufficiently reduced, these degeneracies are split and the underlying “static” molecular symmetry, as seen by X-ray crystallography, becomes apparent. Frequently, however, such rearrangement processes are hidden, even when they become slow on the NMR time-scale, because the molecular point group remains unchanged. Judicious symmetry breaking, such as by substitution of a molecular fragment by a similar, but not identical moiety, or by the incorporation of potentially diastereotopic (chemically non-equivalent nuclei, allows the elucidation of the kinetics and energetics of such processes. Examples are chosen that include a wide range of rotations, migrations and other rearrangements in organic, inorganic and organometallic chemistry.

  11. Multiprobe Spectroscopic Inverstigation of Molecular-level Behavior within Aqueous 1-Butyl-3-methylimidazolium Tetrafluoroborate

    Sarkar, Abhra [Indian Institute of Technology, Delhi; Ali, Maroof [Indian Institute of Technology, Delhi; Baker, Gary A [ORNL; Tetin, Sergey Y. [Abbott Laboratories; Ruan, Qiaoqiao [Abbott Laboratories; Pandey, Siddharth [Indian Institute of Technology, Delhi

    2009-01-01

    In this work, an array of molecular-level solvent featuressincluding solute-solvent/solvent-solvent interactions, dipolarity, heterogeneity, dynamics, probe accessibility, and diffusionswere investigated across the entire composition of ambient mixtures containing the ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate, [bmim][BF4], and pH 7.0 phosphate buffer, based on results assembled for nine different molecular probes utilized in a range of spectroscopic modes. These studies uncovered interesting and unusual solvatochromic probe behavior within this benchmark mixture. Solvatochromic absorbance probessa watersoluble betaine dye (betaine dye 33), N,N-diethyl-4-nitroaniline, and 4-nitroanilineswere employed to determine ET (a blend of dipolarity/polarizability and hydrogen bond donor contributions) and the Kamlet-Taft indices * (dipolarity/polarizability), R (hydrogen bond donor acidity), and (hydrogen bond acceptor basicity) characterizing the [bmim][BF4] + phosphate buffer system. These parameters each showed a marked deviation from ideality, suggesting selective solvation of the individual probe solutes by [bmim][BF4]. Similar conclusions were derived from the responses of the fluorescent polarity-sensitive probes pyrene and pyrene-1-carboxaldehyde. Importantly, the fluorescent microfluidity probe 1,3-bis(1-pyrenyl)propane senses a microviscosity within the mixture that significantly exceeds expectations derived from simple interpolation of the behavior in the neat solvents. On the basis of results from this probe, a correlation between microviscosity and bulk viscosity was established; pronounced solvent-solvent hydrogen-bonding interactions were implicit in this behavior. The greatest deviation from ideal additive behavior for the probes studied herein was consistently observed to occur in the buffer-rich regime. Nitromethane-based fluorescence quenching of pyrene within the [bmim][BF4] + phosphate buffer system showed unusual compliance with a sphere-of-action quenching model, a further manifestation of the microheterogeneity of the system. Fluorescence correlation spectroscopic results for both small (BODIPY FL) and macromolecular (Texas Red-10 kDa dextran conjugate) diffusional probes provide additional evidence in support of microphase segregation inherent to aqueous [bmim][BF4].

  12. Antimicrobial resistance profiling and molecular subtyping of Campylobacter spp. from processed turkey

    Sherwood Julie S

    2009-09-01

    Full Text Available Abstract Background Campylobacter is a major cause of human disease worldwide and poultry are identified as a significant source of this pathogen. Most disease in humans is associated with the consumption of contaminated poultry or cross-contamination with other foods. The primary drugs of choice for treatment of human campylobacteriosis include erythromycin and ciprofloxacin. In this study, we investigated the prevalence of resistance to erythromycin and ciprofloxacin in Campylobacter isolates recovered from turkey carcasses at two processing plants in the Upper Midwest US. Further analysis of a subset of isolates was carried out to assess resistance and genotype profiles. Results Campylobacter isolates from plant A (n = 439; including 196 C. coli and 217 C. jejuni and plant B (n = 362, including 281 C. coli and 62 C. jejuni were tested for susceptibility to ciprofloxacin and erythromycin using agar dilution. C. coli were more frequently resistant than C. jejuni in both plants, including resistance to ciprofloxacin (28% of C. jejuni and 63% of C. coli, plant B; and 11% of C. coli, plant A. Erythromycin resistance was low among C. jejuni (0% plant A and 0.3% plant B compared to C. coli (41%, plant A and 17%, plant B. One hundred resistant and susceptible isolates were selected for additional antimicrobial susceptibility testing, restriction fragment length polymorphism analysis of the flaA gene (fla typing, and pulsed-field gel electrophoresis (PFGE. Fla-PFGE types obtained (n = 37 were associated with a specific plant with the exception of one type that was isolated from both plants. C. coli isolates (n = 65 were grouped into 20 types, while C. jejuni isolates (n = 35 were grouped into 17 types. Most isolates with identical fla-PFGE patterns shared identical or very similar antimicrobial resistance profiles. PFGE alone and composite analysis using fla-PFGE with resistance profiles separated C. jejuni and C. coli into distinct groups. Conclusion Ciprofloxacin and erythromycin resistance in Campylobacter recovered from processed turkey occurred more frequently among C. coli than C. jejuni. Fla-PFGE types were associated with a particular species, antimicrobial resistance profiles, and a specific plant. Molecular subtyping in this study provided more information about the relationships among antimicrobial-resistant Campylobacter at the processing level.

  13. Atomic and molecular processes generated by linearly polarized few-cycle laser pulses

    S-matrix theory is used to analyze different atomic and molecular processes in a linearly polarized few-cycle laser field. The energy spectra of high-order above-threshold ionization (HATI) are presented. Electron-atom potential scattering assisted by a few-cycle laser pulse is also analyzed. It is shown that the plateau structures in the energy spectra of the electron-atom potential scattering are dependent on the carrier-envelope phase (CEP) of the laser pulse, so that the cutoff positions of the plateaus can be controlled by changing the CEP. Regarding our analysis of the molecular HATI process, the angle-resolved spectra, obtained by different theoretical approaches, are also presented. (paper)

  14. An isomerization-induced cage-breaking process in a molecular glass former below Tg

    A recent experimental [P. Karageorgiev, D. Neher, B. Schulz, B. Stiller, U. Pietsch, M. Giersig, L. Brehmer, Nature Mater. 4, 699 (2005)] study has found liquidlike diffusion below the glass-transition temperature in azobenzene-containing materials under irradiation. This result suggests that the isomerization-induced massive mass transport that leads to surface relief gratings formation in these materials, is induced by this huge increase of the matrix diffusion coefficient around the probe. In order to investigate the microscopic origin of the increase of the diffusion, we use molecular dynamics simulations of the photoisomerization of probe dispersed red 1 molecules dispersed inside a glassy molecular matrix. Results show that the increased diffusion is due to an isomerization-induced cage-breaking process. A process that explains the induced cooperative motions recently observed in these photoactive materials.

  15. Ultrasmall volume molecular isothermal amplification in microfluidic chip with advanced surface processing

    Huang, Guoliang; Ma, Li; Yang, Xiaoyong; Yang, Xu

    2011-01-01

    In this paper, we developed a metal micro-fluidic chip with advanced surface processing for ultra-small volume molecular isothermal amplification. This method takes advantages of the nucleic acid amplification with good stability and consistency, high sensitivity about 31 genomic DNA copies and bacteria specific gene identification. Based on the advanced surface processing, the bioreaction assays of nucleic acid amplification was dropped about 392nl in volume. A high numerical aperture confocal optical detection system was advanced to sensitively monitor the DNA amplification with low noise and high power collecting fluorescence near to the optical diffraction limit. A speedy nucleic acid isothermal amplification was performed in the ultra-small volume microfluidic chip, where the time at the inflexions of second derivative to DNA exponential amplified curves was brought forward and the sensitivity was improved about 65 folds to that of in current 25?l Ep-tube amplified reaction, which indicates a promising clinic molecular diagnostics in the droplet amplification.

  16. Theoretical study of the molecular bases that control photochemical processes with biological and nanotechnological interest

    Saur Peris, Vicenta

    2013-01-01

    El trabajo desarrollado en la tesis doctoral que lleva por ttulo "Theoretical study of the molecular bases that control photochemical processes with biological and nanotechnological interest" se enmarca en las lneas de investigacin del grupo QCEXVAL (Quantum Chemistry of the Excited State University of Valencia), que naci en el seno del departamento de Qumica Fsica de la Universitat de Valncia en 1993. Se han abordado temas de inters metodolgico, biolgico y nanotecnolgico. La prime...

  17. On the use of Graphics Processing Units (GPUs) for molecular dynamics simulation of spherical particles

    Cruz-Hidalgo, R. (Raúl); Kanzaki, T.; Alonso-Marroquin, F.; Luding, S.

    2013-01-01

    General-purpose computation on Graphics Processing Units (GPU) on personal computers has recently become an attractive alternative to parallel computing on clusters and supercomputers. We present the GPU-implementation of an accurate molecular dynamics algorithm for a system of spheres. The new hybrid CPU-GPU implementation takes into account all the degrees of freedom, including the quaternion representation of 3D rotations. For additional versatility, the contact interaction bet...

  18. Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit

    Eastman, Peter; Pande, Vijay S.

    2010-01-01

    We describe an algorithm for computing nonbonded interactions with cutoffs on a graphics processing unit (GPU). We have incorporated it into OpenMM, a library for performing molecular simulations on high performance computer architectures. We benchmark it on a variety of systems including boxes of water molecules, proteins in explicit solvent, a lipid bilayer, and proteins with implicit solvent. The results demonstrate that its performance scales linearly with the number of atoms over a wide ...

  19. Acceleration of Early-Photon Fluorescence Molecular Tomography with Graphics Processing Units

    Xin Wang; Bin Zhang; Xu Cao; Fei Liu; Jianwen Luo; Jing Bai

    2013-01-01

    Fluorescence molecular tomography (FMT) with early-photons can improve the spatial resolution and fidelity of the reconstructed results. However, its computing scale is always large which limits its applications. In this paper, we introduced an acceleration strategy for the early-photon FMT with graphics processing units (GPUs). According to the procedure, the whole solution of FMT was divided into several modules and the time consumption for each module is studied. In this strategy, two most...

  20. On the use of graphics processing units (GPUs) for molecular dynamics simulation of spherical particles

    Hidalgo, R. C.; Kanzaki, T.; Alonso-Marroquin, F.; Yu, A.; Dong, K.; Yang, R; Luding, S.

    2013-01-01

    General-purpose computation on Graphics Processing Units (GPU) on personal computers has recently become an attractive alternative to parallel computing on clusters and supercomputers. We present the GPU-implementation of an accurate molecular dynamics algorithm for a system of spheres. The new hybrid CPU-GPU implementation takes into account all the degrees of freedom, including the quaternion representation of 3D rotations. For additional versatility, the contact interaction between particl...

  1. Accelerated molecular dynamics force evaluation on graphics processing units for thermal conductivity calculations

    Fan, Zheyong; Siro, Topi; harju, Ari

    2012-01-01

    In this paper, we develop a highly efficient molecular dynamics code fully implemented on graphics processing units for thermal conductivity calculations using the Green-Kubo formula. We compare two different schemes for force evaluation, a previously used thread-scheme where a single thread is used for one particle and each thread calculates the total force for the corresponding particle, and a new block-scheme where a whole block is used for one particle and each thread in the block calcula...

  2. MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

    Villar-Briones Alejandro; Castillo Sandra; Pluskal Tomáš; Orešič Matej

    2010-01-01

    Abstract Background Mass spectrometry (MS) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. Such approaches are used for systems biology, functional genomics, and biomarker discovery, among others. An ongoing challenge of these molecular profiling approaches, however, is the development of better data processing methods. Here we introduce a new generation of a popular open...

  3. Femtosecond Laser Processing of Germanium: An Ab Initio Molecular Dynamics Study

    Ji, Pengfei; Zhang, Yuwen

    2016-01-01

    An ab initio molecular dynamics study of femtosecond laser processing of germanium is presented in this paper. The method based on the finite temperature density functional theory is adopted to probe the structural change, thermal motion of the atoms, dynamic property of the velocity autocorrelation, and the vibrational density of states. Starting from a cubic system at room temperature (300 K) containing 64 germanium atoms with an ordered arrangement of 1.132 nm in each dimension, the femtos...

  4. Diffusion processes in biological membranes studied by molecular dynamics simulations and analytical models

    Stachura, Slawomir,

    2014-01-01

    Various recent experimental and simulation studies show that the lateral diffusion of molecules in biological membranes exhibits anomalies, in the sense that the molecular mean square displacements increase sub-linearily instead of linearly with time. Mathematically, such diffusion processes can be modeled by generalized diffusion equations which involve an additional fractional time derivative compared to the corresponding normal counterpart. The aim of this thesis is to gain some more physi...

  5. Molecular Mechanisms of Processing Proteome Reorganization of Interphase Chromatin During Stress and Adaptation to Winter in Wheat

    Ivanov R.S.

    2015-06-01

    Full Text Available Research of fundamental molecular and genetic processes of plant interaction with the environment, is a progressive field of understanding the fundamental problems of stress supramolecular biochemistry of developmental biology. The purpose of the work was the analysis of localization shielded to protease processing proteins of suprastructures of interphase chromatin matrix in the conditions of adaptation during vegetative phase of wheat to stressful environment factors. It is shown that in the conditions of perennial adaptation to cold shock of wheat at the level of chromatin suprastructures tightly bound to the nuclear matrix there is a total shielding of arginine-X sites to protease-processing. Perhaps these are zones that affect to the architecture organization of the cell nucleus that can help to survive in complex environmental conditions. According to the priorities in the study of agricultural plants, put forward by EPIC (The Epigenomics of Plants International Consortium in 2011 for the next decade, was included the point of necessity to understand the molecular basis of the interactions of genotype and environment that change the characteristics of plants in different conditions of the environment. These data will be useful for those who involved in the development of mathematical logic schemes of the theory and practice of biological specificity, and it could be included in the ontology of the stages plant growth and development.

  6. Molecular tools for the selective detection of nine diatom species biomarkers of various water quality levels.

    Cimarelli, Lucia; Singh, Kumar Saurabh; Mai, Nguyen Thi Nhu; Dhar, Bidhan Chandra; Brandi, Anna; Brandi, Letizia; Spurio, Roberto

    2015-05-01

    Our understanding of the composition of diatom communities and their response to environmental changes is currently limited by laborious taxonomic identification procedures. Advances in molecular technologies are expected to contribute more efficient, robust and sensitive tools for the detection of these ecologically relevant microorganisms. There is a need to explore and test phylogenetic markers as an alternative to the use of rRNA genes, whose limited sequence divergence does not allow the accurate discrimination of diatoms at the species level. In this work, nine diatom species belonging to eight genera, isolated from epylithic environmental samples collected in central Italy, were chosen to implement a panel of diatoms covering the full range of ecological status of freshwaters. The procedure described in this work relies on the PCR amplification of specific regions in two conserved diatom genes, elongation factor 1-a (eEF1-a) and silicic acid transporter (SIT), as a first step to narrow down the complexity of the targets, followed by microarray hybridization experiments. Oligonucleotide probes with the potential to discriminate closely related species were designed taking into account the genetic polymorphisms found in target genes. These probes were tested, refined and validated on a small-scale prototype DNA chip. Overall, we obtained 17 highly specific probes targeting eEF1-a and SIT, along with 19 probes having lower discriminatory power recognizing at the same time two or three species. This basic array was validated in a laboratory setting and is ready for tests with crude environmental samples eventually to be scaled-up to include a larger panel of diatoms. Its possible use for the simultaneous detection of diatoms selected from the classes of water quality identified by the European Water Framework Directive is discussed. PMID:26006124

  7. Molecular Tools for the Selective Detection of Nine Diatom Species Biomarkers of Various Water Quality Levels

    Lucia Cimarelli

    2015-05-01

    Full Text Available Our understanding of the composition of diatom communities and their response to environmental changes is currently limited by laborious taxonomic identification procedures. Advances in molecular technologies are expected to contribute more efficient, robust and sensitive tools for the detection of these ecologically relevant microorganisms. There is a need to explore and test phylogenetic markers as an alternative to the use of rRNA genes, whose limited sequence divergence does not allow the accurate discrimination of diatoms at the species level. In this work, nine diatom species belonging to eight genera, isolated from epylithic environmental samples collected in central Italy, were chosen to implement a panel of diatoms covering the full range of ecological status of freshwaters. The procedure described in this work relies on the PCR amplification of specific regions in two conserved diatom genes, elongation factor 1-a (eEF1-a and silicic acid transporter (SIT, as a first step to narrow down the complexity of the targets, followed by microarray hybridization experiments. Oligonucleotide probes with the potential to discriminate closely related species were designed taking into account the genetic polymorphisms found in target genes. These probes were tested, refined and validated on a small-scale prototype DNA chip. Overall, we obtained 17 highly specific probes targeting eEF1-a and SIT, along with 19 probes having lower discriminatory power recognizing at the same time two or three species. This basic array was validated in a laboratory setting and is ready for tests with crude environmental samples eventually to be scaled-up to include a larger panel of diatoms. Its possible use for the simultaneous detection of diatoms selected from the classes of water quality identified by the European Water Framework Directive is discussed.

  8. Toxic effects of pesticide mixtures at a molecular level: Their relevance to human health

    Highlights: ► Toxic effects of pesticide mixtures can be independent, dose addition or interaction. ► Metabolic interactions involve inhibition or induction of detoxifying enzymes. ► Organophosphates can potentiate pyrethroid, carbaryl and triazine toxicity. ► Synergism occurs when two active pesticides elicit greater than additive toxicity. ► Endocrine disruptors have the potential for additivity rather than synergism. - Abstract: Pesticides almost always occur in mixtures with other ones. The toxicological effects of low-dose pesticide mixtures on the human health are largely unknown, although there are growing concerns about their safety. The combined toxicological effects of two or more components of a pesticide mixture can take one of three forms: independent, dose addition or interaction. Not all mixtures of pesticides with similar chemical structures produce additive effects; thus, if they act on multiple sites their mixtures may produce different toxic effects. The additive approach also fails when evaluating mixtures that involve a secondary chemical that changes the toxicokinetics of the pesticide as a result of its increased activation or decreased detoxification, which is followed by an enhanced or reduced toxicity, respectively. This review addresses a number of toxicological interactions of pesticide mixtures at a molecular level. Examples of such interactions include the postulated mechanisms for the potentiation of pyrethroid, carbaryl and triazine herbicides toxicity by organophosphates; how the toxicity of some organophosphates can be potentiated by other organophosphates or by previous exposure to organochlorines; the synergism between pyrethroid and carbamate compounds and the antagonism between triazine herbicides and prochloraz. Particular interactions are also addressed, such as those of pesticides acting as endocrine disruptors, the cumulative toxicity of organophosphates and organochlorines resulting in estrogenic effects and the promotion of organophosphate-induced delayed polyneuropathy

  9. Role of molecular dynamics on descriptions of shock-front processes

    By means of a computational approach based on classical molecular dynamics, we can begin to form a realistic picture of shock-induced processes occurring at the shock front and resulting from the detailed, violent motion associated with shock motion on an atomic scale. Prototype studies of phase transitions will be discussed. We will also examine the interaction of the shock front with defects, surfaces, voids, and inclusions, and across grain boundaries. We will focus on the critical question of how mechanical energy imparted to a condensed material by shock loading is converted to the activation energy required to overcome some initial energy barrier in an initiation process

  10. Fixation of radioactive wastes in glass by a process of molecular stuffing

    Research on a process for adding dopants to high-silica porous glass at relatively low temperatures (0C) (Molecular Stuffing Process) has led to a method suitable for the storage of radioactive waste materials. Glass produced by this method has a high concentration of waste in the interior and is free of this waste in a thick surface layer. Silica content is above 75% in the core and above 90 mole % in the surface. The glass exhibits extremely high chemical durability and low diffusion rates for the waste

  11. R-Matrix Theory of Atomic Collisions Application to Atomic, Molecular and Optical Processes

    Burke, Philip George

    2011-01-01

    Commencing with a self-contained overview of atomic collision theory, this monograph presents recent developments of R-matrix theory and its applications to a wide-range of atomic molecular and optical processes. These developments include electron and photon collisions with atoms, ions and molecules required in the analysis of laboratory and astrophysical plasmas, multiphoton processes required in the analysis of superintense laser interactions with atoms and molecules and positron collisions with atoms and molecules required in antimatter studies of scientific and technologial importance. Basic mathematical results and general and widely used R-matrix computer programs are summarized in the appendices.

  12. A quantum mechanical model of the Bloch NMR flow equations for electron dynamics in fluids at the molecular level

    Understanding of processes such as carrier mobility, electron transfer reactions, chemical reactions in fluids, electron solvation in fluids and electron attachment and localization in clusters relies crucially on the understanding of electron dynamics in fluids at the molecular level. Because of its very small mass, an electron is a quantum object and some of its properties such as diffusion coefficient of a solvated electron in water can be explained only by resorting to quantum mechanical formulation. In this study, we have solved the Bloch NMR flow equations to describe the evolution of the wavelike properties and find the wave functions which can be useful to solve a particular fluid flow problem quantum mechanically. Based on the uncertainty principle, a wave packet is assumed to initially describe the fluid particle (electron) under study. Then, when the particle encounters a force (so its potential energy is no longer zero), the force modifies the wave packet. Finding such propagation techniques, and applying them appropriately can provide useful techniques to find solutions to biological, medical and physical problems which otherwise could not be easily solved

  13. Molecularly mediated processing and assembly of nanoparticles: exploring the interparticle interactions and structures.

    Lim, Stephanie I; Zhong, Chuan-Jian

    2009-06-16

    The harnessing of the nanoscale properties of nanoparticles in most technological applications requires the abilities of controlled processing and assembly, which has been an important challenge because of the difficulty in manipulating interparticle properties. Molecularly mediated processing and assembly of nanoparticles have emerged as an important strategy for addressing this challenge. The capability of this strategy in manipulating size, shape, composition, and interparticle properties has significant implications for designing sensing, biosensing, nanoprobing, and many other functional nanostructures. This Account highlights some of the important findings in investigating both interparticle and collective properties as a forum for discussing new opportunities in exploiting nanoparticle-based designs and applications. The concept of mediator-template assembly of nanoparticles explores the combination of the forces from a mediator and a templating molecule for designing and controlling the interparticle interactions. The manipulation of the interparticle interaction properties and the detection of the molecular signatures are two of the key elements in this concept. A series of well-defined molecular mediators ranging from inorganic, organic, supramolecular, to biological molecules have been explored to ascertain how these two elements can be achieved in nanoparticle assemblies. The emphasis is the fundamental understanding of interparticle molecular interactions, such as covalent, electrostatic, hydrogen bonding, multidentate coordination, pi-pi interactions, etc. Each of these molecular interactions has been examined using specific molecules, such as multifunctional ligands, tunable sizes, shapes, or charges, well-defined molecular rigidity and chirality, or spectroscopic signatures, such as fluorescence and Raman scattering. Examples included thiols, thioethers, carboxylic acids, fullerenes, dyes, homocysteines, cysteines, glutathiones, proteins, and DNAs as molecular mediators for the assembly of gold, alloy, and magnetic nanoparticles. The understanding of these systems provided insights into how the unique electrical, optical, magnetic, and spectroscopic properties of the nanoparticle assemblies can be exploited for potential applications. This Account also highlights a few examples in chemical sensing and bioprobing to illustrate the importance of interparticle interactions and structures in exploiting these properties. One example involves thin-film assemblies of metal nanoparticles as biomimetic ion channels or chemiresistor sensing arrays by exploiting the nanostructured ligand framework interactions. Other examples explore the surface-enhanced Raman scattering signature as nanoprobes for the detection of protein binding or the enzyme-based cutting of interparticle DNAs. The detailed understanding of the design and control parameters in these and other systems should have a profound impact on the exploration of nanoparticles in a wide range of technological applications. PMID:19378982

  14. A methodology to assess the maturity level of brewery business processes

    Armendáriz, Mikel

    2010-01-01

    The purpose of this project is to develop a procedure to assess the maturity level of the brewery business processes to be able to determine the required level of process automation & IT for a brewery.This procedure is made up by several tailored questionnaires that have been based on the Process and Enterprise Maturity Model management assessment tool. This tool is described in the article called The Process Audit written by Michael Hammer and published by Harvard Business Review in 2007...

  15. Molecular-level understanding of the water-gas-shift reaction on Rh(111)

    Maestri, Matteo [Politecnico di Milano (Italy); Fritz-Haber-Institut, MPG, Berlin (Germany); Reuter, Karsten [Technische Universitaet, Muenchen (Germany); Fritz-Haber-Institut, MPG, Berlin (Germany)

    2011-07-01

    The identification of the reaction mechanism is the center piece for the atomic-scale understanding of a catalytic process and requires the kinetic assessment of all potential steps at the surface. At this level, processes of technological interest involve a large number of potential reactions and, due to the huge computational costs, are still largely outside the capabilities of a full density-functional theory (DFT) analysis. To this end we propose a hierarchical approach for the identification of prevalent reaction mechanisms by efficiently combining DFT and semi-empirical methods. The obtained computationally undemanding barrier estimates serve as initial approximate input for the identification of the prevalent paths that subsequently require refined kinetic parameters from explicit DFT calculations. As showcase we consider the water-gas-shift (WGS) and reverse reactions on Rh(111). Our results reveal that CO follows different chemical paths depending on the operating conditions. A carboxyl pathway is preferred for the consumption of CO, while its formation proceeds through the direct decomposition of carbon dioxide. These insights into the atomic-scale mechanism allow for a new understanding of the WGS system in full agreement with existing experimental evidence.

  16. Towards system-level understanding of baculovirus host cell interactions: from molecular fundamental studies to large-scale proteomics approaches

    FranciscaMonteiro

    2012-11-01

    Full Text Available Baculoviruses are insect viruses extensively exploited as eukaryotic protein expression vectors. Molecular biology studies have provided exciting discoveries on virus-host interactions, but the application of omic high throughput techniques on the baculovirus-insect cell system has been hampered by the lack of host genome sequencing. While a broader, systems level analysis of biological responses to infection is urgently needed, recent advances on proteomic studies have yielded new insights on the impact of infection on the host cell. These works are reviewed and critically assessed in the light of current biological knowledge of the molecular biology of baculoviruses and insect cells.

  17. The Henry Ford Production System: LEAN Process Redesign Improves Service in the Molecular Diagnostic Laboratory: A Paper from the 2008 William Beaumont Hospital Symposium on Molecular Pathology

    Cankovic, Milena; Varney, Ruan C.; Whiteley, Lisa; Brown, Ron; D'Angelo, Rita; Chitale, Dhananjay; Zarbo, Richard J.

    2009-01-01

    Accurate and timely molecular test results play an important role in patient management; consequently, there is a customer expectation of short testing turnaround times. Baseline data analysis revealed that the greatest challenge to timely result generation occurred in the preanalytic phase of specimen collection and transport. Here, we describe our efforts to improve molecular testing turnaround times by focusing primarily on redesign of preanalytic processes using the principles of LEAN pro...

  18. Processes of DNA condensation induced by multivalent cations: Approximate annealing experiments and molecular dynamics simulations

    The condensation of DNA induced by spermine is studied by atomic force microscopy (AFM) and molecular dynamics (MD) simulation in this paper. In our experiments, an equivalent amount of multivalent cations is added to the DNA solutions in different numbers of steps, and we find that the process of DNA condensation strongly depends on the speed of adding cations. That is, the slower the spermine cations are added, the slower the DNA aggregates. The MD and steered molecular dynamics (SMD) simulation results agree well with the experimental results, and the simulation data also show that the more steps of adding multivalent cations there are, the more compact the condensed DNA structure will be. This investigation can help us to control DNA condensation and understand the complicated structures of DNA—cation complexes. (interdisciplinary physics and related areas of science and technology)

  19. Absence of high-level vancomycin resistance in enterococci isolated from meat-processing facilities.

    Bodnaruk, P. W.; Krakar, P. J.; Tompkin, R. B.

    2001-01-01

    Enterococci isolated from packaging areas of meat-processing facilities that produce ready-to-eat meat products were examined for high-level vancomycin resistance. A total of 406 enterococci isolates from the plants' packaging areas were examined for vancomycin resistance. High-level vancomycin resistance was not demonstrated in any enterococci isolated from 12 meat-processing plants.

  20. An overview of atomic and molecular processes in critical velocity ionization

    Alfven's critical ionization velocity (CIV) is a multi-step process involving plasma physics and plasma chemistry. The authors present an overview of the time development of some atomic and molecular processes in CIV. In the pre-onset stage, metastable states play an important role: they provide an energy pooling mechanism allowing low energy electrons to participate in the ionization processes, and help explain the low energy threshold as well as the fast time scale in the onset of CIV. For a sustaining CIV to occur, an energy requirement and Townsend's criterion have to be satisfied. The kinetic energies of the neutrals are transformed to plasma wave energies via beam-plasma instabilities, and the plasma waves heat the electrons resulting in a tail formation. A parametric domain of beam angle and neutral densities satisfying Townsend's criterion is presented

  1. Insights into the molecular level composition, sources, and formation mechanisms of dissolved organic matter in aerosols and precipitation

    Altieri, Katye Elisabeth

    Atmospheric aerosols scatter and absorb light influencing the global radiation budget and climate, and are associated with adverse effects on human health. Precipitation is an important removal mechanism for atmospheric dissolved organic matter (DOM), and a potentially important input for receiving ecosystems. However, the sources, formation, and composition of atmospheric DOM in aerosols and precipitation are not well understood. This dissertation investigates the composition and formation mechanisms of secondary organic aerosol (SOA) formed through cloud processing reactions, elucidates the composition and sources of DOM in rainwater, and provides links connecting the two. Photochemical batch aqueous-phase reactions of organics with both biogenic and anthropogenic sources (i.e., methylglyoxal, pyruvic acid) and OH radical were performed to simulate cloud processing. The composition of products formed through cloud processing experiments and rainwater collected in New Jersey, USA was investigated using a combination of electrospray ionization mass spectrometry techniques, including ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry. This dissertation has resulted in the first evidence that oligomers form through cloud processing reactions, the first detailed chemical mechanism of aqueous phase oligomerization, the first identification of oligomers, organosulfates, and nitrooxy organosulfates in precipitation, and the first molecular level chemical characterization of organic nitrogen in precipitation. The formation of oligomers in SOA helps to explain the presence of large multifunctional compounds and humic like substances (HULIS) that dominate particulate organic mass. Oligomers have low vapor pressures and remain in the particle phase after cloud evaporation, enhancing SOA. The chemical properties of the oligomers suggest that they are less hygroscopic than the monomeric reaction products (i.e., organic acids). Their elemental ratios are consistent with the hypothesis that oligomers are a large contributor to aged organic aerosol mass. The majority of the compounds identified in rainwater samples by advanced mass spectrometry appear to be products of atmospheric reactions, including known contributors to SOA formed from gas phase, aerosol phase, and in-cloud reactions in the atmosphere. The similarities between the complex organic matter in rainwater and SOA suggest that the large uncharacterized component of SOA is the main contributor to the large uncharacterized component of rainwater DOM.

  2. Seeing the Light: Adapting Luminance Reveals Low-Level Visual Processes in the Attentional Blink

    Giesbrecht, Barry; Bischof, Walter F.; Kingstone, Alan

    2004-01-01

    It is widely assumed that high-level visual processes subserve the attentional blink (AB). Recent evidence from studies of visual masking during the AB that were designed to directly test the contributions of high-level masking effects, however, have failed to provide empirical support for this position.The implication is that low-level visual

  3. Functional genomics in fish: towards understanding stress and immune responses at a molecular level

    Ribas Cabezas, Laia

    2006-01-01

    Aquesta tesis doctoral està basada en estudiar la resposta immunològica dels peixos en models d'estrès i d'activació del sistema immune des la genòmica funcional. L'aplicació de tecnologies moleculars com el Differential Display van permetre identificar y clonar por primera vegada en orades (Sparus aurata) y en altres especies de peix, el gen enolasa. Aquest enzim glucolític s'ha plantejat per primera vegada com un bon marcador molecular per estudiar el benestar dels peixos. Per mitjà de l'ús...

  4. Molecular-level removal of proteinaceous contamination from model surfaces and biomedical device materials by air plasma treatment.

    Banerjee, K K; Kumar, S; Bremmell, K E; Griesser, H J

    2010-11-01

    Established methods for cleaning and sterilising biomedical devices may achieve removal of bioburden only at the macroscopic level while leaving behind molecular levels of contamination (mainly proteinaceous). This is of particular concern if the residue might contain prions. We investigated at the molecular level the removal of model and real-life proteinaceous contamination from model and practical surfaces by air plasma (ionised air) treatment. The surface-sensitive technique of X-ray photoelectron spectroscopy (XPS) was used to assess the removal of proteinaceous contamination, with the nitrogen (N1s) photoelectron signal as its marker. Model proteinaceous contamination (bovine serum albumin) adsorbed on to a model surface (silicon wafer) and the residual proteinaceous contamination resulting from incubating surgical stainless steel (a practical biomaterial) in whole human blood exhibited strong N1ssignals [16.8 and 18.5 atomic percent (at.%), respectively] after thorough washing. After 5min air plasma treatment, XPS detected no nitrogen on the sample surfaces, indicating complete removal of proteinaceous contamination, down to the estimated XPS detection limit 10ng/cm(2). Applying the same plasma treatment, the 7.7at.% nitrogen observed on a clinically cleaned dental bur was reduced to a level reflective of new, as-received burs. Contact angle measurements and atomic force microscopy also indicated complete molecular-level removal of the proteinaceous contamination upon air plasma treatment. This study demonstrates the effectiveness of air plasma treatment for removing proteinaceous contamination from both model and practical surfaces and offers a method for ensuring that no molecular residual contamination such as prions is transferred upon re-use of surgical and dental instruments. PMID:20850199

  5. Advice concerning the advantages of a reference incinerator for low-level and intermediate-level radioactive waste processing

    In this report, an inventory is presented of new incinerators and flue gas filters used in low and intermediate-level radioactive waste combustion. It is argued that a 'reference equipment' for the combustion of solid and liquid low- and intermediate-level wastes best meets existing Dutch radiation protection standards. A cost-benefit analysis of such an equipment is given including annual costs of investment, capital and exploration. A separate combustion process of organic liquids and carrions is considered finally. (G.J.P.)

  6. THE APPLICATION OF FEATURE TECHNOLOGY IN DEVELOPING A CAD-BASED HIGH LEVEL PROCESS PLANNING SYSTEM

    Ade Febransyah

    2005-01-01

    Full Text Available High-level process planning plays an important role in determining candidate process domains at the configuration design stage. Changing the process domains later increases the product development cycle and the product development cost. Therefore, determining the most appropriate manufacturing processes at the beginning stages of the design process becomes critical. However, high-level process planning systems have traditionally lacked integration of design synthesis and design evaluation. The objective of this paper is to propose a CAD-based high-level process planning system that will help designers decide whether or not the designs are worth pursuing. A hybrid approach incorporating design by feature and feature recognition approaches is proposed and implemented. Synergizing both advantages of both approaches will reduce the complexity of feature recognition algorithm without sacrificing the flexibility in creating a part model.

  7. Managing the Bologna Process at the European Level: Institution and Actor Dynamics

    Lazetic, Predrag

    2010-01-01

    This article analyses the work of the Bologna Follow Up Group as the main institution of the Bologna Process and the perceptions of the policy actors involved concerning the character of the process in terms of its functioning in contrast to similar multi-level multi-actor European processes, its modes of communication and consensus seeking, as

  8. On level crossings for a general class of piecewise-deterministic Markov processes

    Borovkov, K. A.; Last, Günter

    2007-01-01

    We consider a piecewise-deterministic Markov process governed by a jump intensity function, a rate function that determines the behaviour between jumps, and a stochastic kernel describing the conditional distribution of jump sizes. We study the point process of upcrossings of a level $b$ by the Markov process. Our main result shows that, under a suitable scaling $\

  9. Statistical mechanics of neocortical interactions: large-scale EEG influences on molecular processes

    Ingber, Lester

    2012-01-01

    Recent calculations further supports the premise that large-scale synchronous firings of neurons may affect molecular processes. The context is scalp electroencephalography (EEG) during short-term memory (STM) tasks. The mechanism considered is $\\mathbf{\\Pi} = \\mathbf{p} + q \\mathbf{A}$ (SI units) coupling, where $\\mathbf{p}$ is the momenta of free $\\mathrm{Ca}^{2+}$ waves $q$ the charge of $\\mathrm{Ca}^{2+}$ in units of the electron charge, and $\\mathbf{A}$ the magnetic vector potential of c...

  10. Low temperature pulse radiolysis as a method to study fast isomerization processes in molecular cations

    Application of the low-temperature pulse radiolysis to the studies of molecular cation transformations has been discussed. It has been shown that such parameters as: concentration of the substrate, ionization potentials of the solution components and the temperature of the matrix play important role in the charge transfer processes. These parameters have to be chosen carefully in order to secure a complete formation of the substrate radical cation prior to observation of its unimolecular transformations. A successful application of the low-temperature pulse radiolytic method to the studies of valence isomerization and conformational rotamerism of radical cations has been reviewed. (author)

  11. Molecular and physiological basic processes in the context of radiation protection

    The aim of this paper is an attempt to answer the question why accumulated knowledge on molecular basis of biological effects of ionizing radiation have not yet resulted in in sufficiently successful chemical radiation protection. In the past decade experimental results which demonstrated a direct regulatory role of some radicals in the main physiological processes such as vascular tone successfully emphasize the significance of old experimental results (the best protection can be achieved through physiological manipulations) connecting them to new data on free radical evolvement and the application of various free radical scavengers in radiation protection, which represents the most appropriate approach to the problem. (author)

  12. Mechanically Processed Alumina Reinforced Ultra-high Molecular Weight Polyethylene (UHMWPE) Matrix Composites

    Elmkharram, Hesham Moh. A.

    2013-01-01

    Alumina particles filled Ultra-high Molecular Weight Polyethylene (UHMWPE), with Al2O3 contents 0, 1, and 2.5 wt% were milled for up to 10 hours by the mechanical alloying (MA) process performed at room temperature to produce composite powders. Compression molding was utilized to produce sheets out of the milled powders. A partial phase transformation from orthorhombic and amorphous phases to monoclinic phase was observed to occur for both the un-reinforced and reinforced UHMWPE in the soli...

  13. Analysis of Pd-Ni Nanobelts Melting Process Using Molecular Dynamics Simulation

    Chen Gang; Zhang Peng; Liu HongWei

    2013-01-01

    The melting process of Pd-Ni alloy nanobelts with different Ni atom content has been simulated by molecular dynamic (MD) method. The radial distribution function, the Lindemann index, and pair analysis method were used to characterize Pd-Ni nanobelt models in simulation. The results indicate that the melting temperature of Pd-Ni nanobelt with composition far from pure metal was lower than that of other models, and the breaking point of the nanobelt can be illustrated by the Lindemann index. P...

  14. Simulating picosecond x-ray diffraction from shocked crystals using post-processing molecular dynamics calculations

    Kimminau, Giles; Nagler, Bob; Higginbotham, Andrew; Murphy, William J; Wark, Justin S [Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU (United Kingdom); Park, Nigel [AWE, Aldermaston, Reading RG7 4PR (United Kingdom); Hawreliak, James; Kalantar, Daniel H; Lorenzana, Hector E; Remington, Bruce A [Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States); Kadau, Kai; Germann, Timothy C [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Bringa, Eduardo M [Institudo de Ciencias Basicas, Universidad Nacional de Cuyo, Mendoza CP 5500 (Argentina)], E-mail: giles.kimminau@physics.ox.ac.uk

    2008-12-17

    Calculations of the patterns of x-ray diffraction from shocked crystals derived from the results of non-equilibrium molecular dynamics (NEMD) simulations are presented. The atomic coordinates predicted from the NEMD simulations combined with atomic form factors are used to generate a discrete distribution of electron density. A fast Fourier transform (FFT) of this distribution provides an image of the crystal in reciprocal space, which can be further processed to produce quantitative simulated data for direct comparison with experiments that employ picosecond x-ray diffraction from laser-irradiated crystalline targets.

  15. Simulating Picosecond X-ray Diffraction from shocked crystals by Post-processing Molecular Dynamics Calculations

    Kimminau, G; Nagler, B; Higginbotham, A; Murphy, W; Park, N; Hawreliak, J; Kadau, K; Germann, T C; Bringa, E M; Kalantar, D; Lorenzana, H; Remington, B; Wark, J

    2008-06-19

    Calculations of the x-ray diffraction patterns from shocked crystals derived from the results of Non-Equilibrium-Molecular-Dynamics (NEMD) simulations are presented. The atomic coordinates predicted by the NEMD simulations combined with atomic form factors are used to generate a discrete distribution of electron density. A Fast-Fourier-Transform (FFT) of this distribution provides an image of the crystal in reciprocal space, which can be further processed to produce quantitative simulated data for direct comparison with experiments that employ picosecond x-ray diffraction from laser-irradiated crystalline targets.

  16. Simulating picosecond x-ray diffraction from shocked crystals using post-processing molecular dynamics calculations

    Kimminau, Giles; Nagler, Bob; Higginbotham, Andrew; Murphy, William J.; Park, Nigel; Hawreliak, James; Kadau, Kai; Germann, Timothy C.; Bringa, Eduardo M.; Kalantar, Daniel H.; Lorenzana, Hector E.; Remington, Bruce A.; Wark, Justin S.

    2008-12-01

    Calculations of the patterns of x-ray diffraction from shocked crystals derived from the results of non-equilibrium molecular dynamics (NEMD) simulations are presented. The atomic coordinates predicted from the NEMD simulations combined with atomic form factors are used to generate a discrete distribution of electron density. A fast Fourier transform (FFT) of this distribution provides an image of the crystal in reciprocal space, which can be further processed to produce quantitative simulated data for direct comparison with experiments that employ picosecond x-ray diffraction from laser-irradiated crystalline targets.

  17. MOLECULAR SIEVES AS CATALYSTS FOR METHANOL DEHYDRATION IN THE LPDMEtm PROCESS

    Andrew W. Wang

    2002-04-01

    Several classes of molecular sieves were investigated as methanol dehydration catalysts for the LPDME{trademark} (liquid-phase dimethyl ether) process. Molecular sieves offer a number of attractive features as potential catalysts for the conversion of methanol to DME. These include (1) a wide range of acid strengths, (2) diverse architectures and channel connectivities that provide latitude for steric control, (3) high active site density, (4) well-investigated syntheses and characterization, and (5) commercial availability in some cases. We directed our work in two areas: (1) a general exploration of the catalytic behavior of various classes of molecular sieves in the LPDME{trademark} system and (2) a focused effort to prepare and test zeolites with predominantly Lewis acidity. In our general exploration, we looked at such diverse materials as chabazites, mordenites, pentasils, SAPOs, and ALPOs. Our work with Lewis acidity sought to exploit the structural advantages of zeolites without the interfering effects of deleterious Broensted sites. We used zeolite Ultrastable Y (USY) as our base material because it possesses a high proportion of Lewis acid sites. This work was extended by modifying the USY through ion exchange to try to neutralize residual Broensted acidity.

  18. MOLECULAR SIEVES AS CATALYSTS FOR METHANOL DEHYDRATION IN THE LPDMEtm PROCESS; TOPICAL

    Several classes of molecular sieves were investigated as methanol dehydration catalysts for the LPDME(trademark) (liquid-phase dimethyl ether) process. Molecular sieves offer a number of attractive features as potential catalysts for the conversion of methanol to DME. These include (1) a wide range of acid strengths, (2) diverse architectures and channel connectivities that provide latitude for steric control, (3) high active site density, (4) well-investigated syntheses and characterization, and (5) commercial availability in some cases. We directed our work in two areas: (1) a general exploration of the catalytic behavior of various classes of molecular sieves in the LPDME(trademark) system and (2) a focused effort to prepare and test zeolites with predominantly Lewis acidity. In our general exploration, we looked at such diverse materials as chabazites, mordenites, pentasils, SAPOs, and ALPOs. Our work with Lewis acidity sought to exploit the structural advantages of zeolites without the interfering effects of deleterious Broensted sites. We used zeolite Ultrastable Y (USY) as our base material because it possesses a high proportion of Lewis acid sites. This work was extended by modifying the USY through ion exchange to try to neutralize residual Broensted acidity

  19. Extending pathways and processes using molecular interaction networks to analyse cancer genome data

    Krasnogor Natalio

    2010-12-01

    Full Text Available Abstract Background Cellular processes and pathways, whose deregulation may contribute to the development of cancers, are often represented as cascades of proteins transmitting a signal from the cell surface to the nucleus. However, recent functional genomic experiments have identified thousands of interactions for the signalling canonical proteins, challenging the traditional view of pathways as independent functional entities. Combining information from pathway databases and interaction networks obtained from functional genomic experiments is therefore a promising strategy to obtain more robust pathway and process representations, facilitating the study of cancer-related pathways. Results We present a methodology for extending pre-defined protein sets representing cellular pathways and processes by mapping them onto a protein-protein interaction network, and extending them to include densely interconnected interaction partners. The added proteins display distinctive network topological features and molecular function annotations, and can be proposed as putative new components, and/or as regulators of the communication between the different cellular processes. Finally, these extended pathways and processes are used to analyse their enrichment in pancreatic mutated genes. Significant associations between mutated genes and certain processes are identified, enabling an analysis of the influence of previously non-annotated cancer mutated genes. Conclusions The proposed method for extending cellular pathways helps to explain the functions of cancer mutated genes by exploiting the synergies of canonical knowledge and large-scale interaction data.

  20. MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

    Villar-Briones Alejandro

    2010-07-01

    Full Text Available Abstract Background Mass spectrometry (MS coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. Such approaches are used for systems biology, functional genomics, and biomarker discovery, among others. An ongoing challenge of these molecular profiling approaches, however, is the development of better data processing methods. Here we introduce a new generation of a popular open-source data processing toolbox, MZmine 2. Results A key concept of the MZmine 2 software design is the strict separation of core functionality and data processing modules, with emphasis on easy usability and support for high-resolution spectra processing. Data processing modules take advantage of embedded visualization tools, allowing for immediate previews of parameter settings. Newly introduced functionality includes the identification of peaks using online databases, MSn data support, improved isotope pattern support, scatter plot visualization, and a new method for peak list alignment based on the random sample consensus (RANSAC algorithm. The performance of the RANSAC alignment was evaluated using synthetic datasets as well as actual experimental data, and the results were compared to those obtained using other alignment algorithms. Conclusions MZmine 2 is freely available under a GNU GPL license and can be obtained from the project website at: http://mzmine.sourceforge.net/. The current version of MZmine 2 is suitable for processing large batches of data and has been applied to both targeted and non-targeted metabolomic analyses.

  1. Digging process in NGC 6951: the molecular disc bumped by the jet

    May, D.; Steiner, J. E.; Ricci, T. V.; Menezes, R. B.; Andrade, I. S.

    2016-03-01

    We present a study of the central 200 pc of the galaxy NGC 6951, SAB(rs)bc, an active twin of the Milky Way, at a distance of 24 Mpc. Its nucleus has been observed in the optical with the Integral Field Unit of the Gemini Multi-Object Spectrograph, showing an outflow, and with the HST/ACS, revealing two extended structures with similar orientation, suggesting the presence of a collimating and/or obscuring structure. In order to ascertain this hypothesis, adaptive optics assisted NIR integral field spectroscopic observations were obtained with the Near-Infrared Integral Field Spectrograph in the Gemini North telescope. We detected a compact structure of H2 molecular gas, interpreted as a nearly edge-on disc with diameter of ˜47 pc, PA = 124° and velocity range from -40 to +40 km s-1. This disc is misaligned by 32° with respect to the radio jet and the ionization cones seen in the optical. There are two regions of turbulent gas, with position angles similar to the jet/cones, seen both in molecular and ionized phases; these regions are connected to the edges of the molecular disc and coincide with a high ratio of [N II]/H α = 5, suggesting that these regions are shock excited, partially ionized or both. We explain these structures as a consequence of a `digging process' that the jet inflicts on the disc, ejecting the molecular gas towards the ionization cones. The dynamical mass within 17 pc is estimated as 6.3 × 106 M⊙. This is an interesting case of an object presenting evidence of a connected feeding-feedback structure.

  2. Towards system-level understanding of baculovirus host cell interactions: from molecular fundamental studies to large-scale proteomics approaches

    FranciscaMonteiro; ManuelJosé TeixeiraCarrondo; VicenteBernal

    2012-01-01

    Baculoviruses are insect viruses extensively exploited as eukaryotic protein expression vectors. Molecular biology studies have provided exciting discoveries on virus-host interactions, but the application of omic high throughput techniques on the baculovirus-insect cell system has been hampered by the lack of host genome sequencing. While a broader, systems level analysis of biological responses to infection is urgently needed, recent advances on proteomic studies have yielded new insights o...

  3. Effects of Freshwater Pollution on the Genetics of Zebra Mussels (Dreissena polymorpha) at the Molecular and Population Level

    Emilia G. Thomas; Maja Šrut; Anamaria Štambuk; Göran I. V. Klobučar; Alfred Seitz; Eva Maria Griebeler

    2014-01-01

    Revealing long-term effects of contaminants on the genetic structure of organisms inhabiting polluted environments should encompass analyses at the population, molecular, and cellular level. Following this concept, we studied the genetic constitution of zebra mussel populations from a polluted (Dp) and reference sites (Cl) at the river Drava, Croatia, and applied microsatellite and DNA damage analyses (Comet assay, micronucleus test (MNT)). Additionally, mussels from both populations were exp...

  4. PET molecular imaging of peripheral and central inflammatory processes targeting the TSPO 18 kDa

    The purpose of this study was to determine the in vivo potential of the TSPO 18 kDa as a bio-marker of inflammation, with the use of its radioligand [18F]DPA-714, to non-invasively quantify the inflammatory state within the scope of various pathologies. Multiple animal models of various inflammatory diseases, to include: inflammatory bowel disease, neuro-inflammation, and septic shock, were developed and put in place by adapted measures. The animals well-being and the subsequent inflammation was evaluated. The inflammatory state was measured using quantitative PET imaging with the TSPO radioligand [18F]DPA-714 and correlated to the expression of conventional inflammatory markers using microscopy. Based on the observed data, we were able to distinguish control groups from treated groups when using [18F]DPA-714. This TSPO radioligand permitted us to quantify the inflammatory level and to observe evolutionary changes in the inflammatory state of the disease in multiple models. The PET results, using the [18F]DPA-714 signal was correlated with an increased TSPO expression at cellular level. Results indicate that [18F]DPA-714 is a suitable tracer for studying inflammation of multiple diseases. [18F]DPA-714 could be a good molecular probe to non-invasively evaluate the level and localization of inflammation. Moreover, in vivo imaging using this TSPO ligand is potentially a powerful tool to stage and certainly to follow the evolution and therapeutic efficiency at molecular level in inflammatory diseases. (author)

  5. Dialkylthio Substitution: An Effective Method to Modulate the Molecular Energy Levels of 2D-BDT Photovoltaic Polymers.

    Yao, Huifeng; Zhang, Hao; Ye, Long; Zhao, Wenchao; Zhang, Shaoqing; Hou, Jianhui

    2016-02-17

    Dialkylthio-substituted thienyl-benzodithiophene (BDT-DST) was designed and synthesized as a building block to modulate the molecular levels of the conjugated polymers, and three copolymers named PDST-BDD, PDST-TT and PDST-DPP were prepared and applied in polymer solar cells (PSCs). Theoretical calculations and electrochemical cyclic voltammetry (CV) measurement suggested that the dialkylthio group could decrease the molecular energy levels of the resulting polymers distinctly. The open-circuit voltage (VOC) of PSC devices based on PDST-BDD, PDST-TT, and PDST-DPP are as high as 1.0, 0.98, and 0.88 V, respectively, which are ?0.15 V higher than those of the corresponding alky-substituted analogues. Moreover, the influence of the dialkylthio group on the absorption spectra, crystalline properties, hole mobilities, and blend morphologies of the polymers was also investigated. The results indicate that the dialkythio substitution is an effective method to modulate the molecular energy levels and that the BDT-DST unit has potential for constructing high-efficiency photovoltaic polymers. PMID:26359953

  6. Spectroscopic investigations on the interactions between isopropanol and trypsin at molecular level

    Hu, Xinxin; Yu, Zehua; Liu, Rutao

    2013-05-01

    The toxicity of hydroxyl group of isopropanol to trypsin in aqueous solution was investigated by techniques including UV-visible absorption spectroscopy, fluorescence spectroscopy, circular dichroism (CD) spectroscopy, enzyme activity assay and molecular docking technology. The results of UV-visible absorption spectroscopy and CD spectra indicate that isopropanol could change the secondary structure of trypsin by increasing the content of α-helix and decreasing the content of β-sheet. The tertiary structure of trypsin was also changed owing to the loss of environmental asymmetry of amino acid residues. Isopropanol bound into a hydrophobic cavity on the surface of trypsin by a hydrogen bond located between the hydrogen atom on the hydroxyl of isopropanol and the oxygen atoms on SER 214 and hydrophobic interaction, as the molecular docking results showed. In addition, isopropanol could affect the function of trypsin by increasing its catalytic activity.

  7. Thickness control of molecular beam epitaxy grown layers at the 0.01–0.1 monolayer level

    Electron tunnelling through semiconductor tunnel barriers is exponentially sensitive to the thickness of the barrier layer, and in the most common system, the AlAs tunnel barrier in GaAs, a one monolayer variation in thickness results in a 300% variation in the tunnelling current for a fixed bias voltage. We use this degree of sensitivity to demonstrate that the level of control at 0.06 monolayer can be achieved in the growth by molecular beam epitaxy, and the geometrical variation of layer thickness across a wafer at the 0.01 monolayer level can be detected. (paper)

  8. Failure of single electron descriptions of molecular orbital collision processes. [Electron promotion mechanism

    Elston, S.B.

    1978-01-01

    Inner-shell excitation occurring in low and moderate (keV range) energy collisions between light atomic and ionic systems is frequently describable in terms of molecular promotion mechanisms, which were extensively explored both theoretically and experimentally. The bulk of such studies have concentrated on processes understandable through the use of single- and independent-electron models. Nonetheless, it is possible to find cases of inner-shell excitation in relatively simple collision systems which involve nearly simultaneous multiple-electron transitions and transitions induced by inherently two-electron interactions. Evidence for these many- and nonindependent-electron phenomena in inner-shell excitation processes and the importance of considering such effects in the interpretation of collisionally induced excitation spectra is discussed. 13 references.

  9. Wavelet analysis of molecular dynamics: Efficient extraction of time-frequency information in ultrafast optical processes

    Prior, Javier; Castro, Enrique [Departamento de Física Aplicada, Universidad Politécnica de Cartagena, Cartagena 30202 (Spain); Chin, Alex W. [Theory of Condensed Matter Group, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE (United Kingdom); Almeida, Javier; Huelga, Susana F.; Plenio, Martin B. [Institut für Theoretische Physik, Albert-Einstein-Allee 11, Universität Ulm, D-89069 Ulm (Germany)

    2013-12-14

    New experimental techniques based on nonlinear ultrafast spectroscopies have been developed over the last few years, and have been demonstrated to provide powerful probes of quantum dynamics in different types of molecular aggregates, including both natural and artificial light harvesting complexes. Fourier transform-based spectroscopies have been particularly successful, yet “complete” spectral information normally necessitates the loss of all information on the temporal sequence of events in a signal. This information though is particularly important in transient or multi-stage processes, in which the spectral decomposition of the data evolves in time. By going through several examples of ultrafast quantum dynamics, we demonstrate that the use of wavelets provide an efficient and accurate way to simultaneously acquire both temporal and frequency information about a signal, and argue that this greatly aids the elucidation and interpretation of physical process responsible for non-stationary spectroscopic features, such as those encountered in coherent excitonic energy transport.

  10. Statistical mechanics of neocortical interactions: Large-scale EEG influences on molecular processes.

    Ingber, Lester

    2016-04-21

    Calculations further support the premise that large-scale synchronous firings of neurons may affect molecular processes. The context is scalp electroencephalography (EEG) during short-term memory (STM) tasks. The mechanism considered is Π=p+qA (SI units) coupling, where p is the momenta of free Ca(2+) waves, q the charge of Ca(2+) in units of the electron charge, and A the magnetic vector potential of current I from neuronal minicolumnar firings considered as wires, giving rise to EEG. Data has processed using multiple graphs to identify sections of data to which spline-Laplacian transformations are applied, to fit the statistical mechanics of neocortical interactions (SMNI) model to EEG data, sensitive to synaptic interactions subject to modification by Ca(2+) waves. PMID:26874226

  11. Induction and reversion process of molecular and cytological alterations after highly irradiated food ingestion in mice

    The molecular and cytological alterations induced in a mammal (Mus musculus) fed ad libitum with a balanced pellet diet irradiated with 50 KGy gamma radiation from weaning, for different periods, are analyzed. The transient chromosomal changes that recall tumor-like phenomena could be the expression of the damage and repair processes induced by changed molecules present in irradiated food. The reversible alterations of DNA structure and cytoplasmatic soluble proteins observed in mice fed with irradiated pellet diet could be interpreted as a result of the enhancement of the repair processes which could also explain the significant increase of the radioresistance of DNA found at 200 days after irradiated food ingestion. Finally, our results would suggest an induction of a pseudo-neoplasia due to a prolongated and exclusive ingestion of food irradiated with sterilizing gamma dose. Moreover, the maintenance of the irradiated diet induce the reversion of the observed phenomena by an eventual activation of the repair mechanisms. (Author)

  12. Molecular Interdiffusion between Stacked Layers by Solution and Thermal Annealing Processes in Organic Light Emitting Devices.

    Ohisa, Satoru; Pu, Yong-Jin; Yamada, Norifumi L; Matsuba, Go; Kido, Junji

    2015-09-23

    In organic light emitting devices (OLEDs), interfacial structures between multilayers have large impacts on the characteristics of OLEDs. Herein, we succeeded in revealing the interdiffusion in solution processed and thermal annealed OLEDs by neutron reflectometry. We investigated interfaces between a polymer under layer and small molecules upper layer. The small molecules diffused into the swollen polymer layer during the interfacial formation by the solution process, but the polymer did not diffuse into the small molecules layer. At temperatures close to the glass transition temperatures of the materials, asymmetric molecular diffusion was observed. We elucidated the effects of the interdiffusion on the characteristics of OLEDs. Partially mixing the interface improved the current efficiencies due to suppressed triplet-polaron quenching at the interface. Controlling and understanding the interfacial structures of the miultilayers will be more important to improve the OLED characteristics. PMID:26331696

  13. Femtosecond Laser Processing of Germanium: An Ab Initio Molecular Dynamics Study

    Ji, Pengfei

    2016-01-01

    An ab initio molecular dynamics study of femtosecond laser processing of germanium is presented in this paper. The method based on the finite temperature density functional theory is adopted to probe the structural change, thermal motion of the atoms, dynamic property of the velocity autocorrelation, and the vibrational density of states. Starting from a cubic system at room temperature (300 K) containing 64 germanium atoms with an ordered arrangement of 1.132 nm in each dimension, the femtosecond laser processing is simulated by imposing the Nose Hoover thermostat to the electronic subsystem lasting for ~100 fs and continuing with microcanonical ensemble simulation of ~200 fs. The simulation results show solid, liquid and gas phases of germanium under adjusted intensities of the femtosecond laser irradiation. We find the irradiated germanium distinguishes from the usual germanium crystal by analyzing their melting and dynamic properties.

  14. Anthraquinone-based demultiplexer and other multiple operations at the molecular level

    Navneet Kaur; Subodh Kumar

    2014-01-01

    Anthraquinone-based chemosensor L with pyridine units as additional functional groups has been found to show pH-dependent multiple coordinationmodes towards differentmetal ions (Co2+, Ni2+ and Cu2+). Based on these different absorption changes, this differential colorimetric chemosensor L has found promising applications as a multiple-mode molecular logic system, i.e., OR, three - input NOR, three - input INHIBIT, TRANSFER and 1:2 DEMUX.

  15. MILLIMETER-SCALE GENETIC GRADIENTS AND COMMUNITY-LEVEL MOLECULAR CONVERGENCE IN A HYPERSALINE MICROBIAL MAT

    Fenner, Marsha W; Kunin, Victor; Raes, Jeroen; Harris, J. Kirk; Spear, John R.; Walker, Jeffrey J.; Ivanova, Natalia; Mering, Christian von; Bebout, Brad M.; Pace, Norman R.; Bork, Peer; Hugenholtz, Philip

    2008-04-30

    To investigate the extent of genetic stratification in structured microbial communities, we compared the metagenomes of 10 successive layers of a phylogenetically complex hypersaline mat from Guerrero Negro, Mexico. We found pronounced millimeter-scale genetic gradients that are consistent with the physicochemical profile of the mat. Despite these gradients, all layers displayed near identical and acid-shifted isoelectric point profiles due to a molecular convergence of amino acid usage indicating that hypersalinity enforces an overriding selective pressure on the mat community.

  16. Molecular Tools for the Selective Detection of Nine Diatom Species Biomarkers of Various Water Quality Levels

    Lucia Cimarelli; Kumar Saurabh Singh; Nguyen Thi Nhu Mai; Bidhan Chandra Dhar; Anna Brandi; Letizia Brandi; Roberto Spurio

    2015-01-01

    Our understanding of the composition of diatom communities and their response to environmental changes is currently limited by laborious taxonomic identification procedures. Advances in molecular technologies are expected to contribute more efficient, robust and sensitive tools for the detection of these ecologically relevant microorganisms. There is a need to explore and test phylogenetic markers as an alternative to the use of rRNA genes, whose limited sequence divergence does not allow the...

  17. Einstein–Bohr recoiling double-slit gedanken experiment performed at the molecular level

    Liu, X-J; Miao, Q.; Gel'mukhanov, F.; Patanen, M.; Travnikova, O; C. Nicolas; Ågren, H; Ueda, K.; Miron, C.

    2015-01-01

    Double-slit experiments illustrate proof for wave–particle complementarity. The essence of Einstein–Bohr's debate about wave–particle duality was whether the momentum transfer between a particle and a recoiling slit could mark the path, thus destroying the interference. We realized this recoiling double-slit gedanken experiment by resonant X-ray photoemission from molecular oxygen for geometries near equilibrium (coupled slits) and in a dissociative state far away from equilibrium (decoupled ...

  18. Ultrasmall volume molecular isothermal amplification in microfluidic chip with advanced surface processing

    In this paper, we developed a metal micro-fluidic chip with advanced surface processing for ultra-small volume molecular isothermal amplification. This method takes advantages of the nucleic acid amplification with good stability and consistency, high sensitivity about 31 genomic DNA copies and bacteria specific gene identification. Based on the advanced surface processing, the bioreaction assays of nucleic acid amplification was dropped about 392nl in volume. A high numerical aperture confocal optical detection system was advanced to sensitively monitor the DNA amplification with low noise and high power collecting fluorescence near to the optical diffraction limit. A speedy nucleic acid isothermal amplification was performed in the ultra-small volume microfluidic chip, where the time at the inflexions of second derivative to DNA exponential amplified curves was brought forward and the sensitivity was improved about 65 folds to that of in current 25μl Ep-tube amplified reaction, which indicates a promising clinic molecular diagnostics in the droplet amplification.

  19. Molecular dynamics simulation of the melting process in Ag27Cu13 coreshell nanoalloy

    Highlights: Melting process of Ag27Cu13 nanoalloy is studied by molecular dynamics simulation. Different criteria are used to analyze thermal behavior of nanoalloy. Steepest descent quenching method coupled to the isothermal MD simulations. Multiple histogram method is used to remove the non-ergodicity problem. - Abstract: Molecular dynamics simulation in NVT ensemble coupled to steepest descent quenching method for studying melting mechanism of Ag27Cu13 nanoalloy, using thermodynamical, geometrical and dynamical criteria. Heat capacity values showed a strong fluctuation at temperatures of the phase coexistence region due to non-ergodicity in the simulation. Hence, in order to remove the non-ergodicity problem, multiple histogram method has been used. Heat capacity curve shows a shoulder peak at 620 K due to pre-melting of the surface atoms. Furthermore, at T = 840 K the melting behavior intensity of the atoms reaches to its maximum value, indicating that the melting process is completed. Considering the melting of 620 K for the nanoalloy, Lindemann parameter showed solidsolid isomerization at T = 480 K. Calculating ?shell and ?core proved that the corresponding solidsolid isomerization is only due to the shell atoms rearrangement. This fact is verified by quenching the configuration of the atoms by using steepest descent quenching method as well

  20. Quantum control of a molecular ionization process by using Fourier-synthesized laser fields

    Ohmura, Hideki; Saito, Naoaki

    2015-11-01

    In photoexcitation processes, if the motion of excited electrons can be precisely steered by the instantaneous electric field of an arbitrary waveform of a Fourier-synthesized laser field, the resultant matter response can be achieved within one optical cycle, usually within the attosecond (1 as =10-18s) regime. Fourier synthesis of laser fields has been achieved in various ways. However, the general use of Fourier-synthesized laser fields for the control of matter is extremely limited. Here, we report the quantum control of a nonlinear response of a molecular ionization process by using Fourier-synthesized laser fields. The directionally asymmetric molecular tunneling ionization induced by intense (5.0 ×1012W /c m2) Fourier-synthesized laser fields consisting of fundamental, second-, third-, and fourth-harmonic light achieves the orientation-selective ionization; we utilized the orientation-selective ionization for measurement of the relative phase differences between the fundamental and each harmonic light. Our findings impact not only light-wave engineering but also the control of matter, possibly triggering the creation and establishment of a new methodology that uses Fourier-synthesized laser fields.

  1. Global plant-responding mechanisms to salt stress: physiological and molecular levels and implications in biotechnology.

    Tang, Xiaoli; Mu, Xingmin; Shao, Hongbo; Wang, Hongyan; Brestic, Marian

    2015-12-01

    The increasing seriousness of salinization aggravates the food, population and environmental issues. Ameliorating the salt-resistance of plants especially the crops is the most effective measure to solve the worldwide problem. The salinity can cause damage to plants mainly from two aspects: hyperosmotic and hyperionic stresses leading to the restrain of growth and photosynthesis. To the adverse effects, the plants derive corresponding strategies including: ion regulation and compartmentalization, biosynthesis of compatible solutes, induction of antioxidant enzymes and plant hormones. With the development of molecular biology, our understanding of the molecular and physiology knowledge is becoming clearness. The complex signal transduction underlying the salt resistance is being illuminated brighter and clearer. The SOS pathway is the central of the cell signaling in salt stress. The accumulation of the compatible solutes and the activation of the antioxidant system are the effective measures for plants to enhance the salt resistance. How to make full use of our understanding to improve the output of crops is a huge challenge for us, yet the application of the genetic engineering makes this possible. In this review, we will discuss the influence of the salt stress and the response of the plants in detail expecting to provide a particular account for the plant resistance in molecular, physiological and transgenic fields. PMID:24738851

  2. Optimization of preservation and processing of sea anemones for microbial community analysis using molecular tools.

    Rocha, Joana; Coelho, Francisco J R C; Peixe, Luísa; Gomes, Newton C M; Calado, Ricardo

    2014-01-01

    For several years, knowledge on the microbiome associated with marine invertebrates was impaired by the challenges associated with the characterization of bacterial communities. With the advent of culture independent molecular tools it is possible to gain new insights on the diversity and richness of microorganisms associated with marine invertebrates. In the present study, we evaluated if different preservation and processing methodologies (prior to DNA extraction) can affect the bacterial diversity retrieved from snakelocks anemone Anemonia viridis. Denaturing gradient gel electrophoresis (DGGE) community fingerprints were used as proxy to determine the bacterial diversity retrieved (H'). Statistical analyses indicated that preservation significantly affects H'. The best approach to preserve and process A. viridis biomass for bacterial community fingerprint analysis was flash freezing in liquid nitrogen (preservation) followed by the use of a mechanical homogenizer (process), as it consistently yielded higher H'. Alternatively, biomass samples can be processed fresh followed by cell lyses using a mechanical homogenizer or mortar &pestle. The suitability of employing these two alternative procedures was further reinforced by the quantification of the 16S rRNA gene; no significant differences were recorded when comparing these two approaches and the use of liquid nitrogen followed by processing with a mechanical homogenizer. PMID:25384534

  3. Study the sensitivity of molecular functional groups to bioethanol processing in lipid biopolymer of co-products using DRIFT molecular spectroscopy

    Yu, Peiqiang

    2011-11-01

    To date, there is no study on bioethanol processing-induced changes in molecular structural profiles mainly related to lipid biopolymer. The objectives of this study were to: (1) determine molecular structural changes of lipid related functional groups in the co-products that occurred during bioethanol processing; (2) relatively quantify the antisymmetric CH 3 and CH 2 (ca. 2959 and 2928 cm -1, respectively), symmetric CH 3 and CH 2 (ca. 2871 and 2954 cm -1, respectively) functional groups, carbonyl C dbnd O ester (ca. 1745 cm -1) and unsaturated groups (CH attached to C dbnd C) (ca. 3007 cm -1) spectral intensities as well as their ratios of antisymmetric CH 3 to antisymmetric CH 2, and (3) illustrate the molecular spectral analyses as a research tool to detect for the sensitivity of individual moleculars to the bioethanol processing in a complex plant-based feed and food system without spectral parameterization. The hypothesis of this study was that bioethanol processing changed the molecular structure profiles in the co-products as opposed to original cereal grains. These changes could be detected by infrared molecular spectroscopy and will be related to nutrient utilization. The results showed that bioethanol processing had effects on the functional groups spectral profiles in the co-products. It was found that the CH 3-antisymmetric to CH 2-antisymmetric stretching intensity ratio was changed. The spectral features of carbonyl C dbnd O ester group and unsaturated group were also different. Since the different types of cereal grains (wheat vs. corn) had different sensitivity to the bioethanol processing, the spectral patterns and band component profiles differed between their co-products (wheat DDGS vs. corn DDGS). The multivariate molecular spectral analyses, cluster analysis and principal component analysis of original spectra (without spectral parameterization), distinguished the structural differences between the wheat and wheat DDGS and between the corn and corn DDGS in the antisymmetric and symmetric CH 3 and CH 2 spectral region (ca. 2994-2800 cm -1) and unsaturated group band region (3025-2996 cm -1). Further study is needed to quantify molecular structural changes in relation to nutrient utilization of lipid biopolymer.

  4. Molecular mechanism of the adsorption process of an iodide anion into liquid-vapor interfaces of water-methanol mixtures

    Annapureddy, Harsha V. R.; Dang, Liem X.

    2012-12-01

    To enhance our understanding of the molecular mechanism of ion adsorption to the interface of mixtures, we systematically carried out a free energy calculations study involving the transport of an iodide anion across the interface of a water-methanol mixture. Many body affects are taken into account to describe the interactions among the species. The surface propensities of I- at interfaces of pure water and methanol are well understood. In contrast, detailed knowledge of the molecular level adsorption process of I- at aqueous mixture interfaces has not been reported. In this paper, we explore how this phenomenon will be affected for mixed solvents with varying compositions of water and methanol. Our potential of mean force study as function of varying compositions indicated that I- adsorption free energies decrease from pure water to pure methanol but not linearly with the concentration of methanol. We analyze the computed density profiles and hydration numbers as a function of concentrations and ion positions with respect to the interface to further explain the observed phenomenon.

  5. Molecular Mechanism of the Adsorption Process of an Iodide Anion into Liquid-Vapor Interfaces of Water-Methanol Mixtures

    Annapureddy, Harsha V.; Dang, Liem X.

    2012-12-07

    To enhance our understanding of the molecular mechanism of ion adsorption to the interface of mixtures, we systematically carried out a free energy calculations study involving the transport of an iodide anion across the interface of a water-methanol mixture. Many body affects are taken into account to describe the interactions among the species. The surface propensities of I- at interfaces of pure water and methanol are well understood. In contrast, detailed knowledge of the molecular level adsorption process of I- at aqueous mixture interfaces has not been reported. In this paper, we explore how this phenomenon will be affected for mixed solvents with varying compositions of water and methanol. Our potential of mean force study as function of varying compositions indicated that I- adsorption free energies decrease from pure water to pure methanol but not linearly with the concentration of methanol. We analyze the computed density profiles and hydration numbers as a function of concentrations and ion positions with respect to the interface to further explain the observed phenomenon. This work was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences (BES), Division of Chemical Sciences, Geosciences, and Biosciences. Pacific Northwest National Laboratory is a multiprogram national laboratory operated for DOE by Battelle. The calculations were carried out using computer resources provided by BES.

  6. Low-level wastewater treatment facility process control operational test report

    Bergquist, G.G.

    1996-04-08

    This test report documents the results obtained while conducting operational testing of a new TK 102 level controller and total outflow integrator added to the NHCON software that controls the Low-Level Wastewater Treatment Facility (LLWTF). The test was performed with WHC-SD-CP-OTP 154, PFP Low-Level Wastewater Treatment Facility Process Control Operational Test. A complete test copy is included in appendix A. The new TK 102 level controller provides a signal, hereafter referred to its cascade mode, to the treatment train flow controller which enables the water treatment process to run for long periods without continuous operator monitoring. The test successfully demonstrated the functionality of the new controller under standard and abnormal conditions expected from the LLWTF operation. In addition, a flow totalizer is now displayed on the LLWTF outlet MICON screen which tallies the process output in gallons. This feature substantially improves the ability to retrieve daily process volumes for maintaining accurate material balances.

  7. Low-level wastewater treatment facility process control operational test report

    This test report documents the results obtained while conducting operational testing of a new TK 102 level controller and total outflow integrator added to the NHCON software that controls the Low-Level Wastewater Treatment Facility (LLWTF). The test was performed with WHC-SD-CP-OTP 154, PFP Low-Level Wastewater Treatment Facility Process Control Operational Test. A complete test copy is included in appendix A. The new TK 102 level controller provides a signal, hereafter referred to its cascade mode, to the treatment train flow controller which enables the water treatment process to run for long periods without continuous operator monitoring. The test successfully demonstrated the functionality of the new controller under standard and abnormal conditions expected from the LLWTF operation. In addition, a flow totalizer is now displayed on the LLWTF outlet MICON screen which tallies the process output in gallons. This feature substantially improves the ability to retrieve daily process volumes for maintaining accurate material balances

  8. Algorithms and programs for processing of satellite data on ozone layer and UV radiation levels

    Some algorithms and programs for automatic retrieving and processing ozone layer satellite data are discussed. These techniques are used for reliable short-term UV-radiation levels forecasting. (authors)

  9. Multi-level Governance and Security: The Security Sector Reform Process in the Central African Republic

    BAGAYOKO-PENONE, Niagalé

    2010-01-01

    Analysing how the SSR process in CAR has been defined and then implemented, this article puts emphasis on the international interactions between institutional actors who may be geographically/territorially situated at different levels of the policy-making process in different places around the world, thus suggesting ways to grasp multi-actor and multi-sited governance. Therefore, it advocates an approach which consists of expanding the agenda of the traditional multi-level governance approach...

  10. An instrumentation and control philosophy for high-level nuclear waste processing facilities

    The purpose of this paper is to present an instrumentation and control philosophy which may be applied to high-level nuclear waste processing facilities. This philosophy describes the recommended criteria for automatic/manual control, remote/local control, remote/local display, diagnostic instrumentation, interlocks, alarm levels, and redundancy. Due to the hazardous nature of the process constituents of a high-level nuclear waste processing facility, it is imperative that safety and control features required for accident-free operation and maintenance be incorporated. A well-instrumented and controlled process, while initially more expensive in capital and design costs, is generally safer and less expensive to operate. When the long term cost savings of a well designed process is coupled with the high savings enjoyed by accident avoidance, the benefits far outweigh the initial capital and design costs

  11. Paving the Way to Understand Autoantibody-Mediated Epilepsy on the Molecular Level.

    Seebohm, Guiscard; Piccini, Ilaria; Strutz-Seebohm, Nathalie

    2015-01-01

    Correct function of neuronal networks is enabled by a delicate interplay among neurons communicating with each other. One of the keys is the communication at chemical synapses where neurotransmitters like glutamate, GABA, and glycine enable signal transfer over the synaptic cleft. Thereby, the neurotransmitters are released from the presynapse and bind as ligands to specific receptors at the postsynaptic side to allow for modulation of the postsynaptic membrane potentials. The postsynaptic electrical signal, which is highly modulated by voltage-gated ion channels, spreads over the dendritic tree and is thus integrated to allow for generation of action potentials at the axon hillock. This concert of receptors and voltage-gated ion channels depends on correct function of all its components. Misfunction of receptors and/or voltage-gated potassium channels (VGKC) leads to diverse adverse effects in patients. Such malfunctions can be the result of inherited genetic alterations or pharmacological side effects by drugs. Recently, autoantibodies targeting receptor or channel complexes like NMDAR, AMPAR, GABA-receptors, glycine receptors, LGI1 or CASPR2 (previously termed as VGKC-complex antibodies) have been discovered. The presence of specific autoantibodies against these targets associates with severe forms of antibody-mediated encephalitis. Understanding the molecular details of autoantibody actions on receptor and VGKC complexes is highly desirable and may open the path to develop specific therapies to treat humoral autoimmune encephalitis. Here, we summarize the current knowledge and discuss technical approaches to fill the gap of knowledge. These techniques include electrophysiology, biochemical approaches for epitope mapping, and in silico modeling to simulate molecular interactions between autoantibody and its molecular target. PMID:26217297

  12. ToF-SIMS imaging of molecular-level alteration mechanisms in Le Bonheur de vivre by Henri Matisse

    Voras, Zachary E.; Wiggins, Marcie B.; Beebe, Thomas P. [University of Delaware, Department of Chemistry and Biochemistry, Newark, DE (United States); University of Delaware, UD Surface Analysis Facility, Newark, DE (United States); DeGhetaldi, Kristin [University of Delaware, Department of Art Conservation, Newark, DE (United States); Winterthur-University of Delaware Program in Art Conservation, Winterthur, DE (United States); Buckley, Barbara [The Barnes Foundation, Department of Conservation, Philadelphia, PA (United States); Baade, Brian [University of Delaware, Department of Art Conservation, Newark, DE (United States); Mass, Jennifer L. [Winterthur Museum, Scientific Research and Analysis Laboratory, Conservation Department, Winterthur, DE (United States)

    2015-11-15

    Time-of-flight secondary ion mass spectrometry (ToF-SIMS) has recently been shown to be a valuable tool for cultural heritage studies, especially when used in conjunction with established analytical techniques in the field. The ability of ToF-SIMS to simultaneously image inorganic and organic species within a paint cross section at micrometer-level spatial resolution makes it a uniquely qualified analytical technique to aid in further understanding the processes of pigment and binder alteration, as well as pigment-binder interactions. In this study, ToF-SIMS was used to detect and image both molecular and elemental species related to CdS pigment and binding medium alteration on the painting Le Bonheur de vivre (1905-1906, The Barnes Foundation) by Henri Matisse. Three categories of inorganic and organic components were found throughout Le Bonheur de vivre and co-localized in cross-sectional samples using high spatial resolution ToF-SIMS analysis: (1) species relating to the preparation and photo-induced oxidation of CdS yellow pigments (2) varying amounts of long-chain fatty acids present in both the paint and primary ground layer and (3) specific amino acid fragments, possibly relating to the painting's complex restoration history. ToF-SIMS's ability to discern both organic and inorganic species via cross-sectional imaging was used to compare samples collected from Le Bonheur de vivre to artificially aged reference paints in an effort to gather mechanistic information relating to alteration processes that have been previously explored using μXANES, SR-μXRF, SEM-EDX, and SR-FTIR. The relatively high sensitivity offered by ToF-SIMS imaging coupled to the high spatial resolution allowed for the positive identification of degradation products (such as cadmium oxalate) in specific paint regions that have before been unobserved. The imaging of organic materials has provided an insight into the extent of destruction of the original binding medium, as well as identifying unexpected organic materials in specific paint layers. (orig.)

  13. ToF-SIMS imaging of molecular-level alteration mechanisms in Le Bonheur de vivre by Henri Matisse

    Time-of-flight secondary ion mass spectrometry (ToF-SIMS) has recently been shown to be a valuable tool for cultural heritage studies, especially when used in conjunction with established analytical techniques in the field. The ability of ToF-SIMS to simultaneously image inorganic and organic species within a paint cross section at micrometer-level spatial resolution makes it a uniquely qualified analytical technique to aid in further understanding the processes of pigment and binder alteration, as well as pigment-binder interactions. In this study, ToF-SIMS was used to detect and image both molecular and elemental species related to CdS pigment and binding medium alteration on the painting Le Bonheur de vivre (1905-1906, The Barnes Foundation) by Henri Matisse. Three categories of inorganic and organic components were found throughout Le Bonheur de vivre and co-localized in cross-sectional samples using high spatial resolution ToF-SIMS analysis: (1) species relating to the preparation and photo-induced oxidation of CdS yellow pigments (2) varying amounts of long-chain fatty acids present in both the paint and primary ground layer and (3) specific amino acid fragments, possibly relating to the painting's complex restoration history. ToF-SIMS's ability to discern both organic and inorganic species via cross-sectional imaging was used to compare samples collected from Le Bonheur de vivre to artificially aged reference paints in an effort to gather mechanistic information relating to alteration processes that have been previously explored using μXANES, SR-μXRF, SEM-EDX, and SR-FTIR. The relatively high sensitivity offered by ToF-SIMS imaging coupled to the high spatial resolution allowed for the positive identification of degradation products (such as cadmium oxalate) in specific paint regions that have before been unobserved. The imaging of organic materials has provided an insight into the extent of destruction of the original binding medium, as well as identifying unexpected organic materials in specific paint layers. (orig.)

  14. ToF-SIMS imaging of molecular-level alteration mechanisms in Le Bonheur de vivre by Henri Matisse

    Voras, Zachary E.; deGhetaldi, Kristin; Wiggins, Marcie B.; Buckley, Barbara; Baade, Brian; Mass, Jennifer L.; Beebe, Thomas P.

    2015-11-01

    Time-of-flight secondary ion mass spectrometry (ToF-SIMS) has recently been shown to be a valuable tool for cultural heritage studies, especially when used in conjunction with established analytical techniques in the field. The ability of ToF-SIMS to simultaneously image inorganic and organic species within a paint cross section at micrometer-level spatial resolution makes it a uniquely qualified analytical technique to aid in further understanding the processes of pigment and binder alteration, as well as pigment-binder interactions. In this study, ToF-SIMS was used to detect and image both molecular and elemental species related to CdS pigment and binding medium alteration on the painting Le Bonheur de vivre (1905-1906, The Barnes Foundation) by Henri Matisse. Three categories of inorganic and organic components were found throughout Le Bonheur de vivre and co-localized in cross-sectional samples using high spatial resolution ToF-SIMS analysis: (1) species relating to the preparation and photo-induced oxidation of CdS yellow pigments (2) varying amounts of long-chain fatty acids present in both the paint and primary ground layer and (3) specific amino acid fragments, possibly relating to the painting's complex restoration history. ToF-SIMS's ability to discern both organic and inorganic species via cross-sectional imaging was used to compare samples collected from Le Bonheur de vivre to artificially aged reference paints in an effort to gather mechanistic information relating to alteration processes that have been previously explored using μXANES, SR-μXRF, SEM-EDX, and SR-FTIR. The relatively high sensitivity offered by ToF-SIMS imaging coupled to the high spatial resolution allowed for the positive identification of degradation products (such as cadmium oxalate) in specific paint regions that have before been unobserved. The imaging of organic materials has provided an insight into the extent of destruction of the original binding medium, as well as identifying unexpected organic materials in specific paint layers.

  15. Selected materials of the international workshop on radiation risk and its origin at molecular and cellular level

    The workshop ''International Workshop on Radiation Risk and its Origin at Molecular and Cellular Level'' was held at The Tokai Research Establishment, Japan Atomic Energy Research Institute, on the 6th and 7th of February 2003. The Laboratory of Radiation Risk Analysis of JAERI organized it. This international workshop attracted scientists from several different scientific areas, including radiation physics, radiation biology, molecular biology, crystallography of biomolecules, modeling and bio-informatics. Several foreign and domestic keynote speakers addresses the very fundamental areas of radiation risk and tried to establish a link between the fundamental studies at the molecular and cellular level and radiation damages at the organism. The symposium consisted of 13 oral lectures, 10 poster presentations and panel discussion. The 108 participants attended the workshop. This publication comprises of proceedings of oral and poster presentations where available. For the rest of contributions the abstracts or/and selections of presentation materials are shown instead. The 5 papers are indexed individually. (J.P.N.)

  16. Glucocorticoid-like effects of antihepatocarcinogen Rotenone are mediated via enhanced serum corticosterone levels: Molecular Fitting and Receptor Activation Studies

    Youssef Jihan

    2003-02-01

    Full Text Available Abstract Background Recent studies suggest that rotenone alters cell signal transduction pathways in a manner similar to glucocorticoids. Histological and biochemical markers of glucocorticoid effects in vivo, evaluated in our laboratories, provide further evidence for similarities in the activity of glucocorticoids and rotenone. The purpose of this study was to investigate the mechanism by which rotenone produces glucocorticoid-like effects. Methods Male B6C3F1 mice were treated for 7 days with rotenone (600 ppm in diet, the glucocorticoid antagonist RU486 (2 mg/kg/day, ip, corticosterone (2 mg/kg/day, ip, or both rotenone and RU 486. Control mice received drug-free diet and the vehicle (corn oil, ip. Following preservation in 10% neutral buffered formalin, tissues were embedded in paraffin. Sections were stained with hematoxylin, eosin, and were examined by light microscopy. Tissue sections were processed for in situ enzymatic end labeling of 3'-hydroxy-DNA strand breaks, a measure of apoptosis. Corticosterone was quantified in sera, using a solid phase radioimmunoassay kit. Cells (cell line 1470.2 derived from C127 mouse mammary adenocarcinoma cells were transiently transfected with 5 ?g of pLTRLuc and 1 ?g of ?-Galactosidase expression vectors using a BTX square-wave pulser at 155 V, 4 pulses (40 ms each. Cells were then treated with dexamethasone, rotenone, or a mixture of both for 6 hr, harvested and assayed for luciferase and ?-Galactosidase activity. Using Root Mean Square (RMS fit analysis (Alchemy, Tripose, Inc., St Louis, MO, we assessed possible structural similarities between rotenone and corticosterone, dehydrocorticosterone, glucocorticoid antagonists ZK 98.299, and RU 486. RMS fit was calculated by selecting three atoms in each of the molecules, followed by calculating the distance between these atoms. An RMS value of zero between two molecules indicates identical molecular characteristics. A positive value suggests diminished similarity with a value of 1 or higher excluding any such similarities. Results Although the stimulatory effect exerted by rotenone on hepatocellular apoptosis was in the opposite direction of that produced by the glucocorticoid antagonist RU 486, data suggested that rotenone does not directly activate the glucocorticoid receptor. Molecular fitting of rotenone to glucocorticoid receptor agonists and antagonists as well as examination of the transcriptional activation of a glucocorticoid-responsive reporter gene (Mouse MammaryTumorVirus in response to rotenone indicated that it is highly unlikely that rotenone interacts directly with the glucocorticoid receptor. However, feeding male B6C3F1 mice a diet containing rotenone (600 ppm for 7 days resulted in a 3-fold increase in serum levels of corticosterone relative to control animals. Corticosterone is the major glucocorticoid in rodents. Conclusion Rotenone does not interact directly with the glucocorticoid receptor. Elevation of serum corticosterone levels in response to rotenone may explain the glucocorticoid-like effects of this compound, and may play a role in its anti-hepatocarcinogenic effect.

  17. Relationship between processing and mechanical properties of injection molded high molecular mass polyethylene + hydroxyapatite composites

    Reis, R.L.; Cunha, A.M.; Oliveira, M.J.; Campos, A.R. [Dept. of Polymer Engineering, University of Minho, Guimaraes (Portugal); Bevis, M.J. [Wolfson Center for Materials Processing, Brunel Univ., Uxbridge (United Kingdom)

    2001-04-01

    We apply a macromolecular-orientation approach to produce high molecular weight polyethylene (HMWPE) + hydroxyapatite (HA) ductile composites with the stiffness and strength within the range of human cortical bone. Our composites are produced with different amounts (10 to 50% by weight) of the reinforcement by two procedures: bi-axial rotating drum and twin screw extrusion (TSE). The processing is by conventional injection molding and by Scorim (shear controlled orientation in injection molding) under a wide range of processing windows. Tensile testing is performed and the corresponding performance related to the morphology evaluated by polarized light microscopy and scanning electron microscopy. The control of the processing parameters led to significant improvements of the tensile properties. Compounding by TSE and then processing by Scorim produces the maximum modulus of 7.4 GPa and the ductility as high as 19%, for the HA weight fraction of 30%. These mechanical properties match those of bone, and were obtained with much smaller amounts of HA reinforcement then has been previously reported in literature. Our PE + HA composites present the additional benefit of being ductile even for 50% HA amounts. The use Scorim is a unique way of inducing anisotropy to thick sections and to produce very stiff composites that may be used in biomedical applications with important mechanical loads. This fact, combined with the bioactive behavior of the HA phase, makes our composite usable for orthopedic load-bearing implants. (orig.)

  18. Low-Volatility Model Demonstrates Humidity Affects Environmental Toxin Deposition on Plastics at a Molecular Level.

    Hankett, Jeanne M; Collin, William R; Yang, Pei; Chen, Zhan; Duhaime, Melissa

    2016-02-01

    Despite the ever-increasing prevalence of plastic debris and endocrine disrupting toxins in aquatic ecosystems, few studies describe their interactions in freshwater environments. We present a model system to investigate the deposition/desorption behaviors of low-volatility lake ecosystem toxins on microplastics in situ and in real time. Molecular interactions of gas-phase nonylphenols (NPs) with the surfaces of two common plastics, poly(styrene) and poly(ethylene terephthalate), were studied using quartz crystal microbalance and sum frequency generation vibrational spectroscopy. NP point sources were generated under two model environments: plastic on land and plastic on a freshwater surface. We found the headspace above calm water provides an excellent environment for NP deposition and demonstrate significant NP deposition on plastic within minutes at relevant concentrations. Further, NP deposits and orders differently on both plastics under humid versus dry environments. We attributed the unique deposition behaviors to surface energy changes from increased water content during the humid deposition. Lastly, nanograms of NP remained on microplastic surfaces hours after initial NP introduction and agitating conditions, illustrating feasibility for plastic-bound NPs to interact with biota and surrounding matter. Our model studies reveal important interactions between low-volatility environmental toxins and microplastics and hold potential to correlate the environmental fate of endocrine disrupting toxins in the Great Lakes with molecular behaviors. PMID:26752114

  19. SILVER NANOPARTICLES AND EXPERESSION OF MOLECULAR MARKERS IN LYMPHOCYTE ACTIVATION AND MARKER OF AUTOIMMUNE PROCESSES IN PERIPHERAL BLOOD OF PATIENTS WITH VIRAL CORNEAL PATHOLOGY

    Ulyanov V.A.

    2015-08-01

    Full Text Available The influence of the nanoparticles of silver on the expression of molecular markers activation of lymphoid cells CD7+, CD25+, CD38+, CD45+, CD54+, CD95+, CD150+ and CD5+ – marker of the autoimmune process, as well as on phagocytic activity of neutrophils in patients with viral pathologies of the cornea was studied in vitro. In the Laboratory of Immunology, SI Institute of Eye Diseases and Tissue Therapy NAMS of Ukraine was developed technique of cultivation of peripheral blood lymphocytes with immunomodulation drugs, followed by determination of changes in the level of expression of molecular markers of lymphocyte activation. Assessment of the level of expression of molecular markers of activation of peripheral blood lymphocytes was performed method using a panel of monoclonal antibodies, CD5+, CD7+, CD25+, CD38+, CD45+, CD54+, CD95+ and CD 150+. The study was conducted in vitro with the peripheral lymphocytes the blood of 23 patients of viral pathology of the cornea. Our studies of the effects of nanosilver particles in vitro on the state of expression of molecular markers of activation of peripheral blood lymphocytes and phagocytic activity of neutrophils in patients with viral corneal pathology, showed a significant increase in the level of expression of the CD7+, CD25+, CD45+ and phagocytic activity of neutrophils after application silver nanoparticles.

  20. Single-walled carbon nanotube bucky paper/epoxy composites: Molecular dynamics simulation and process development

    Gou, Jihua

    The discovery of carbon nanotubes by Iijima in 1991 has initiated a large number of scientific investigations to explore their unique properties and potential applications. One of the major applications is nanocomposites with nanotubes as the reinforcing material. Currently, nanotube composites are fabricated by using the direct mixing technique. However, this technique is limited by low weight fraction of nanotubes and uncontrollable nanostructures in the composite. This dissertation research presents a new nanocomposite processing method in which single-walled nanotubes (SWNTs) are first preformed into nanotube bucky papers (NBPs) and then liquid epoxy resins are infiltrated through the NBPs and cured to fabricate the composite. The major technical challenges for developing the NBP/Epoxy nanocomposite include (1) understanding of the molecular interactions between nanotubes and epoxy resin at the nanometer scale; (2) fabricating NBPs with uniform nano-scaled rope size and pore size; and (3) realizing resin infiltration through the nanoporous structure of NBPs. Molecular dynamics (MD) simulations were used to examine the important molecular interactions, including affinity and interfacial bonding. The affinities of two kinds of epoxy systems were examined. Unlike the DGEBA/DETA epoxy system, both EPON 862 epoxy resin and DETDA molecules had good affinities with SWNT and were chosen as the matrix material in the nanocomposites. Pullout simulations of a SWNT from cured epoxy resins were performed to investigate the stress transfer potential of the SWNT/Epoxy interface. The estimated interfacial shear stress is up to 75 MPa. The MD simulation results were found useful to guide the process development and property prediction of NBP/Epoxy nanocomposites. Experimentally, the fabrication process for NBPs was analyzed and optimized using the design of experiments (DOE) approach. The SEM and AFM image analyses of the resultant nanocomposites indicated observable wetting and bonding between nanotubes and the epoxy resin. The dynamics mechanic analysis (DMA) showed that a 200--250% increase of the storage modulus was achieved in the nanocomposites. This research is the first attempt to make nanocomposites using nanotube bucky papers.

  1. Dynamics of cooperative emissions in a cascade three-level molecular system driven by an ultrashort laser pulse

    This paper investigates the dynamics of cooperative emissions in a cascade three-level system driven by an ultrashort laser pulse by solving numerically the full-wave Maxwell–Bloch equations. The 4, 4'-bis(dimethylamino) stilbene molecule is used as the model molecule because of its strong two-photon absorption property. The two-colour cooperative emissions are studied as functions of molecular number density and dephasing rate of the dipole coherence. The propagation effects on the evolution of the cooperative radiations are also taken into account. The cooperative radiations are enhanced for large number density of the molecule, while the fast dephasing of the dipole coherence reduces the intensity of the cooperative radiations and delays the emission times or even inhibits the formation of the emissions. The delay time of the radiation decreases with the increase of the molecular number density and the propagation distance. (classical areas of phenomenology)

  2. Study on the toxic interaction of methanol, ethanol and propanol against the bovine hemoglobin (BHb) on molecular level

    Jun, Chai; Xue, Yan; Liu, Rutao; Wang, Meijie

    2011-09-01

    The toxic interaction of methanol, ethanol and propanol with bovine hemoglobin (BHb) at protein molecular level was studied by resonance light scattering (RLS), fluorescence, ultraviolet-visible absorption (UV-vis) and circular dichroism (CD) techniques. The experimental results showed that the three alcohols all had toxic effects on BHb and the effects increased along with the increasing alcohol dose. The results of RLS and fluorescence spectroscopy showed that alcohols can denature BHb. They changed the microenvironment of amino acid residues and led to molecular aggregation. The decreasing order of the influence is propanol, ethanol and methanol. The results of UV-vis and CD spectra revealed that alcohols led to conformational changes of BHb, including the loosening of the skeleton structure and the decreasing of α-helix in the second structure. The changes generated by propanol were much larger than those by methanol and ethanol.

  3. Molecular reordering processes on ice (0001) surfaces from long timescale simulations

    Pedersen, Andreas, E-mail: andped10@gmail.com [Faculty of Physical Sciences and Science Institute, University of Iceland, VR-III, 107 Reykjavík (Iceland); Integrated Systems Laboratory, ETH Zurich, 8092 Zurich (Switzerland); Wikfeldt, Kjartan T. [Science Institute, University of Iceland, VR-III, 107 Reykjavík (Iceland); NORDITA, AlbaNova University Center, S-10691 Stockholm (Sweden); Karssemeijer, Leendertjan; Cuppen, Herma [Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Jónsson, Hannes [Faculty of Physical Sciences and Science Institute, University of Iceland, VR-III, 107 Reykjavík (Iceland); Department of Applied Physics, Aalto University, Espoo FI-00076 (Finland)

    2014-12-21

    We report results of long timescale adaptive kinetic Monte Carlo simulations aimed at identifying possible molecular reordering processes on both proton-disordered and ordered (Fletcher) basal plane (0001) surfaces of hexagonal ice. The simulations are based on a force field for flexible molecules and span a time interval of up to 50 μs at a temperature of 100 K, which represents a lower bound to the temperature range of earth's atmosphere. Additional calculations using both density functional theory and an ab initio based polarizable potential function are performed to test and refine the force field predictions. Several distinct processes are found to occur readily even at this low temperature, including concerted reorientation (flipping) of neighboring surface molecules, which changes the pattern of dangling H-atoms, and the formation of interstitial defects by the downwards motion of upper-bilayer molecules. On the proton-disordered surface, one major surface roughening process is observed that significantly disrupts the crystalline structure. Despite much longer simulation time, such roughening processes are not observed on the highly ordered Fletcher surface which is energetically more stable because of smaller repulsive interaction between neighboring dangling H-atoms. However, a more localized process takes place on the Fletcher surface involving a surface molecule transiently leaving its lattice site. The flipping process provides a facile pathway of increasing proton-order and stabilizing the surface, supporting a predominantly Fletcher-like ordering of low-temperature ice surfaces. Our simulations also show that eventual proton-disordered patches on the surface may induce significant local reconstructions. Further, a subset of the molecules on the Fletcher surface are susceptible to forming interstitial defects which might provide active sites for various chemical reactions in the atmosphere.

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

    Holton, L.K.; Larson, D.E.; Partain, W.L.; Treat, R.L.

    1981-10-01

    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.

  5. Comparisons between molecular dynamics and hydrodynamics treatment of nonstationary thermal processes in a liquid

    Okumura, Hisashi; Heyes, David M.

    2004-12-01

    Molecular dynamics (MD) and Navier-Stokes hydrodynamics have been performed to model thermal relaxation processes arising from an initially established nonequilibrium stationary state. A nanoscale two-layer Lennard-Jones (LJ) liquid system was constructed in which the two parts were initially at a different temperature, with a narrow transitional zone between the two layers that was spatially linear in temperature. The highest-temperature layer had widths of five or 20 LJ particle diameters. The hydrodynamics model used parametrized MD-derived transport coefficients and the LJ equation of state as input functions. The temporal and spatial temperature and density profiles produced by the two methods show good agreement, indicating that a hydrodynamics description is reliable even for nonstationary phenomena down to the scale of a few molecular diameters. We found that at certain locations the Navier-Stokes solution predicted that the pressure and temperature profiles relaxed in a damped oscillatory manner, which we could discern despite the fluctuations in the MD data.

  6. Processing of meteoritic organic materials as a possible analog of early molecular evolution in planetary environments.

    Pizzarello, Sandra; Davidowski, Stephen K; Holland, Gregory P; Williams, Lynda B

    2013-09-24

    The composition of the Sutter's Mill meteorite insoluble organic material was studied both in toto by solid-state NMR spectroscopy of the powders and by gas chromatography-mass spectrometry analyses of compounds released upon their hydrothermal treatment. Results were compared with those obtained for other meteorites of diverse classifications (Murray, GRA 95229, Murchison, Orgueil, and Tagish Lake) and found to be so far unique in regard to the molecular species released. These include, in addition to O-containing aromatic compounds, complex polyether- and ester-containing alkyl molecules of prebiotic appeal and never detected in meteorites before. The Sutter's Mill fragments we analyzed had likely been altered by heat, and the hydrothermal conditions of the experiments realistically mimic early Earth settings, such as near volcanic activity or impact craters. On this basis, the data suggest a far larger availability of meteoritic organic materials for planetary environments than previously assumed and that molecular evolution on the early Earth could have benefited from accretion of carbonaceous meteorites both directly with soluble compounds and, for a more protracted time, through alteration, processing, and release from their insoluble organic materials. PMID:24019471

  7. Study of a hydrogen-bombardment process for molecular cross-linking within thin films

    A low-energy hydrogen bombardment method, without using any chemical additives, has been designed for fine tuning both physical and chemical properties of molecular thin films through selectively cleaving C-H bonds and keeping other bonds intact. In the hydrogen bombardment process, carbon radicals are generated during collisions between C-H bonds and hydrogen molecules carrying ∼10 eV kinetic energy. These carbon radicals induce cross-linking of neighboring molecular chains. In this work, we focus on the effect of hydrogen bombardment on dotriacontane (C32H66) thin films as growing on native SiO2 surfaces. After the hydrogen bombardment, XPS results indirectly explain that cross-linking has occurred among C32H66 molecules, where the major chemical elements have been preserved even though the bombarded thin film is washed by organic solution such as hexane. AFM results show the height of the perpendicular phase in the thin film decreases due to the bombardment. Intriguingly, Young's modulus of the bombarded thin films can be increased up to ∼6.5 GPa, about five times of elasticity of the virgin films. The surface roughness of the thin films can be kept as smooth as the virgin film surface after thorough bombardment. Therefore, the hydrogen bombardment method shows a great potential in the modification of morphological, mechanical, and tribological properties of organic thin films for a broad range of applications, especially in an aggressive environment.

  8. Adaptation and learning of molecular networks as a description of cancer development at the systems-level: Potential use in anti-cancer therapies

    Gyurko, David M; Modos, Dezso; Lenti, Katalin; Korcsmaros, Tamas; Csermely, Peter

    2013-01-01

    There is a widening recognition that cancer cells are products of complex developmental processes. Carcinogenesis and metastasis formation are increasingly described as systems-level, network phenomena. Here we propose that malignant transformation is a two-phase process, where an initial increase of system plasticity is followed by a decrease of plasticity at late stages of carcinogenesis as a model of cellular learning. We describe the hallmarks of increased system plasticity of early, tumor initiating cells, such as increased noise, entropy, conformational and phenotypic plasticity, physical deformability, cell heterogeneity and network rearrangements. Finally, we argue that the large structural changes of molecular networks during cancer development necessitate a rather different targeting strategy in early and late phase of carcinogenesis. Plastic networks of early phase cancer development need a central hit, while rigid networks of late stage primary tumors or established metastases should be attacked b...

  9. Process description and plant design for preparing ceramic high-level waste forms

    The ceramics process flow diagram has been simplified and upgraded to utilize only two major processing steps - fluid-bed calcination and hot isostatic press consolidating. Full-scale fluid-bed calcination has been used at INEL to calcine high-level waste for 18 y; and a second-generation calciner, a fully remotely operated and maintained calciner that meets ALARA guidelines, started calcining high-level waste in 1982. Full-scale hot isostatic consolidation has been used by DOE and commercial enterprises to consolidate radioactive components and to encapsulate spent fuel elements for several years. With further development aimed at process integration and parametric optimization, the operating knowledge of full-scale demonstration of the key process steps should be rapidly adaptable to scale-up of the ceramic process to full plant size. Process flowsheets used to prepare ceramic and glass waste forms from defense and commercial high-level liquid waste are described. Preliminary layouts of process flow diagrams in a high-level processing canyon were prepared and used to estimate the preliminary cost of the plant to fabricate both waste forms. The estimated costs for using both options were compared for total waste management costs of SRP high-level liquid waste. Using our design, for both the ceramic and glass plant, capital and operating costs are essentially the same for both defense and commercial wastes, but total waste management costs are calculated to be significantly less for defense wastes using the ceramic option. It is concluded from this and other studies that the ceramic form may offer important advantages over glass in leach resistance, waste loading, density, and process flexibility. Preliminary economic calculations indicate that ceramics must be considered a leading candidate for the form to immobilize high-level wastes

  10. Deciphering Membrane-Associated Molecular Processes in Target Tissue of Autoimmune Uveitis by Label-Free Quantitative Mass Spectrometry*

    Hauck, Stefanie M.; Dietter, Johannes; Kramer, Roxane L.; Hofmaier, Florian; Zipplies, Johanna K.; Amann, Barbara; Feuchtinger, Annette; Deeg, Cornelia A.; Ueffing, Marius

    2010-01-01

    Autoimmune uveitis is a blinding disease presenting with autoantibodies against eye-specific proteins as well as autoagressive T cells invading and attacking the immune-privileged target tissue retina. The molecular events enabling T cells to invade and attack the tissue have remained elusive. Changes in membrane protein expression patterns between diseased and healthy stages are especially interesting because initiating events of disease will most likely occur at membranes. Since disease progression is accompanied with a break-down of the blood-retinal barrier, serum-derived proteins mask the potential target tissue-related changes. To overcome this limitation, we used membrane-enriched fractions derived from retinas of the only available spontaneous animal model for the disease equine recurrent uveitis, and compared expression levels by a label-free LC-MSMS-based strategy to healthy control samples. We could readily identify a total of 893 equine proteins with 57% attributed to the Gene Ontology project term membrane. Of these, 179 proteins were found differentially expressed in equine recurrent uveitis tissue. Pathway enrichment analyses indicated an increase in proteins related to antigen processing and presentation, TNF receptor signaling, integrin cell surface interactions and focal adhesions. Additionally, loss of retina-specific proteins reflecting decrease of vision was observed as well as an increase in Mller glial cell-specific proteins indicating glial reactivity. Selected protein candidates (caveolin 1, integrin alpha 1 and focal adhesion kinase) were validated by immunohistochemistry and tissue staining pattern pointed to a significant increase of these proteins at the level of the outer limiting membrane which is part of the outer blood-retinal barrier. Taken together, the membrane enrichment in combination with LC-MSMSbased label-free quantification greatly increased the sensitivity of the comparative tissue profiling and resulted in detection of novel molecular pathways related to equine recurrent uveitis. PMID:20601722

  11. Deciphering membrane-associated molecular processes in target tissue of autoimmune uveitis by label-free quantitative mass spectrometry.

    Hauck, Stefanie M; Dietter, Johannes; Kramer, Roxane L; Hofmaier, Florian; Zipplies, Johanna K; Amann, Barbara; Feuchtinger, Annette; Deeg, Cornelia A; Ueffing, Marius

    2010-10-01

    Autoimmune uveitis is a blinding disease presenting with autoantibodies against eye-specific proteins as well as autoagressive T cells invading and attacking the immune-privileged target tissue retina. The molecular events enabling T cells to invade and attack the tissue have remained elusive. Changes in membrane protein expression patterns between diseased and healthy stages are especially interesting because initiating events of disease will most likely occur at membranes. Since disease progression is accompanied with a break-down of the blood-retinal barrier, serum-derived proteins mask the potential target tissue-related changes. To overcome this limitation, we used membrane-enriched fractions derived from retinas of the only available spontaneous animal model for the disease equine recurrent uveitis, and compared expression levels by a label-free LC-MSMS-based strategy to healthy control samples. We could readily identify a total of 893 equine proteins with 57% attributed to the Gene Ontology project term "membrane." Of these, 179 proteins were found differentially expressed in equine recurrent uveitis tissue. Pathway enrichment analyses indicated an increase in proteins related to antigen processing and presentation, TNF receptor signaling, integrin cell surface interactions and focal adhesions. Additionally, loss of retina-specific proteins reflecting decrease of vision was observed as well as an increase in Mller glial cell-specific proteins indicating glial reactivity. Selected protein candidates (caveolin 1, integrin alpha 1 and focal adhesion kinase) were validated by immunohistochemistry and tissue staining pattern pointed to a significant increase of these proteins at the level of the outer limiting membrane which is part of the outer blood-retinal barrier. Taken together, the membrane enrichment in combination with LC-MSMS-based label-free quantification greatly increased the sensitivity of the comparative tissue profiling and resulted in detection of novel molecular pathways related to equine recurrent uveitis. PMID:20601722

  12. A Wafer Level Vacuum Encapsulated Capacitive Accelerometer Fabricated in an Unmodified Commercial MEMS Process

    Adel Merdassi; Peng Yang; Chodavarapu, Vamsy P.

    2015-01-01

    We present the design and fabrication of a single axis low noise accelerometer in an unmodified commercial MicroElectroMechanical Systems (MEMS) process. The new microfabrication process, MEMS Integrated Design for Inertial Sensors (MIDIS), introduced by Teledyne DALSA Inc. allows wafer level vacuum encapsulation at 10 milliTorr which provides a high Quality factor and reduces noise interference on the MEMS sensor devices. The MIDIS process is based on high aspect ratio bulk micromachining of...

  13. Role of intrinsic molecular dipole in energy level alignment at organic interfaces

    Lindell, Linda; ćakır, Deniz; Brocks, Geert; Fahlman, Mats; Braun, Slawomir

    2013-06-01

    The energy level alignment in metal-organic and organic-organic junctions of the widely used materials tris-(8-hydroxyquinoline)aluminum (Alq3) and 1,4,5,8-naphthalenetetracarboxylic dianhydride (NTCDA) is investigated. The measured alignment schemes for single and bilayer films of Alq3 and NTCDA are interpreted with the integer charge transfer (ICT) model. Single layer films of Alq3 feature a constant vacuum level shift of ˜0.2-0.4 eV in the absence of charge transfer across the interface. This finding is attributed to the intrinsic dipole of the Alq3 molecule and (partial) ordering of the molecules at the interfaces. The vacuum level shift changes the onset of Fermi level pinning, as it changes the energy needed for equilibrium charge transfer across the interface.

  14. Tank waste remediation system phase I high-level waste feed processability assessment report

    Lambert, S.L.; Stegen, G.E., Westinghouse Hanford

    1996-08-01

    This report evaluates the effects of feed composition on the Phase I high-level waste immobilization process and interim storage facility requirements for the high-level waste glass.Several different Phase I staging (retrieval, blending, and pretreatment) scenarios were used to generate example feed compositions for glass formulations, testing, and glass sensitivity analysis. Glass models and data form laboratory glass studies were used to estimate achievable waste loading and corresponding glass volumes for various Phase I feeds. Key issues related to feed process ability, feed composition, uncertainty, and immobilization process technology are identified for future consideration in other tank waste disposal program activities.

  15. Electron spin resonance studies on reduction process of nitroxyl spin radicals used in molecular imaging

    The Electron spin resonance studies on the reduction process of nitroxyl spin probes were carried out for 1mM 14N labeled nitroxyl radicals in pure water and 1 mM concentration of ascorbic acid as a function of time. The electron spin resonance parameters such as signal intensity ratio, line width, g-value, hyperfine coupling constant and rotational correlation time were determined. The half life time was estimated for 1mM 14N labeled nitroxyl radicals in 1 mM concentration of ascorbic acid. The ESR study reveals that the TEMPONE has narrowest line width and fast tumbling motion compared with TEMPO and TEMPOL. From the results, TEMPONE has long half life time and high stability compared with TEMPO and TEMPOL radical. Therefore, this study reveals that the TEMPONE radical can act as a good redox sensitive spin probe for molecular imaging

  16. A domain decomposition parallel processing algorithm for molecular dynamics simulations of polymers

    Brown, David; Clarke, Julian H. R.; Okuda, Motoi; Yamazaki, Takao

    1994-10-01

    We describe in this paper a domain decomposition molecular dynamics algorithm for use on distributed memory parallel computers which is capable of handling systems containing rigid bond constraints and three- and four-body potentials as well as non-bonded potentials. The algorithm has been successfully implemented on the Fujitsu 1024 processor element AP1000 machine. The performance has been compared with and benchmarked against the alternative cloning method of parallel processing [D. Brown, J.H.R. Clarke, M. Okuda and T. Yamazaki, J. Chem. Phys., 100 (1994) 1684] and results obtained using other scalar and vector machines. Two parallel versions of the SHAKE algorithm, which solves the bond length constraints problem, have been compared with regard to optimising the performance of this procedure.

  17. Molecular dynamics simulations of mixed lubrication with smooth particle post-processing

    Eder, S; Vernes, A; Vorlaufer, G [Austrian Center of Competence for Tribology, Viktor-Kaplan-Strasse 2, 2700 Wiener Neustadt (Austria); Betz, G [Institute of Applied Physics, Vienna University of Technology, Wiedner Hauptstrasse 8-10/134, 1040 Vienna (Austria)

    2011-05-04

    A post-processing method for molecular dynamics (MD) simulations of friction based on the smooth particle approach is proposed, allowing-among other features-the introduction and evaluation of a solid-solid contact area arising due to direct asperity interaction. In order to illustrate the feasibility of this scheme, a large number of MD calculations of lubricated nanotribological systems with various asperity geometries and carefully selected numbers of lubricant molecules were carried out and analysed. In this manner, it is shown that the friction force as a function of load agrees very well with a three-parameter friction law which, in addition to the adhesion- and the load-controlled terms, contains a load-independent offset.

  18. Molecular simulation evidence for processive motion of Trichoderma reesei Cel7A during cellulose depolymerization

    Zhao, Xiongce; Rignall, Tauna R.; McCabe, Clare; Adney, William S.; Himmel, Michael E.

    2008-07-01

    We present free energy calculations for the Trichoderma reesei Cel7A (cellobiohydrolase I) linker peptide from molecular dynamics simulations directed towards understanding the linker role in cellulose hydrolysis. The calculations predict an energy storage mechanism of the linker under stretching/compression that is consistent with processive depolymerization. The linker exhibits two stable states at lengths of 2.5 nm and 5.5 nm during extension/compression, with a free energy difference of 10.5 kcal/mol between the two states separated by an energy barrier. The switching between stable states supports the hypothesis that the linker peptide has the capacity to store energy in a manner similar to a spring.

  19. Vibrational spectroscopy to support the link between rheology and continuous twin-screw melt granulation on molecular level: A case study.

    Monteyne, Tinne; Heeze, Liza; Oldörp, Klaus; Vervaet, Chris; Remon, Jean-Paul; De Beer, Thomas

    2016-06-01

    Twin screw hot melt granulation (TSHMG) is an innovative and continuous drug formulation process allowing granulation of moisture sensitive drugs. However, due to the lack of experience and in-depth process understanding, this technique is not yet widely used. During the TSHMG process, the microstructure of the granules is generated and modified and strongly depends on the flow behavior of the material. Hence, rheology might be a suitable tool to simulate and examine this process. However, chemical interactions of the material are influencing the physical properties leading to the microstructure. In this research project it is spectroscopically investigated whether the heat applied in a rheometer induces the same molecular effects as these occurring during TSHMG of the model formulation caffeine anhydrous/Soluplus®. Hence, it is evaluated whether rheology can be used as a simulation tool to improve the understanding of the material behavior at molecular level during continuous melt granulation. Therefore, in-line Raman spectroscopy is executed during TSHMG and in situ Fourier Transform Infra-red (FTIR) during oscillatory rheological experiments. The results from the in-line Raman monitoring revealed polymorph transition of caffeine anhydrous during twin screw melt granulation with Soluplus® which is stimulated depending on the binder concentration and/or granulation temperature. A correlation was seen between the FTIR spectra obtained during the rheological temperature ramp and the in-line collected Raman spectra during the melt granulation runs. The polymorphic conversion of caffeine anhydrous could be detected in the same temperature range with both techniques, proving the comparability of plate-plate rheometry and hot melt granulation (HMG) for this case with the used parameter settings. Process simulation using rheology combined with in situ FTIR seems a promising approach to increase process understanding and to facilitate binder and parameter selection for TSHMG. PMID:27040975

  20. Shocks in dense clouds. IV. Effects of grain-grain processing on molecular line emission

    Anderl, S; Forêts, G Pineau des; Flower, D R

    2014-01-01

    Grain-grain processing has been shown to be an indispensable ingredient of shock modelling in high density environments. For densities higher than \\sim10^5 cm-3, shattering becomes a self-enhanced process that imposes severe chemical and dynamical consequences on the shock characteristics. Shattering is accompanied by the vaporization of grains, which can directly release SiO to the gas phase. Given that SiO rotational line radiation is used as a major tracer of shocks in dense clouds, it is crucial to understand the influence of vaporization on SiO line emission. We have developed a recipe for implementing the effects of shattering and vaporization into a 2-fluid shock model, resulting in a reduction of computation time by a factor \\sim100 compared to a multi-fluid modelling approach. This implementation was combined with an LVG-based modelling of molecular line radiation transport. Using this model we calculated grids of shock models to explore the consequences of different dust-processing scenarios. Grain-...

  1. Early stage oxynitridation process of Si(001) surface by NO gas: Reactive molecular dynamics simulation study

    Cao, Haining; Srivastava, Pooja; Choi, Keunsu; Kim, Seungchul; Lee, Kwang-Ryeol

    2016-03-01

    Initial stage of oxynitridation process of Si substrate is of crucial importance in fabricating the ultrathin gate dielectric layer of high quality in advanced MOSFET devices. The oxynitridation reaction on a relaxed Si(001) surface is investigated via reactive molecular dynamics (MD) simulation. A total of 1120 events of a single nitric oxide (NO) molecule reaction at temperatures ranging from 300 to 1000 K are statistically analyzed. The observed reaction kinetics are consistent with the previous experimental or calculation results, which show the viability of the reactive MD technique to study the NO dissociation reaction on Si. We suggest the reaction pathway for NO dissociation that is characterized by the inter-dimer bridge of a NO molecule as the intermediate state prior to NO dissociation. Although the energy of the inter-dimer bridge is higher than that of the intra-dimer one, our suggestion is supported by the ab initio nudged elastic band calculations showing that the energy barrier for the inter-dimer bridge formation is much lower. The growth mechanism of an ultrathin Si oxynitride layer is also investigated via consecutive NO reactions simulation. The simulation reveals the mechanism of self-limiting reaction at low temperature and the time evolution of the depth profile of N and O atoms depending on the process temperature, which would guide to optimize the oxynitridation process condition.

  2. Molecular dynamics simulation of moderately coupled Yukawa liquids on graphics processing units

    Complete text of publication follows. During the past decade Graphic Processing Unit (GPU) architectures have seen not only continuous performance increase, but a completely new horizon through general purpose computing as well. Thus, being integrated inside personal computers (PC), besides high-performance graphics applications, they provide a new platform for scientific computing, too, at moderate cost. Single instruction multiple data (SIMD) parallelism of GPUs is attractive for molecular simulations, as particle methods can largely be parallelized. We have developed a molecular dynamics (MD) simulation code for the NVIDIA Compute Unified Device Architecture (CUDA) GPU architecture that allows massive parallel computing, thereby permitting relatively big systems to be simulated on PC class computers, compared to the traditional Central Processing Unit (CPU) computations. We have carried out simulations of moderately coupled (01. ≤ Γ ≤ 10) 3-dimensional Yukawa liquids [2], using particle numbers in the 105-106 range. Besides the MD simulations we have as well obtained pair correlation functions using the Hypernetted Chain (HNC) Approximation, and have compared the results with the GPU-MD data. The analysis of the asymptotic long-range behaviour of the pair correlation functions (transition between monotonic vs. oscillating decay) confirmed the results of [3]. Figure 1 shows pair correlation functions obtained from the numerical simulations and the theoretical HNC method, in which the bridge function was set to zero. We find a very good agreement between the curves at Γ=0.1 and 1, over several orders of magnitude. The only difference seen at Γ = 10 is the (expected) slightly higher correlation peak amplitude obtained from the MD simulation, compared to the HNC result. We thank OTKA for supporting this work (grant K77653) and Dr A. Archer for useful discussions.

  3. Gene Expression Profiles of the NCI-60 Human Tumor Cell Lines Define Molecular Interaction Networks Governing Cell Migration Processes

    Kohn, Kurt W.; Zeeberg, Barry R; Reinhold, William C.; Sunshine, Margot; Luna, Augustin; Pommier, Yves

    2012-01-01

    Although there is extensive information on gene expression and molecular interactions in various cell types, integrating those data in a functionally coherent manner remains challenging. This study explores the premise that genes whose expression at the mRNA level is correlated over diverse cell lines are likely to function together in a network of molecular interactions. We previously derived expression-correlated gene clusters from the database of the NCI-60 human tumor cell lines and assoc...

  4. Molecular design of new P3HT derivatives: Adjusting electronic energy levels for blends with PCBM

    An intensive search is underway for new materials to make more efficient organic solar cells through improvements in thin film morphology, transport properties, and adjustments to the energy of frontier electronic levels. The use of chemical modifications capable of modifying the electronic properties of materials already known is an interesting approach, as it can, in principle, provide a more adequate adjustment of the frontier electronic levels while preserving properties such as solubility. Based on this idea, we performed a theoretical study of poly(3-hexylthiophene) (P3HT) and 13 new derivatives obtained by substitution with electron acceptor and donor groups, in order to understand how the energy levels of the frontier orbitals are modified. The results show that it is possible to deduce the modification of the electronic levels in accordance with the substituent's acceptor/donor character. We also evaluated how the substituents influence the open circuit voltage and the exciton binding energy. - Highlights: • Prediction of P3HT derivatives properties for bulk-heterojunction solar cells. • Correlating substituent properties with electronic levels of P3HT derivatives. • Fluorinated P3HT improves open circuit voltage and stability

  5. Molecular design of new P3HT derivatives: Adjusting electronic energy levels for blends with PCBM

    Oliveira, Eliezer Fernando [UNESP Univ Estadual Paulista, POSMAT Programa de Ps-Graduao em Cincia e Tecnologia de Materiais, Bauru, SP (Brazil); Lavarda, Francisco Carlos, E-mail: lavarda@fc.unesp.br [UNESP Univ Estadual Paulista, POSMAT Programa de Ps-Graduao em Cincia e Tecnologia de Materiais, Bauru, SP (Brazil); Faculdade de Cincias, UNESP Univ Estadual Paulista, Departamento de Fsica, Av. Eng. Luiz Edmundo Carrijo Coube, 14-01, 17033-360 Bauru, SP (Brazil)

    2014-12-15

    An intensive search is underway for new materials to make more efficient organic solar cells through improvements in thin film morphology, transport properties, and adjustments to the energy of frontier electronic levels. The use of chemical modifications capable of modifying the electronic properties of materials already known is an interesting approach, as it can, in principle, provide a more adequate adjustment of the frontier electronic levels while preserving properties such as solubility. Based on this idea, we performed a theoretical study of poly(3-hexylthiophene) (P3HT) and 13 new derivatives obtained by substitution with electron acceptor and donor groups, in order to understand how the energy levels of the frontier orbitals are modified. The results show that it is possible to deduce the modification of the electronic levels in accordance with the substituent's acceptor/donor character. We also evaluated how the substituents influence the open circuit voltage and the exciton binding energy. - Highlights: Prediction of P3HT derivatives properties for bulk-heterojunction solar cells. Correlating substituent properties with electronic levels of P3HT derivatives. Fluorinated P3HT improves open circuit voltage and stability.

  6. The Influence of Metal Carbides on the Oxidation Processes of 1-Octene by Molecular Oxygen and tert-Butyl Hydroperoxide

    Oksana Makota; Lidiya Bulgakova

    2012-01-01

    The influence of metal carbides, TiC, VC, ZrC, Mo2C, TaC, and WC, on the liquid-phase oxidation processes of 1-octene by molecular oxygen and tert-butyl hydroperoxide was investigated. It was established that vanadium carbide is the most active in the oxidation process of 1-octene by molecular oxygen as well as in the tert-butyl hydroperoxide unproductive decomposition process in the hydroperoxide oxidation reaction. It was shown that there is a correlation among the activities of metal carbi...

  7. Recent Process and Equipment Improvements to Increase High Level Waste Throughput at The Defense Waste Processing Facility (DWPF)

    The Savannah River Site's (SRS) Defense Waste Processing Facility (DWPF) began stabilizing high level waste (HLW) in a glass matrix in 1996. Over the past few years, there have been several process and equipment improvements at the DWPF to increase the rate at which the high level waste can be stabilized. These improvements have either directly increased waste processing rates or have desensitized the process to upsets, thereby minimizing downtime and increasing production. Improvements due to optimization of waste throughput with increased HLW loading of the glass resulted in an 8 % waste throughput increase over the standard 28 % waste loading based upon operational efficiencies. Improvements in canister production include the pour spout heated bellows liner (7 %), glass surge (siphon) protection software (2 %), melter feed pump software logic change to prevent spurious interlocks of the feed pump with subsequent dilution of feed stock (2 %) and optimization of the steam atomized scrubber (SAS) operation to minimize downtime (3 %) for a total increase in canister production of 14 %. A number of process recovery efforts have allowed continued operation. These include the off gas system pluggage and restoration, slurry mix evaporator (SME) tank repair and replacement, remote cleaning of melter top head center nozzle, remote melter internal inspection, SAS pump J-Tube recovery, inadvertent pour scenario resolutions, dome heater transformer bus bar cooling water leak repair and new Infra-red camera for determination of glass height in the canister are discussed. (authors)

  8. RECENT PROCESS AND EQUIPMENT IMPROVEMENTS TO INCREASE HIGH LEVEL WASTE THROUGHPUT AT THE DEFENSE WASTE PROCESSING FACILITY

    The Savannah River Site's (SRS) Defense Waste Processing Facility (DWPF) began stabilizing high level waste (HLW) in a glass matrix in 1996. Over the past few years, there have been several process and equipment improvements at the DWPF to increase the rate at which the high level waste can be stabilized. These improvements have either directly increased waste processing rates or have desensitized the process to upsets, thereby minimizing downtime and increasing production. Improvements due to optimization of waste throughput with increased HLW loading of the glass resulted in a 6% waste throughput increase based upon operational efficiencies. Improvements in canister production include the pour spout heated bellows liner (5%), glass surge (siphon) protection software (2%), melter feed pump software logic change to prevent spurious interlocks of the feed pump with subsequent dilution of feed stock (2%) and optimization of the steam atomized scrubber (SAS) operation to minimize downtime (3%) for a total increase in canister production of 12%. A number of process recovery efforts have allowed continued operation. These include the off gas system pluggage and restoration, slurry mix evaporator (SME) tank repair and replacement, remote cleaning of melter top head center nozzle, remote melter internal inspection, SAS pump J-Tube recovery, inadvertent pour scenario resolutions, dome heater transformer bus bar cooling water leak repair and new Infra-red camera for determination of glass height in the canister are discussed

  9. RECENT PROCESS AND EQUIPMENT IMPROVEMENTS TO INCREASE HIGH LEVEL WASTE THROUGHPUT AT THE DEFENSE WASTE PROCESSING FACILITY

    Odriscoll, R; Allan Barnes, A; Jim Coleman, J; Timothy Glover, T; Robert Hopkins, R; Dan Iverson, D; Jeff Leita, J

    2008-01-15

    The Savannah River Site's (SRS) Defense Waste Processing Facility (DWPF) began stabilizing high level waste (HLW) in a glass matrix in 1996. Over the past few years, there have been several process and equipment improvements at the DWPF to increase the rate at which the high level waste can be stabilized. These improvements have either directly increased waste processing rates or have desensitized the process to upsets, thereby minimizing downtime and increasing production. Improvements due to optimization of waste throughput with increased HLW loading of the glass resulted in a 6% waste throughput increase based upon operational efficiencies. Improvements in canister production include the pour spout heated bellows liner (5%), glass surge (siphon) protection software (2%), melter feed pump software logic change to prevent spurious interlocks of the feed pump with subsequent dilution of feed stock (2%) and optimization of the steam atomized scrubber (SAS) operation to minimize downtime (3%) for a total increase in canister production of 12%. A number of process recovery efforts have allowed continued operation. These include the off gas system pluggage and restoration, slurry mix evaporator (SME) tank repair and replacement, remote cleaning of melter top head center nozzle, remote melter internal inspection, SAS pump J-Tube recovery, inadvertent pour scenario resolutions, dome heater transformer bus bar cooling water leak repair and new Infra-red camera for determination of glass height in the canister are discussed.

  10. Role of intrinsic molecular dipole in energy level alignment at organic interfaces

    Lindell, Linda; Cakir, Deniz; Brocks, Geert; Fahlman, Mats; Braun, Slawomir

    2013-01-01

    The energy level alignment in metal-organic and organic-organic junctions of the widely used materials tris-(8-hydroxyquinoline)aluminum (Alq3) and 1,4,5,8-naphthalenetetracarboxylic dianhydride (NTCDA) is investigated. The measured alignment schemes for single and bilayer films of Alq3 and NTCDA are interpreted with the integer charge transfer (ICT) model. Single layer films of Alq3 feature a constant vacuum level shift of ∼0.2–0.4 eV in the absence of charge transfer across the interface. T...

  11. Comparison of cryoconite organic matter composition from Arctic and Antarctic glaciers at the molecular-level

    Pautler, Brent G.; Dubnick, Ashley; Sharp, Martin J.; Simpson, André J.; Simpson, Myrna J.

    2013-03-01

    Glacier surfaces are reservoirs that contain organic and inorganic debris referred to as cryoconite. Solar heating of this material results in the formation of water-filled depressions that are colonized by a variety of microbes and are hypothesized to play a role in carbon cycling in glacier ecosystems. Recent studies on cryoconite deposits have focused on their contribution to carbon fluxes to determine whether they are a net source or sink for atmospheric CO2. To better understand carbon cycling in these unique ecosystems, the molecular constituents of cryoconite organic matter (COM) require further elucidation. COM samples from four glaciers were analyzed by targeted extraction of plant- and microbial-derived biomarkers in conjunction with non-targeted NMR experiments to determine the COM composition and potential sources. Several molecular proxies were applied to assess COM degradation and microbial activity using samples from Greenland, the Canadian Arctic, and Antarctica. COM from Canadian (John Evans glacier) and Greenlandic (Leverett glacier) locations was more chemically heterogeneous than that from the Antarctic likely due to inputs from higher plants, mosses and Sphagnum as suggested by the solvent-extractable alkyl lipids and sterols and the detection of lignin- and Sphagnum-derived phenols after cupric oxide chemolysis. Solid-state 13C nuclear magnetic resonance (NMR) experiments highlighted the bulk chemical functional groups of COM allowing for a general assessment of its degradation stage from the alkyl/O-alkyl proxy whereas solution-state 1H NMR highlighted both microbial and plant contributions to base-soluble extracts from these COM samples. The dominance of 1H NMR signals from microbial protein/peptides in base-soluble extracts of COM from Antarctica (Joyce glacier and Garwood glacier), phospholipid fatty acid (PLFA) biomarker detection and the absence of plant-derived biomarkers in both the solvent and cupric oxide extracts suggests that this COM is dominated by microbial-derived material. These results indicate that COM carbon composition is dependent on the local glacier environment which may have a profound impact on carbon cycling and sequestration on glacier surfaces.

  12. Fermi level alignment in molecular nanojunctions and its relation to charge transfer

    Stadler, Robert; Jacobsen, Karsten Wedel

    2006-01-01

    calculations. For bipyridine the charge distribution is defined by a balance between electrostatic repulsion effects and the filling of the LUMO, where the molecule loses electrons to the leads. BPDT, on the other hand, gains electrons. As a direct consequence the Fermi level of the metal is found at the...

  13. Molecular level crossing and the geometric phase effect from the optical Hanle perspective

    Glenn, R.; Dantus, M.

    2016-04-01

    Level-crossing spectroscopy involves lifting the degeneracy of an excited state and using the interference of two nearly degenerate levels to measure the excited-state lifetime. Here we use the idea of interference between different pathways to study the momentum-dependent wave-packet lifetime due an excited-state level crossing (conical intersection) in a molecule. Changes in population from the wave-packet propagation are reflected in the detected fluorescence. We use a chirped pulse to control the wave-packet momentum. Increasing the chirp rate increases the transition to the lower state through the conical intersection. It also increases the interference of different pathways in the upper electronic state due to the geometric phase acquired. Therefore, increasing the chirp rate decreases the population of the upper electronic state and its fluorescence yield. This suggests that there is a finite momentum-dependent lifetime of the wave packet through the level crossing as a function of chirp. We dub this lifetime the wave-packet-momentum lifetime.

  14. Molecular Level-Crossing and the Geometric Phase Effect from the Optical Hanle Perspective

    Glenn, R

    2016-01-01

    Level-crossing spectroscopy involves lifting the degeneracy of an excited state and using the interference of two nearly degenerate levels to measure the excited state lifetime. Here we use the idea of interference between different pathways to study the momentum-dependent wave packet lifetime due an excited state level-crossing (conical intersection) in a molecule. Changes in population from the wave packet propagation are reflected in the detected fluorescence. We use a chirped pulse to control the wave packet momentum. Changing the chirp rate affects the transition to the lower state through the conical intersection. It also affects the interference of different pathways in the upper electronic state, due to the geometric phase acquired. Increasing the chirp rate decreases the coherence of the wave packet in the upper electronic state. This suggests that there is a finite momentum dependent lifetime of the wave packet through the level-crossing as function of chirp. We dub this lifetime the wave packet mom...

  15. New molecular markers for fungal phylogenetics: Two genes for species level systematics in the Sordariomycetes (Ascomycota)

    Although significant progress has been made resolving deep branches of the fungal tree of life in recent works, many fungal systematists are interested in species-level questions to both define species and to assess fungal biodiversity. Fungal genome sequences are a useful resource to systematic bio...

  16. Critical assessment of methods for treating airborne effluents from high-level waste solidification processes

    Christian, J.D.; Pence, D.T.

    1977-06-01

    Off-gas treatment systems are reviewed for high-temperature processes which are being developed for the solidification of high-level liquid wastes from nuclear fuel reprocessing plants. A brief description of each of the processes is given and detailed analyses are made of the expected magnitudes of airborne effluent release rates from each system. The estimated release rates of the various processes are compared with present and anticipated regulatory limits. A number of recommendations are made for additional development studies to better understand and control certain airborne effluents from the solidification processes.

  17. Site selection and characterization processes for deep geologic disposal of high level nuclear waste

    In this paper, the major elements of the site selection and characterization processes used in the US high level waste program are discussed. While much of the evolution of the site selection and characterization processes have been driven by the unique nature of the US program, these processes, which are well defined and documented, could be used as an initial basis for developing site screening, selection, and characterization programs in other countries. Thus, this paper focuses more on the process elements than the specific details of the US program

  18. Site selection and characterization processes for deep geologic disposal of high level nuclear waste

    In this paper, the major elements of the site selection and characterization processes used in the U. S. high level waste program are discussed. While much of the evolution of the site selection and characterization processes have been driven by the unique nature of the U. S. program, these processes, which are well-defined and documented, could be used as an initial basis for developing site screening, selection, and characterization programs in other countries. Thus, this paper focuses more on the process elements than the specific details of the U. S. program. (author). 3 refs., 2 tabs., 5 figs

  19. Processing of water level derived from water pressure data at the Time Series Station Spiekeroog

    Holinde, L.; Badewien, T. H.; Freund, J. A.; Stanev, E. V.; Zielinski, O.

    2015-10-01

    The quality of water level time series data strongly varies with periods of high- and low-quality sensor data. In this paper we are presenting the processing steps which were used to generate high-quality water level data from water pressure measured at the Time Series Station (TSS) Spiekeroog. The TSS is positioned in a tidal inlet between the islands of Spiekeroog and Langeoog in the East Frisian Wadden Sea (southern North Sea). The processing steps will cover sensor drift, outlier identification, interpolation of data gaps and quality control. A central step is the removal of outliers. For this process an absolute threshold of 0.25 m 10 min-1 was selected which still keeps the water level increase and decrease during extreme events as shown during the quality control process. A second important feature of data processing is the interpolation of gappy data which is accomplished with a high certainty of generating trustworthy data. Applying these methods a 10-year data set (December 2002-December 2012) of water level information at the TSS was processed resulting in a 7-year time series (2005-2011). Supplementary data are available at doi:10.1594/PANGAEA.843740.

  20. Molecular imaging in oncology

    Dzik-Jurasz, A S K

    2004-01-01

    Cancer is a genetic disease that manifests in loss of normal cellular homeostatic mechanisms. The biology and therapeutic modulation of neoplasia occurs at the molecular level. An understanding of these molecular processes is therefore required to develop novel prognostic and early biomarkers of response. In addition to clinical applications, increased impetus for the development of such technologies has been catalysed by pharmaceutical companies investing in the development of molecular ther...

  1. Non-Radiative Carrier Recombination Enhanced by Two-Level Process: A First-Principles Study

    Yang, Ji-Hui; Shi, Lin; Wang, Lin-Wang; Wei, Su-Huai

    2016-02-01

    Non-radiative recombination plays an important role in the performance of optoelectronic semiconductor devices such as solar cells and light-emitting diodes. Most textbook examples assume that the recombination process occurs through a single defect level, where one electron and one hole are captured and recombined. Based on this simple picture, conventional wisdom is that only defect levels near the center of the bandgap can be effective recombination centers. Here, we present a new two-level recombination mechanism: first, one type of carrier is captured through a defect level forming a metastable state; then the local defect configuration rapidly changes to a stable state, where the other type of carrier is captured and recombined through another defect level. This novel mechanism is applied to the recombination center in CdTe. We show that this two-level process can significantly increase the recombination rate (by three orders of magnitude) in agreement with experiments. We expect that this two-level recombination process can exist in a wide range of semiconductors, so its effect should be carefully examined in characterizing optoelectronic materials.

  2. Framework for sustainability assessment of industrial processes with multi-scale technology at design level: microcapsules production process

    Navarro Rosa, Jennifer

    2009-01-01

    In a world with limited resources and serious environmental, social and economical impacts, a more sustainable life style is everyday more important. Therefore, the general objective of this work is to develop a methodological procedure for eco-efficiency and sustainability assessment of industrial processes with multi-scale technology at design level. The methodology developed follows the ISO 14040 series for environmental LCA standard. To integrate the three pillars of sustainability the an...

  3. Active microrheology reveals molecular-level variations in the viscoelastic properties of Chaetopterus mucus

    Weigand, William; Messmore, Ashley; Anderson, Rae

    The sea annelid, Chaetopterus Variopedatus, secretes a bioluminescent mucus that also exhibits complex viscoelastic properties. The constituents of the mucus are relatively unknown but it does play an important role in the development of the worms' parchment-like housing tubes. In order to determine how and why this mucus can exhibit material properties ranging from fluidity to rigidity we perform microrheology experiments. We determine the microscale viscoelastic properties by using optical tweezers to produce small oscillations in the mucus which allow us to determine both the linear storage and loss moduli (G',G'') along with the viscosity of the fluid. By varying the size of the microspheres (2-10 µm) and oscillation amplitude (.5-10 µm) we are able to determine the dominant intrinsic length scales of the molecular mesh comprising the mucus. By varying the oscillation frequency (1-15Hz) we determine the crossover frequency at which G' surpasses G'', to quantify the longest relaxation time of the mesh network. Initial results show a strong dependence on bead size which indicate that the dominant entanglement lengthscale of the mucus mesh is ~5 um. Microspheres of this size exhibit a wide variety of stress responses in different regions of the mucus demonstrating the substantial microscale heterogeneity of the mucus. We carry out measurements on a population of worms of varying size and age to determine mucus variability between worms.

  4. Towards a molecular level understanding of the sulfanilamide-soil organic matter-interaction.

    Ahmed, Ashour A; Thiele-Bruhn, Sören; Leinweber, Peter; Kühn, Oliver

    2016-07-15

    Sorption experiments of sulfanilamide (SAA) on well-characterized samples of soil size-fractions were combined with the modeling of SAA-soil-interaction via quantum chemical calculations. Freundlich unit capacities were determined in batch experiments and it was found that they increase with the soil organic matter (SOM) content according to the order fine silt > medium silt > clay > whole soil > coarse silt > sand. The calculated binding energies for mass-spectrometrically quantified sorption sites followed the order ionic species > peptides > carbohydrates > phenols and lignin monomers > lignin dimers > heterocyclic compounds > fatty acids > sterols > aromatic compounds > lipids, alkanes, and alkenes. SAA forms H-bonds through its polar centers with the polar SOM sorption sites. In contrast dispersion and π-π-interactions predominate the interaction of the SAA aromatic ring with the non-polar moieties of SOM. Moreover, the dipole moment, partial atomic charges, and molecular volume of the SOM sorption sites are the main physical properties controlling the SAA-SOM-interaction. Further, reasonable estimates of the Freundlich unit capacities from the calculated binding energies have been established. Consequently, we suggest using this approach in forthcoming studies to disclose the interactions of a wide range of organic pollutants with SOM. PMID:27088516

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

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

    2015-01-01

    [Abridged] We have recently reported on the collapse and fragmentation properties of the northernmost part of this structure, located ~2.4pc north of Orion KL -- the Orion Molecular Cloud 3 (OMC 3, Takahashi et al. 2013). As part of our project to study the integral-shaped filament, we analyze the fragmentation properties of the northern OMC 1 filament. This filament is a dense structure previously identified by JCMT/SCUBA submillimeter continuum and VLA ammonia observations and shown to have fragmented into clumps. We observed OMC1 n with the Submillimeter Array (SMA) at 1.3mm and report on our analysis of the continuum data. We discovered 24 new compact sources, ranging in mass from 0.1 to 2.3, in size from 400 to 1300au, and in density from 2.6 x 10^7 to 2.8 x 10^6 cm^{-3}. The masses of these sources are similar to those of the SMA protostars in OMC3, but their typical sizes and densities are lower by a factor of ten. Only 8% of the new sources have infrared counterparts, yet there are five associated CO ...

  6. Molecular-level tuning of cellular autonomy controls the collective behaviors of cell populations

    Maire, Théo

    2016-01-01

    A rigorous understanding of how multicellular behaviors arise from the actions of single cells requires quantitative frameworks that bridge the gap between genetic circuits, the arrangement of cells in space, and population-level behaviors. Here, we provide such a framework for a ubiquitous class of multicellular systems - namely, "secrete-and-sense cells" that communicate by secreting and sensing a signaling molecule. By using formal, mathematical arguments and introducing the concept of a phenotype diagram, we show how these cells tune their degrees of autonomous and collective behavior to realize distinct single-cell and population-level phenotypes; these phenomena have biological analogs, such as quorum sensing or paracrine signaling. We also define the "entropy of population," a measurement of the number of arrangements that a population of cells can assume, and demonstrate how a decrease in the entropy of population accompanies the formation of ordered spatial patterns. Our conceptual framework ties tog...

  7. High-level waste processing at the Savannah River Site: An update

    The Defense Waste Processing Facility (DWPF) at the Savannah River Site (SRS) in Aiken, SC mg began immobilizing high-level radioactive waste in borosilicate glass in 1996. Currently, the radioactive glass is being produced as a ''sludge-only'' composition by combining washed high-level waste sludge with glass frit. The glass is poured in stainless steel canisters which will eventually be disposed of in a permanent, geological repository. To date, DWPF has produced about 100 canisters of vitrified waste. Future processing operations will, be based on a ''coupled'' feed of washed high-level waste sludge, precipitated cesium, and glass frit. This paper provides an update of the processing activities completed to date, operational/flowsheet problems encountered, and programs underway to increase production rates

  8. Aquatic ecotoxicology: from the ecosystem to the cellular and molecular levels.

    Boudou, A.; Ribeyre, F.

    1997-01-01

    This review of aquatic ecotoxicology is presented in three parts. First, we discuss the fundamental concepts and stress the importance of its ecological basis and the complexity and diversity of the field of investigation, which result from actions and interactions between the physicochemical characteristics of the biotopes, the structural and functional properties of the living organisms, and the contamination modalities. Ecotoxicological mechanisms, regardless of the level of biological com...

  9. Recent Advances in Photoinduced Electron Transfer Processes of Fullerene-Based Molecular Assemblies and Nanocomposites

    Osamu Ito

    2012-05-01

    Full Text Available Photosensitized electron-transfer processes of fullerenes hybridized with electron donating or other electron accepting molecules have been surveyed in this review on the basis of the recent results reported mainly from our laboratories. Fullerenes act as photo-sensitizing electron acceptors with respect to a wide variety of electron donors; in addition, fullerenes in the ground state also act as good electron acceptors in the presence of light-absorbing electron donors such as porphyrins. With single-wall carbon nanotubes (SWCNTs, the photoexcited fullerenes act as electron acceptor. In the case of triple fullerene/porphyrin/SWCNT architectures, the photoexcited porphyrins act as electron donors toward the fullerene and SWCNT. These mechanisms are rationalized with the molecular orbital considerations performed for these huge supramolecules. For the confirmation of the electron transfer processes, transient absorption methods have been used, in addition to time-resolved fluorescence spectral measurements. The kinetic data obtained in solution are found to be quite useful to predict the efficiencies of photovoltaic cells.

  10. A hybrid PSO-PID approach for trajectory tracking application of a liquid level control process

    Turker Tekin Erguzel

    2015-07-01

    Full Text Available Water level control is a crucial step for steam generators (SG which are widely used to control the temperature of nuclear power plants. The control process is therefore a challenging task to improve the performance of water level control system. The performance assessment is another consideration to underline. In this paper, in order to get better control of water level, the nonlinear process was first expressed in terms of a transfer function (TF, a proportional-integral-derivative (PID controller was then attached to the model. The parameters of the PID controller was finally optimized using particle swarm optimization (PSO. Simulation results indicate that the proposed approach can make an effective tracking of a given level set or reference trajectory.

  11. Characteristics of conventional STI process-related deep-level traps in Silicon

    Kang, In Man; Kwon, Hyuck In; Lee, Myung Won; Park, Byung Gook; Lee, Jong Duk [Seoul National University, Seoul (Korea, Republic of); Park, Sang Sik [Sejong University, Seoul (Korea, Republic of); Ahn, Jung Chak; Lee, Yong Hee [Samsung Electronics Industries Co., Ltd., Yongin (Korea, Republic of)

    2004-01-15

    The deep-level traps in Si substrates caused by the shallow trench isolation (STI) process have been investigated using deep level transient spectroscopy (DLTS). For the DLTS measurements, test patterns consisting of the STI arrays fabricated on p-type epitaxy wafers are proposed. Based on the DLTS measurements, four kinds of deep level traps, which are thought to be related to the STI process, are detected at E{sub v} + 0.16 eV, E{sub c} - 0.23 eV, E{sub c} - 0.55 eV, and E{sub v} + 0.58 eV, respectively. The deep levels at E{sub c} - 0.55 eV and E{sub v} + 0.58 eV can act as generation-recombination centers. The density of traps was significantly reduced after low-temperature annealing.

  12. Bidirectional Five-Level Power Processing Interface for Low Voltage Battery Energy Storage System

    Huang, Jain-Yi; Jou, Hurng-Liahng; Wu, Kuen-Der; Lin, You-Si; Wu, Jinn-Chang

    A bidirectional five-level power processing interface for low voltage battery energy storage system (BESS) is developed in this paper. This BESS consists of a bidirectional five-level DC-AC converter, a bidirectional dual boost/buck DC-DC converter and a battery set. This five-level DC-AC converter includes a bidirectional full-bridge converter and a bidirectional dual buck DC-DC converter. The five-level power processing interface can charge power to the battery set form the utility or discharge the power from the battery set to the utility depending on the demanded operation of user. A hardware prototype is developed to verify the performance of this BESS. Experimental results show the performance of the developed BESS is as expected.

  13. Research of serum total and high-molecular-weight adiponectin levels in patients with type 2 diabetic retinopathy

    Yuan Zhang

    2016-03-01

    Full Text Available AIM:To explore the levels of serum total adiponectin, high-molecular-weight(HMWadiponectin and its ratio in type 2 diabetic retinopathy and to investigate risk factors of non-proliferative diabetic retinopathy.METHODS:Three hundred and seventy-four subjects were recruited from an epidemiological survey, including 88 patients with proliferative diabetic retinopathy, 124 patients with non-proliferative diabetic retinopathy, 78 patients only with type 2 diabetes mellitus and 84 healthy volunteers. Demographics, physical and laboratory parameters were collected. Serum total and HMW adiponectin levels were detected by ELISA. The main statistical analysis included covariance analysis and cumulative logit model.RESULTS:Total adiponectin level was higher in healthy group than in groups of only diabetes, non-proliferative and proliferative diabetic retinopathy(harmonic mean, 5.717, 3.310, 3.288, 3.822 μg/ml, F=18.792, PPF=14.025, PP>0.05. The ratio of HMW adiponectin and total adiponectin had no differences among four groups(F=0.650, P>0.05. Drug history, high levels of high density lipoprotein cholesterol, total and HMW adiponectin had protective effects to the non-proliferative diabetic retinopathy(PCONCLUSION:The lower concentrations of serum total and HMW adiponectin may result in the occurrence of non-proliferative diabetic retinopathy. And the total adiponectin level was related to the severity of diabetic retinopathy.

  14. Review process of PSA Level 2 of KBR. Concept and experience

    In Germany, a periodic safety review (PSR) has to be performed every 10 years by the utility. In the past, a PSR only included a plant-specific probabilistic safety analysis (PSA) Level 1 study. For the NPP Brokdorf (KBR) PSA Level 2 project, an agreement was reached between all parties involved that the study will be performed not as a part of the PSR process, but supplementary to it. Since a revised version of the German PSA guideline has been released in 2005, these plant-specific PSAs have to include a PSA Level 2, too. This paper will focus on conclusions and findings from a ongoing parallel review process of the first full scope PSA Level 2 performed by the utility for KBR, a typical German PWR-1300. The responsible authority 'Ministerium fuer Soziales, Gesundheit, Familie, Jugend und Senioren des Landes Schleswig-Holstein (MSGF)' (Ministry of Social Affairs, Health, Family, Youth and Senior Citizens of Schleswig-Holstein) initiated this parallel review process in agreement with the utility KBR and the E.ON Kernkraft in 2006. The project will be completed soon. Such a review process allows that essential steps of the PSA will be reviewed and commented before the PSA Level 2 will be finished. So the benefit from this parallel review process is a significant enhancement of the quality and completeness of the PSA Level 2 study as the majority of the recommendations given by the review team has been taken over by the utility and the developer of the PSA, the Areva NP company. Further, a common understanding and agreement will be reached at the end between all parties involved on the major topics of the PSA Level 2 study. (orig.)

  15. Fragile X and autism: Intertwined at the molecular level leading to targeted treatments

    Hagerman Randi

    2010-09-01

    Full Text Available Abstract Fragile X syndrome (FXS is caused by an expanded CGG repeat (> 200 repeats in the 5' untranslated portion of the fragile mental retardation 1 gene (FMR1, leading to deficiency or absence of the FMR1 protein (FMRP. FMRP is an RNA carrier protein that controls the translation of several other genes that regulate synaptic development and plasticity. Autism occurs in approximately 30% of FXS cases, and pervasive developmental disorder, not otherwise specified (PDD-NOS occurs in an additional 30% of cases. Premutation repeat expansions (55 to 200 CGG repeats may also give rise to autism spectrum disorders (ASD, including both autism and PDD-NOS, through a different molecular mechanism that involves a direct toxic effect of the expanded CGG repeat FMR1 mRNA. RNA toxicity can also lead to aging effects including tremor, ataxia and cognitive decline, termed fragile X-associated tremor ataxia syndrome (FXTAS, in premutation carriers in late life. In studies of mice bearing premutation expansions, there is evidence of early postnatal neuronal cell toxicity, presenting as reduced cell longevity, decreased dendritic arborization and altered synaptic morphology. There is also evidence of mitochondrial dysfunction in premutation carriers. Many of the problems with cellular dysregulation in both premutation and full mutation neurons also parallel the cellular abnormalities that have been documented in autism without fragile X mutations. Research regarding dysregulation of neurotransmitter systems in FXS, including the metabotropic glutamate receptor (mGluR1/5 pathway and ? aminobutyric acid (GABAA pathways, have led to new targeted treatments for FXS. Preliminary evidence suggests that these new targeted treatments will also be beneficial in non-fragile X forms of autism.

  16. Molecular and Genomic Characterization of Vibrio mimicus Isolated from a Frozen Shrimp Processing Facility in Mexico

    Guardiola-Avila, Iliana; Acedo-Felix, Evelia; Sifuentes-Romero, Itzel; Yepiz-Plascencia, Gloria; Gomez-Gil, Bruno; Noriega-Orozco, Lorena

    2016-01-01

    Vibrio mimicus is a gram-negative bacterium responsible for diseases in humans. Three strains of V. mimicus identified as V. mimicus 87, V. mimicus 92 and V. mimicus 93 were isolated from a shrimp processing facility in Guaymas, Sonora, Mexico. The strains were analyzed using several molecular techniques and according to the cluster analysis they were different, their similarities ranged between 51.3% and 71.6%. ERIC-PCR and RAPD (vmh390R) were the most discriminatory molecular techniques for the differentiation of these strains. The complete genomes of two strains (V. mimicus 87, renamed as CAIM 1882, and V. mimicus 92, renamed as CAIM 1883) were sequenced. The sizes of the genomes were 3.9 Mb in both strains, with 2.8 Mb in ChI and 1.1 Mb in ChII. A 12.7% difference was found in the proteome content (BLAST matrix). Several virulence genes were detected (e.g. capsular polysaccharide, an accessory colonization factor and genes involved in quorum-sensing) which were classified in 16 categories. Variations in the gene content between these genomes were observed, mainly in proteins and virulence genes (e.g., hemagglutinin, mobile elements and membrane proteins). According to these results, both strains were different, even when they came from the same source, giving an insight of the diversity of V. mimicus. The identification of various virulence genes, including a not previously reported V. mimicus gene (acfD) in ChI in all sequenced strains, supports the pathogenic potential of this species. Further analysis will help to fully understand their potential virulence, environmental impact and evolution. PMID:26730584

  17. Molecular and Genomic Characterization of Vibrio mimicus Isolated from a Frozen Shrimp Processing Facility in Mexico.

    Guardiola-Avila, Iliana; Acedo-Felix, Evelia; Sifuentes-Romero, Itzel; Yepiz-Plascencia, Gloria; Gomez-Gil, Bruno; Noriega-Orozco, Lorena

    2016-01-01

    Vibrio mimicus is a gram-negative bacterium responsible for diseases in humans. Three strains of V. mimicus identified as V. mimicus 87, V. mimicus 92 and V. mimicus 93 were isolated from a shrimp processing facility in Guaymas, Sonora, Mexico. The strains were analyzed using several molecular techniques and according to the cluster analysis they were different, their similarities ranged between 51.3% and 71.6%. ERIC-PCR and RAPD (vmh390R) were the most discriminatory molecular techniques for the differentiation of these strains. The complete genomes of two strains (V. mimicus 87, renamed as CAIM 1882, and V. mimicus 92, renamed as CAIM 1883) were sequenced. The sizes of the genomes were 3.9 Mb in both strains, with 2.8 Mb in ChI and 1.1 Mb in ChII. A 12.7% difference was found in the proteome content (BLAST matrix). Several virulence genes were detected (e.g. capsular polysaccharide, an accessory colonization factor and genes involved in quorum-sensing) which were classified in 16 categories. Variations in the gene content between these genomes were observed, mainly in proteins and virulence genes (e.g., hemagglutinin, mobile elements and membrane proteins). According to these results, both strains were different, even when they came from the same source, giving an insight of the diversity of V. mimicus. The identification of various virulence genes, including a not previously reported V. mimicus gene (acfD) in ChI in all sequenced strains, supports the pathogenic potential of this species. Further analysis will help to fully understand their potential virulence, environmental impact and evolution. PMID:26730584

  18. Solution processable small molecular host materials for blue and white phosphorescence OLEDs

    Lee, Yi-Ting; Chang, Yung-Ting; Chen, Chin-Ti; Chen, Chao-Tsen

    2013-09-01

    Three new solution processable small molecular host materials based on bis-[3,5-di(9H-carbazol-9-yl)phenyl] structural moiety have been developed for blue phosphorescence (FIrpic dopant) organic light-emitting diodes. Whereas N,N-bis-[3,5-di(9H-carbazol-9-yl)phenyl]methylamine (CzPAMe) has the highest solid state triplet energy gap (ET) of 2.73 eV, tetrakis-[3,3',5,5'-(9H-carbazol-9-yl)]triphenylphosphine oxide (CzPPO) and N,N-bis-[3,5-di(9H-carbazol-9-yl)phenyl]pyrimidin-2-amine (CzPAPm) are two host materials potentially being bipolar for charge transport due to the electron deficient unit of phenylphosphine oxide and pyrimidine, respectively. Due to the insufficient ET (2.56 eV) of CzPAPm, CzPPO or CzPAMe devices are significantly better than CzPAPm devices with or without 1,3-bis[(4-tert-butylphenyl)-1,3,4-oxadiazolyl]phenylene (OXD-7) co-host. Particularly, having no OXD-7 co-host and no vacuum-thermal-deposited extra electron transporting layer, single-layer devices of CzPPO surpassing CzPAMe devices reach current efficiency as high as 9.32 cd/A (or power efficiency of 4.97 lm/W), which is one of the highest of the kind. Corresponding single-layer white phosphorescence OLEDs are also fabricated with the small molecular host material demonstrated herein.

  19. QCD Factorization of Semi-Inclusive DIS Process at Operator Level

    Zhou, Gao-Liang

    2016-02-01

    The operator level proof of factorization theorem exhibited in [arXiv:hep-ph/1307.4194] is extended to the semi-inclusive deep inelastic scattering process(SIDIS). Factorization theorem can be proved at operator level if there are not detected soft hadrons. The key point is that the initial one-nucleon state is the eigenstate of QCD. Supported by the National Nature Science Foundation of China under Grant No. 11275242

  20. An optimal retrieval, processing, and blending strategy for immobilization of Hanford high-level tank waste

    Hanford tank waste will be separated into high-level and low-level portions; each portion will then be vitrified (other waste forms are also being considered for low-level waste) to produce a stable glass form for disposal. Because of the wide variability in the tank waste compositions, blending is being considered as a way to reduce the number of distinct compositions that must be vitrified and to minimize the resultant volume of vitrified waste. Three years of computational glass formulation and blending studies have demonstrated that blending of the high-level waste before vitrification can reduce the volume of high-level waste glass required by as much as 50 percent. This level of reduction would be obtained if all the high-level waste were blended together (Total Blend) prior to vitrification, requiring the retrieval and pretreatment of all tank waste before high-level vitrification was started. This paper will present an overall processing strategy that should be able to match the blending performance of the Total Blend and be more logistically feasible. The strategy includes retrieving, pretreating, blending and vitrifying Hanford tank waste. This strategy utilizes blending both before and after pretreatment. Similar wastes are blended before pretreatment, so as not to dilute species targeted for removal. The high-level portions of these pretreated early blends are then selectively blended to produce a small number of high-level vitrification feed streams

  1. Molecular-Level Simulation of Solubility and Speciation in Aqueous Electrolytes

    Jirsák, Jan; Škvor, J.; Moučka, F.; Smith, W.R.; Nezbeda, Ivo

    - : -, 2010, s. 91. ISBN N. [International Symposium on Solubility Phenomena & Related Equilibrium Processes /14./. Leoben (AT), 25.07.2010-30.07.2010] R&D Projects: GA AV ČR IAA400720802 Grant ostatní: NSERC(CA) OGP1041 Institutional research plan: CEZ:AV0Z40720504 Keywords : electrolytes * water * copper-chlorine cycle Subject RIV: CF - Physical ; Theoretical Chemistry

  2. False memory and level of processing effect: an event-related potential study.

    Beato, Maria Soledad; Boldini, Angela; Cadavid, Sara

    2012-09-12

    Event-related potentials (ERPs) were used to determine the effects of level of processing on true and false memory, using the Deese-Roediger-McDermott (DRM) paradigm. In the DRM paradigm, lists of words highly associated to a single nonpresented word (the 'critical lure') are studied and, in a subsequent memory test, critical lures are often falsely remembered. Lists with three critical lures per list were auditorily presented here to participants who studied them with either a shallow (saying whether the word contained the letter 'o') or a deep (creating a mental image of the word) processing task. Visual presentation modality was used on a final recognition test. True recognition of studied words was significantly higher after deep encoding, whereas false recognition of nonpresented critical lures was similar in both experimental groups. At the ERP level, true and false recognition showed similar patterns: no FN400 effect was found, whereas comparable left parietal and late right frontal old/new effects were found for true and false recognition in both experimental conditions. Items studied under shallow encoding conditions elicited more positive ERP than items studied under deep encoding conditions at a 1000-1500 ms interval. These ERP results suggest that true and false recognition share some common underlying processes. Differential effects of level of processing on true and false memory were found only at the behavioral level but not at the ERP level. PMID:22811058

  3. Correlation test to assess low-level processing of high-density oligonucleotide microarray data

    Bergh Jonas

    2005-03-01

    Full Text Available Abstract Background There are currently a number of competing techniques for low-level processing of oligonucleotide array data. The choice of technique has a profound effect on subsequent statistical analyses, but there is no method to assess whether a particular technique is appropriate for a specific data set, without reference to external data. Results We analyzed coregulation between genes in order to detect insufficient normalization between arrays, where coregulation is measured in terms of statistical correlation. In a large collection of genes, a random pair of genes should have on average zero correlation, hence allowing a correlation test. For all data sets that we evaluated, and the three most commonly used low-level processing procedures including MAS5, RMA and MBEI, the housekeeping-gene normalization failed the test. For a real clinical data set, RMA and MBEI showed significant correlation for absent genes. We also found that a second round of normalization on the probe set level improved normalization significantly throughout. Conclusion Previous evaluation of low-level processing in the literature has been limited to artificial spike-in and mixture data sets. In the absence of a known gold-standard, the correlation criterion allows us to assess the appropriateness of low-level processing of a specific data set and the success of normalization for subsets of genes.

  4. Evaluation of high-level waste pretreatment processes with an approximate reasoning model

    The development of an approximate-reasoning (AR)-based model to analyze pretreatment options for high-level waste is presented. AR methods are used to emulate the processes used by experts in arriving at a judgment. In this paper, the authors first consider two specific issues in applying AR to the analysis of pretreatment options. They examine how to combine quantitative and qualitative evidence to infer the acceptability of a process result using the example of cesium content in low-level waste. They then demonstrate the use of simple physical models to structure expert elicitation and to produce inferences consistent with a problem involving waste particle size effects

  5. A novel technique for die-level post-processing of released optical MEMS

    Elsayed, Mohannad Y.; Beaulieu, Philippe-Olivier; Briere, Jonathan; Ménard, Michaël; Nabki, Frederic

    2016-05-01

    This work presents a novel die-level post-processing technique for dies including released movable structures. The procedure was applied to microelectromechanical systems (MEMS) chips that were fabricated in a commercial process, SOIMUMPs from MEMSCAP. It allows the performance of a clean DRIE etch of sidewalls on the diced chips enabling the optical testing of the pre-released MEMS mirrors through the chip edges. The etched patterns are defined by photolithography using photoresist spray coating. The photoresist thickness is tuned to create photoresist bridges over the pre-released gaps, protecting the released structures during subsequent wet processing steps. Then, the chips are subject to a sequence of wet and dry etching steps prior to dry photoresist removal in O2 plasma. Processed micromirrors were tested and found to rotate similarly to devices without processing, demonstrating that the post-processing procedure does not affect the mechanical performance of the devices significantly.

  6. Isolating Neural Indices of Continuous Speech Processing at the Phonetic Level.

    Di Liberto, Giovanni M; Lalor, Edmund C

    2016-01-01

    The human ability to understand speech across an enormous range of listening conditions is underpinned by a hierarchical auditory processing system whose successive stages process increasingly complex attributes of the acoustic input. In order to produce a categorical perception of words and phonemes, it has been suggested that, while earlier areas of the auditory system undoubtedly respond to acoustic differences in speech tokens, later areas must exhibit consistent neural responses to those tokens. Neural indices of such hierarchical processing in the context of continuous speech have been identified using low-frequency scalp-recorded electroencephalography (EEG) data. The relationship between continuous speech and its associated neural responses has been shown to be best described when that speech is represented using both its low-level spectrotemporal information and also the categorical labelling of its phonetic features (Di Liberto et al., Curr Biol 25(19):2457-2465, 2015). While the phonetic features have been proven to carry extra-information not captured by the speech spectrotemporal representation, the causes of this EEG activity remain unclear. This study aims to demonstrate a framework for examining speech-specific processing and for disentangling high-level neural activity related to intelligibility from low-level activity in response to spectrotemporal fluctuations of speech. Preliminary results suggest that neural measure of processing at the phonetic level can be isolated. PMID:27080674

  7. Planning and organization of the learning process in art education at primary level

    Jakopin, Nives

    2011-01-01

    Planning and organization in any learning process is difficult. It consists of accepted curriculum, organization of the school and local community. In what extent and how the teachers will implement formal directions into the classroom planning, depends on the teacher as the individual and his planning of the pedagogical process. (Uljens, 1997) Theoretical part of the thesis will present education at primary level in the Republic of Slovenia. It will present the documents in primary school...

  8. Developmental Family Processes and Interparental Conflict: Patterns of Micro-level Influences

    Schermerhorn, Alice C.; Chow, Sy-Miin; CUMMINGS, E. MARK

    2010-01-01

    Although frequent calls are made for the study of effects of children on families and mutual influence processes within families, little empirical progress has been made. We address these questions at the level of micro processes during marital conflict, including children’s influence on marital conflict and parents’ influence on each other. Participants were 111 cohabiting couples with a child (55 males, 56 females) aged 8 – 16 years. Data were drawn from parents’ diary reports of interparen...

  9. The Effect of Sea Level Changes on Geomorphological Processes Along the Coast.

    Kapule, D.E.

    1991-01-01

    Geomorphological processes at work on the coastal landforms are influenced by a number of environmental factors. The coastal area is a scene of interaction between different spheres of the earth like hydrosphere, lithosphere, atmosphere, biosphere and technosphere. Each of these spheres has its own influence on the development of the coastal landforms. This paper tries to explain the effect of the sea level change on geomorphological processes taking into account the influence imparted by eac...

  10. Operational nanometric gas counters for nuclear risk assessment at the bio-molecular level

    The practical implementation of the system for protection of persons against exposure to ionizing radiation requires that appropriate radiation detectors be designed to produce an output signal which can be related to the risk of deleterious biological effect. At present, conventional dosimeters are used to assess the risk either by measurement of macroscopic quantities such as energy imparted, modified by appropriately evaluated weighting factors, or by microdosimeters which can measure simultaneously the dose and a quality factor obtained from the stochastic distribution of dose, e.g. the lineal energy of microdosimetry. Both types of dosimeter now have recognised limitations which inhibit their accuracy for damage assessment. This is because in practice their radiation response functions could not take account of advances in our understanding of the radiobiological damage mechanisms which involve 'target' sizes of sub-micron dimensions, less than 30 nm, and probably as small as molecular dimensions of 2 nm e.g. a segment of the DNA. If radiation detectors can be designed to simulate the response of relevant biological material by allowing for the dimensions and multiplicity of the radiosensitive target sizes, then there are good prospects of achieving significant improvements in dosimetry instrumentation which, in principle, could lead to direct measurement of risk in unknown radiation fields without the need for arbitrary modifying factors or knowledge of the radiation type. In this context of the foregoing, a prototype of a nanodosimetric counter has been built and used to measure the ionization cluster size distributions for energetic ?-particles in tissue equivalent gases with a spatial resolution of 1 nm. The total and double differential electron scattering cross-sections of the components of the tissue equivalent gases have been measured absolutely for electron energies up to 5 keV and for scattering angles from 30 deg to 120 deg by applying a new method. These cross-sections are implemented in a Monte Carlo code which is developed for realistic simulation of the stochastic nature of the radiation interactions on the scale of the DNA size. The agreement of the experimental data with the results of the Monte Carlo simulation is satisfactory and encouraging (author)

  11. Excitation and deexcitation of N2 molecular levels. Induced fluorescence by electrons and laser

    The electron impact excitation followed by fluorescence induced by N2-laser absorption was used to study the lifetime of the lowest vibrational level of the B 3πg electronic state of N2. The experimental result of this work is 13 + 1 μs. To measure the lifetime of B 3πg (v=2,3,5,6,7,8) levels the delayed coincidence method by electron impact was use. The lifetime values were compared with recent experimental and theoretical results. The relative intensi-ties of 3πg --- A 3ΣΩ+ system bands, in the range (6540-10500 Ao) was measured using a hollow cathode lamp as spectral source. The relative transition moments and its dependence versus the r-centroid was obtained. Total cross sections for electron scattering by N molecules in the range 600 - 5000 eV have been obtained from measurements of the attenuation of a linear electron beam. The results have been compared with available experimental cross sections and with theoretical calculations based on the first Born approximation. (Author)

  12. Ceramic process and plant design for high-level nuclear waste immobilization

    In the last 3 years, significant advances in ceramic technology for high-level nuclear waste solidification have been made. Product quality in terms of leach-resistance, compositional uniformity, structural integrity, and thermal stability promises to be superior to borosilicate glass. This paper addresses the process effectiveness and preliminary designs for glass and ceramic immobilization plants. The reference two-step ceramic process utilizes fluid-bed calcination (FBC) and hot isostatic press (HIP) consolidation. Full-scale demonstration of these well-developed processing steps has been established at DOE and/or commercial facilities for processing radioactive materials. Based on Savannah River-type waste, our model predicts that the capital and operating cost for the solidification of high-level nuclear waste is about the same for the ceramic and glass options. However, when repository costs are included, the ceramic option potentially offers significantly better economics due to its high waste loading and volume reduction. Volume reduction impacts several figures of merit in addition to cost such as system logistics, storage, transportation, and risk. The study concludes that the ceramic product/process has many potential advantages, and rapid deployment of the technology could be realized due to full-scale demonstrations of FBC and HIP technology in radioactive environments. Based on our finding and those of others, the ceramic innovation not only offers a viable backup to the glass reference process but promises to be a viable future option for new high-level nuclear waste management opportunities

  13. Energy level decay processes in Ho3+-doped tellurite glass relevant to the 3-µm transition

    Milanese, Daniel; Boetti, Nadia Giovanna; Lousteau, Joris

    2011-01-01

    The primary excited state decay processes relating to the 5I6 --> 5I7 at 2.9 um laser transition in singly Ho3+-doped tellurite (TZBG) glass have been investigated in detail using time-resolved fluorescence spectroscopy. Selective laser excitation of the 5I6 energy level at 1151 nm and 5I7 energy level at 1958 nm has established that the rate of energy transfer up-conversion between holmium ions excited to the 5I7 level is negligible for Ho3+ concentrations up to 4 mol. %. Excited state absor...

  14. Molecular-Level Computer Simulation of a Vapor-Compression Refrigeration Cycle

    Figueroa-Gerstenmaier, S.; Francova, M.; Kowalski, M.; Lísal, Martin; Nezbeda, Ivo; Smith, W.R.

    2007-01-01

    Roč. 259, č. 2 (2007), s. 195-200. ISSN 0378-3812 R&D Projects: GA ČR(CZ) GA203/05/0725; GA AV ČR 1ET400720409; GA AV ČR 1ET400720507 Grant ostatní: NRCC(CA) OGP 1041 Institutional research plan: CEZ:AV0Z40720504 Source of funding: V - iné verejné zdroje Keywords : alternative refrigerants * joule- thomson expansion * adiabatic process Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.506, year: 2007

  15. Description of Cognitive and Competence Processes Involved in the Levels of Reading Comprehension in College Students

    Charles Romel Yáñez Botello

    2013-12-01

    Full Text Available This is a descriptive research whose main objective was to describe the cognitive processes involved in reading and its relation to different levels of reading comprehension. For doing so, it was chosen a sample of 124 college students of Bogotá city. Participants- men and women between 16 and 30 years old- were studying first semester of psychology. The Evaluation Test for Reading Comprehension by Arenas (2007 was applied in order to describe cognitive operations. Moreover, results related to comprehension levels were analyzed through the Rasch Model. Besides, the Angof Methodology was used to specify the competence levels. It was concluded that there are five levels of reading comprehension. It must be said that most of the students were classified in the literal and inferential reading levels. Finally, the findings and limitations of the research were discussed.

  16. Molecular mapping to species level of the tonsillar crypt microbiota associated with health and recurrent tonsillitis

    Jensen, Anders; Fag-Olsen, Helena; Srensen, Christian Hjort; Kilian, Mogens

    2013-01-01

    level. A complex microbiota consisting of between 42 and 110 taxa was demonstrated in both children and adults. This included a core microbiome of 12 abundant genera found in all samples regardless of age and health status. Yet, Haemophilus influenzae, Neisseria species, and Streptococcus pneumoniae...... and included species that are considered putative pathogens in periodontal diseases, i.e. Porphyromonas gingivalis, Porphyromonas endodontalis, and Tannerella forsythia. Unifrac analysis showed that recurrent tonsillitis is associated with a shift in the microbiota of the tonsillar crypts...... tonsillitis is a polymicrobial infection in which interactions within consortia of taxa play an etiologic role. The study contributes to the human microbiome data, to the understanding of the etiology of infections affecting the tonsils, and forms a basis for further insight into the consequences of the...

  17. Effect of Chayotte Extract on the Biochemical Determinations and on Molecular and Cellular Levels

    M.L. Gomes

    2004-01-01

    Full Text Available The use of natural products occurs around the world. The labeling of blood constituents with technetium-99m (99m Tc has been influenced by natural extracts. We evaluated the influence of a chayotte(Sechium edule extract on the labeling of blood elements with 99m Tc, in the structural conformation of DNA, in the biochemistry of blood and in the measurement of. blood pressure. The animals were treated with chayotte during 15 days and samples of blood were withdrawn. The samples were incubated with stannous chloride and with 99mTc. Plasma(P and blood cells (BC were isolated, also precipitated with trichloroacetic acid and soluble(SF and insoluble fractions(IF separated. There was a decrease in the radioactivity in IF-P(from 83.96 ± 4.28 to 53.26 ± 6.69. Samples of blood from the treated group were carried out with specific biochemistry kits and the blood biochemistry analysis compounds was done. It was analyzed the level of uric acid, albumin, cholesterol, creatinine, glucose, high density lipoprotein (HDL, globulin and trigliceridics. The gauging of the blood pressure of the animals was taken. Our results showed a reduction on the level of glucose (from 118.40 ± 10.69 to 97.20 ± 4.32 and globulin (3.52 ± 0.13 to 3.08 ± 0.19 as well as in the diastolic pressure (from 123.80 ± 9.12 to 84.40 ± 3.85. It was observed that the referred extract has induced lesions on the DNA molecule. The effect of chayotte extract probably, could be explained by the metabolization of the chayotte that could be capable to induce the generation of active metabolites with oxidant properties.

  18. High level model predictive control for plug-and-play process control with stability guaranty

    Michelsen, Axel Gottlieb; Stoustrup, Jakob

    2010-01-01

    In this paper a method for designing a stabilizing high level model predictive controller for a hierarchical plug- and-play process is presented. This is achieved by abstracting the lower layers of the controller structure as low order models with uncertainty and by using a robust model predictive...... controller for generating the references for these. A simulation example, in which the actuators in a process control system are changed, is reported to show the potential of this approach for plug and play process control....

  19. Nested Hierarchical Dirichlet Processes for Multi-Level Non-Parametric Admixture Modeling

    Tekumalla, Lavanya Sita; Agrawal, Priyanka; Bhattacharya, Indrajit

    2015-01-01

    Dirichlet Process(DP) is a Bayesian non-parametric prior for infinite mixture modeling, where the number of mixture components grows with the number of data items. The Hierarchical Dirichlet Process (HDP), is an extension of DP for grouped data, often used for non-parametric topic modeling, where each group is a mixture over shared mixture densities. The Nested Dirichlet Process (nDP), on the other hand, is an extension of the DP for learning group level distributions from data, simultaneousl...

  20. An innovative approach to solid Low Level Radioactive Waste processing and disposal

    This paper will focus on a new system of Low Level Radioactive Waste (LLW) accumulation, processing and packaging, as-well as the implementation of a Laboratory-wide training program used to introduce new waste accumulation containers to all of the on-site radioactive waste generators, and to train them on the requirements of this innovative waste characterization and documentation program

  1. Facilities for processing and solidification of intermediate- and low-level liquid radioactive wastes

    For intermediate- and low-level liquid radioactive wastes processing two units are proposed. Technological schemes of both units include primary purification of solutions from solids, waste reagent treatment , preparation of waste concentrated product, evaporation of concentrated product and remainder drying. Difference between unit 1 and 2 is in methods used for preparation of concentrated product: unit 1 - settling, unit 2 - filtration

  2. Level of Processing Modulates the Neural Correlates of Emotional Memory Formation

    Ritchey, Maureen; LaBar, Kevin S.; Cabeza, Roberto

    2011-01-01

    Emotion is known to influence multiple aspects of memory formation, including the initial encoding of the memory trace and its consolidation over time. However, the neural mechanisms whereby emotion impacts memory encoding remain largely unexplored. The present study used a levels-of-processing manipulation to characterize the impact of emotion on…

  3. Pedagogical Technology of Improving the Students' Viability Levels in the Process of Mastering Foreign Language

    Dmitrienko, Nadezhda; Ershova, Svetlana; Konovalenko, Tatiana; Kutsova, Elvira; Yurina, Elena

    2015-01-01

    The article points out that the process of mastering foreign language stimulates students' personal, professional and cultural growth, improving linguistic, communicative competences and viability levels. A proposed pedagogical technology of modeling different communicative situations has a serious synergetic potential for students' self organized

  4. "Assessment Drives Learning": Do Assessments Promote High-Level Cognitive Processing?

    Bezuidenhout, M. J.; Alt, H.

    2011-01-01

    Students tend to learn in the way they know, or think, they will be assessed. Therefore, to ensure deep, meaningful learning, assessments must be geared to promote cognitive processing that requires complex, contextualised thinking to construct meaning and create knowledge. Bloom's taxonomy of cognitive levels is used worldwide to assist in…

  5. Greater-than-class C low-level waste characterization technical review process

    The objective of this paper is to present the technical review process that has been used to complete projections of commercial Greater-Than-Class C low-level waste (GTCC LLW). Accurate projections are necessary in order to support planning for management of GTCC LLW, including storage, treatment, and disposal. The projections include estimates of volumes, activities, radionuclides, waste generators, and waste types

  6. Reactivity of the calcite–water-interface, from molecular scale processes to geochemical engineering

    Highlights: • The current state of some aspects of calcite–water-interface chemistry is reviewed. • The interface structure is characterized at a molecular scale. • Experimental and theoretical studies on contaminant sorption at calcite are presented. • The influence of phosphonates on calcite growth is investigated. • The effect of limestone on the workability of cement suspensions is addressed. - Abstract: Surface reactions on calcite play an important role in geochemical and environmental systems, as well as many areas of industry. In this review, we present investigations of calcite that were performed in the frame of the joint research project “RECAWA” (reactivity of calcite–water-interfaces: molecular process understanding for technical applications). As indicated by the project title, work within the project comprised a large range of length scales. The molecular scale structure of the calcite (1 0 4)–water-interface is refined based on surface diffraction data. Structural details are related to surface charging phenomena, and a simplified basic stern surface complexation model is proposed. As an example for trace metal interactions with calcite surfaces we review and present new spectroscopic and macroscopic experimental results on Selenium interactions with calcite. Results demonstrate that selenate (SeO42−) shows no significant interaction with calcite at our experimental conditions, while selenite (SeO32−) adsorbs at the calcite surface and can be incorporated into the calcite structure. Atomistic calculations are used to assess the thermodynamics of sulfate (SO42−), selenate (SeO42−), and selenite (SeO32−) partitioning in calcite and aragonite. The results show that incorporation of these oxo-anions into the calcite structure is so highly endothermic that incorporation is practically impossible at bulk equilibrium and standard conditions. This indicates that entrapment processes are involved when coprecipitation is observed experimentally. The relevance of nano-scale surface features is addressed in an investigation of calcite growth and precipitation in the presence of phosphonates, demonstrating the influence of phosphonates on the morphology of growth spirals and macroscopic growth rates. It is investigated how physical properties of limestone containing cement suspensions may influence the workability of the cement suspensions and thus the efficacy of limestone in industrial applications. The largest scale is reached in iron filtration experiments in a water-purification-pilot-plant using limestone as filter material, which appeared to be highly effective for removing iron from drinking water. Investigations presented cover a whole series of methods to study the calcite–water-interface. Many calcite related topics are addressed, demonstrating how broad the field of calcite–water-interface research is and how manifold the applications are, for which calcite–water-interface phenomena are of major relevance

  7. The disposal of intermediate-level radioactive liquid waste by hydraulic fracturing process

    The hydraulic fracturing process is characterized by combination of the treatment with the disposal of ILLW (intermediate-level liquid waste). It is of cement solidification in deep geology stratum. First of all, it is necessary to select a suitable disposal site with detailed information on geology and hydrogeology. The process has such advantages as simple, low cost, large capacity of disposal, safe and reliable in technology. It is an attractive process of ILLW. Since 1980's, the research and the concept design of the hydraulic fracturing process have been initiated for disposal of ILLW. It is demonstrated by the field tests. The authors considered that the geological structure near Sichuan Nuclear Fuel Plant fits the disposal of ILLW by the hydraulic fracturing process

  8. Unravelling Doping Effects on PEDOT at the Molecular Level: From Geometry to Thermoelectric Transport Properties.

    Shi, Wen; Zhao, Tianqi; Xi, Jinyang; Wang, Dong; Shuai, Zhigang

    2015-10-14

    Tuning carrier concentration via chemical doping is the most successful strategy to optimize the thermoelectric figure of merit. Nevertheless, how the dopants affect charge transport is not completely understood. Here we unravel the doping effects by explicitly including the scattering of charge carriers with dopants on thermoelectric properties of poly(3,4-ethylenedioxythiophene), PEDOT, which is a p-type thermoelectric material with the highest figure of merit reported. We corroborate that the PEDOT exhibits a distinct transition from the aromatic to quinoid-like structure of backbone, and a semiconductor-to-metal transition with an increase in the level of doping. We identify a close-to-unity charge transfer from PEDOT to the dopant, and find that the ionized impurity scattering dominates over the acoustic phonon scattering in the doped PEDOT. By incorporating both scattering mechanisms, the doped PEDOT exhibits mobility, Seebeck coefficient and power factors in very good agreement with the experimental data, and the lightly doped PEDOT exhibits thermoelectric properties superior to the heavily doped one. We reveal that the thermoelectric transport is highly anisotropic in ordered crystals, and suggest to utilize large power factors in the direction of polymer backbone and low lattice thermal conductivity in the stacking and lamellar directions, which is viable in chain-oriented amorphous nanofibers. PMID:26406937

  9. Fortuitous description of hemoglobin Hope in a high-level Tunisian athlete: molecular diagnosis and origin.

    Bibi, Amina; Touhemi, Imed; Sahli, Chaima; Siala, Hajer; Bartagi, Zakia; Koubaa, Donia; Le Gallais, Daniel; Fattoum, Slaheddine; Messaoud, Taieb

    2012-01-01

    In this study we report the fortuitous description of hemoglobin (Hb) Hope in a Tunisian athlete. This Hb is one of hemoglobin variants that show a lower stability and oxygen affinity that is beneficial to tissue oxygen delivery. Hb Hope was isolated by automated high performance liquid chromatography and was unequivocally found to be Hb Hope using DNA-based methods: polymerase chain reaction, denaturing gradient gel electrophoresis, direct DNA sequencing. Restriction haplotype showed that this Hb was supported by the Mediterranean haplotype I. Hb Hope was identified at first in a black African-American family and later in several other black and non black ethnic groups. All these descriptions raise the question of the Hb Hope origin. Recently, Hb Hope was reported in Thai in association with the same Mediterranean haplotype I. This favors that Tunisian and Thai Hb Hope would share a common Mediterranean origin, thus suggesting the possibility of a Mediterranean gene flow. On another hand, the observation of Hb Hope in a high level athlete would suggest a selection pressure of this Hb variant due to higher physical aptitude. PMID:22565177

  10. Study of AFM-based nanometric cutting process using molecular dynamics

    Three-dimensional molecular dynamics (MD) simulations are conducted to investigate the atomic force microscope (AFM)-based nanometric cutting process of copper using diamond tool. The effects of tool geometry, cutting depth, cutting velocity and bulk temperature are studied. It is found that the tool geometry has a significant effect on the cutting resistance. The friction coefficient (cutting resistance) on the nanoscale decreases with the increase of tool angle as predicted by the macroscale theory. However, the friction coefficients on the nanoscale are bigger than those on the macroscale. The simulation results show that a bigger cutting depth results in more material deformation and larger chip volume, thus leading to bigger cutting force and bigger normal force. It is also observed that a higher cutting velocity results in a larger chip volume in front of the tool and bigger cutting force and normal force. The chip volume in front of the tool increases while the cutting force and normal force decrease with the increase of bulk temperature.

  11. Beyond Fullerenes: Designing Alternative Molecular Electron Acceptors for Solution-Processable Bulk Heterojunction Organic Photovoltaics.

    Sauv, Genevive; Fernando, Roshan

    2015-09-17

    Organic photovoltaics (OPVs) are promising candidates for providing a low cost, widespread energy source by converting sunlight into electricity. Solution-processable active layers have predominantly consisted of a conjugated polymer donor blended with a fullerene derivative as the acceptor. Although fullerene derivatives have been the acceptor of choice, they have drawbacks such as weak visible light absorption and poor energy tuning that limit overall efficiencies. This has recently fueled new research to explore alternative acceptors that would overcome those limitations. During this exploration, one question arises: what are the important design principles for developing nonfullerene acceptors? It is generally accepted that acceptors should have high electron affinity, electron mobility, and absorption coefficient in the visible and near-IR region of the spectra. In this Perspective, we argue that alternative molecular acceptors, when blended with a conjugated polymer donor, should also have large nonplanar structures to promote nanoscale phase separation, charge separation and charge transport in blend films. Additionally, new material design should address the low dielectric constant of organic semiconductors that have so far limited their widespread application. PMID:26722869

  12. Adopted levels and derived limits for Ra-226 and the decision making processes concerning TENORM releases

    A fraction of a primary dose limit can be, in general, agreed upon as a dose related level to be adopted in decision-making processes. In the case of TENORM releases, fractions of primary dose levels for 226Ra, 228Ra, and 210Po may be of particular importance to establish adopted levels and derived limits to guide decision making processes. Thus, for example, a registration level for 226Ra could be adopted at the highest portion of the natural background variation. Above such level, intervention and remedial action levels could also be adopted. All those levels would be fractions of the primary level, but translated in terms of derived limits expressed in practical units. Derived limits would then be calculated by using environmental models. In such approach 'critical groups' would have to be carefully defined and identified. In addition, the size of a critical group would be chosen to be used in environmental modeling. Site specific environmental models and parameters are desirable, though unavailable, or very difficult to obtain, in most cases. Thus, mathematical models and parameters of more generic nature are often used. A sensitive parametric analysis can make a ranking of the parameters used in a model, allowing one to choose how important each parameter will be for the model output. The paper will point out that when using the adopted levels and derived limits, as suggested above, the uncertainties and importance of the parameters entering an environmental model can make the difference for decision makers to take the right or wrong decision, as far as radiological protection is concerned. (author)

  13. Simulation modeling of nuclear steam generator water level process--a case study

    Zhao; Ou; Du

    2000-01-01

    Simulation modeling of the nuclear steam generator (SG) water level process in Qinshan Nuclear Power Plant (QNPP) is described in this paper. A practical methodology was adopted so that the model is both simple and accurate for control engineering implementation. The structure of the model is in the form of a transfer function, which was determined based on first-principles analysis and expert experience. The parameters of the model were obtained by taking advantage of the recorded historical response curves under the existing closed-loop control system. The results of process dimensional data verification and experimental tests demonstrate that the simulation model depicts the main dynamic characteristics of the SG water level process and is in accordance with the field recorded response curves. The model has been successfully applied to the design and test of an advanced digital feedwater control system in QNPP. PMID:10871210

  14. New treatment facility for low level process effluents at the Savannah River site

    A new facility, the F/H Effluent Treatment Facility (F/H ETF) is under construction at the Savannah River site. It will decontaminate process effluents containing low levels of radionuclides and hazardous chemicals prior to discharge to a surface stream. These effluents, which are currently discharged to seepage basins, originate in the chemical separations and high-level radioactive waste processing areas, known as F-Area and H-Area. The new facility will allow closure of the basins in order to meet the provisions of the Resource Conservation and Recovery Act by November 1988. A high degree of reliability is expected from this design as a result of extensive process development work that has been conducted at the Savannah River Laboratory. This work has included both bench scale testing of individual unit operations and pilot scale testing of an integrated facility, 150 to 285 L/min (40 to 75 gpm), that contains the major operations

  15. Optimization of sorption technology processing of liquid radioactive waste of low and middle activity level

    A substantial amount of liquid radioactive wastes (LRW) is formed during the regeneration of irradiated nuclear fuel (INF). Liquid wastes of low activity level (LAL) include: wash water and leakages; water for hydrotransport; water in storage basins; water from special laundries and disinfestation posts; and waste deactivation solutions. The radioactivity of these LRWs is equal to 1 x 10-7 1 x 10-5 Ci/l. Depending on the sources of the water supply for processing of INF, as well as technology and time (seasons) of processing, productivity and other factors, variations exist in the chemical and radiochemical compositions of LAL. This article discusses various processing treatments for low and intermediate level radioactive wastes

  16. A molecular dynamics simulation study of dynamic process and mesoscopic structure in liquid mixture systems

    Yang, Peng

    The focus of this dissertation is the Molecular Dynamics (MD) simulation study of two different systems. In thefirst system, we study the dynamic process of graphene exfoliation, particularly graphene dispersion using ionic surfactants (Chapter 2). In the second system, we investigate the mesoscopic structure of binary solute/ionic liquid (IL) mixtures through the comparison between simulations and corresponding experiments (Chapter 3 and 4). In the graphene exfoliation study, we consider two separation mechanisms: changing the interlayer distance and sliding away the relative distance of two single-layer graphene sheets. By calculating the energy barrier as a function of separation (interlayer or sliding-away) distance and performing sodium dodecyl sulfate (SDS) structure analysis around graphene surface in SDS surfactant/water + bilayer graphene mixture systems, we find that the sliding-away mechanism is the dominant, feasible separation process. In this process, the SDS-graphene interaction gradually replaces the graphene-graphene Van der Waals (VdW) interaction, and decreases the energy barrier until almost zero at critical SDS concentration. In solute/IL study, we investigate nonpolar (CS2) and dipolar (CH 3CN) solute/IL mixture systems. MD simulation shows that at low concentrations, IL is nanosegregated into an ionic network and nonpolar domain. It is also found that CS2 molecules tend to be localized into the nonpolar domain, while CH3CN interacts with nonpolar domain as well as with the charged head groups in the ionic network because of its amphiphilicity. At high concentrations, CH3CN molecules eventually disrupt the nanostructural organization. This dissertation is organized in four chapters: (1) introduction to graphene, ionic liquids and the methodology of MD; (2) MD simulation of graphene exfoliation; (3) Nanostructural organization in acetonitrile/IL mixtures; (4) Nanostructural organization in carbon disulfide/IL mixtures; (5) Conclusions. Results of MD simulations of liquid mixture systems car-ried out in this research explain observed experiments and show the details of nanostructural organizations in small solute molecules/IL mixture. Additionally, the research successfully reveals the correct mechanism of graphene exfoliation process in liquid solution. (This will be summarized in Chapter 5.) The research presented in this dissertation enhances our understanding of the microscopic behaviors in complex liquid systems as well as the theoretical method to explore them.

  17. Effectiveness of sensory processing strategies on activity level in inclusive preschool classrooms

    Lin CL

    2012-10-01

    Full Text Available Chien-Lin Lin,1,2 Yu-Fan Min,3 Li-Wei Chou,1,2,* Chin-Kai Lin,4,* 1Department of Physical Medicine and Rehabilitation, China Medical University Hospital, Taichung, Taiwan; 2School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; 3Faith, Hope and Love, Center for Children and Adults With Disabilities, Taichung, Taiwan; 4Program of Early Intervention, Department of Early Childhood Education, National Taichung University of Education, Taichung, Taiwan*These authors contributed equally to this workBackground: The purpose of this study was to investigate the effectiveness of sensory processing strategies in improving the activity level of children with sensory integration dysfunction.Methods: The study used a matching-only pretest–posttest control group design, which requires random matching of sensory integration dysfunction to the corresponding intervention group (n = 18 and control group (n = 18. The intervention group comprised 3–6-year-old children who received an 8-week school-day intervention during implementation of the theme curriculum.Results: The 8-week treatment significantly reduced the activity level and foot-swinging episodes in children with sensory integration dysfunction, and obtained a medium-effect size. However, the level of improvement in the control group did not show any statistically significant change.Conclusion: Sensory processing strategies could improve activity levels in children with sensory integration dysfunction. However, this study was unable to exclude a developmental effect. The social validity results show that sensory processing strategies can be integrated into the theme curriculum and improve activity levels in children.Keywords: activity level, preschool inclusive classroom, sensory integration dysfunction, sensory processing strategy

  18. Adopted levels and derived limits for Ra-226 and the decision making processes concerning TENORM releases

    A fraction of a primary dose limit can be, in general, agreed upon as a dose related level to be adopted in decision-making processes. In the case of TENORM releases, fractions of primary dose levels for 226Ra, 228Ra, and 210Po may be of particular importance to establish adopted levels for 226Ra could be adopted at the highest portion of the natural background variation. Above such level, intervention and remedial action levels could also be adopted. All those levels would be fractions of the primary level, but translated in terms of derived limits expressed in practical units. Derived limits would then be calculated by using environmental models. In such approach 'critical groups' would have to be carefully defined and identified. In addition, the size of a critical group would be chosen to be used in environmental modeling. Site specific environmental models and parameters are desirable, though unavailable, or very difficult to obtain, in most cases. Thus, mathematical models and parameters of more generic nature are often used. A sensitive parametric analysis can make a ranking of the parameters used in a model, allowing one to choose how important each parameter will be for the model output. The paper will point out that when using the adopted levels and derived limits, as suggested above, the uncertainties and importance of the parameters entering an environmental model can make the difference for decision makers to take the right or wrong decision, as far as radiological protection is concerned. (author)

  19. The role of atomic and molecular collision processes in plasmas - and vice versa

    Gans, Timo

    2008-10-01

    A broad base of accurate data of atomic and molecular collision processes is essential for reliable modelling, simulation, and diagnostics of plasmas. This is particularly important for plasmas at elevated pressures close to atmosphere. This regime attracts rapidly growing attention due to both - promising innovative technological applications as well as new fundamental scientific phenomena. The collision dominated environment and decreasing dimensions down to microscale plasmas with extremely high surface to volume ratios significantly increase the demand for collisional deactivation and surface interaction processes. Cross sections for collisional deactivation can be determined from the effective lifetime of excited states. Direct excitation using short pulse laser systems are most reliable however limited by optical selection rules and available photon energies. Recently improved understanding of the dynamics of electron impact excitation in radio-frequency discharges allows alternative strategies using space and phase resolved optical emission spectroscopy measurements coupled with careful modelling of the population dynamics of excited states. This method based on electron impact excitation is not limited by optical selection rules and also provides access to high energetic electronic states which are not accessible with common laser systems. Data for surface interactions is inherently delicate since it strongly depends on surface properties such as coverage and temperature. Nevertheless, reliable data for recombination of radicals and metastable states, and coefficients for secondary electron emission are highly desirable for consistent modelling and simulation. An alternative approach is the active implementation of experimentally measured surface sensitive parameters such as atomic radical densities and excitation structures caused by secondary electrons. These experimentally accessible quantities can be used as fixed input parameters in improved self-consistent modelling.

  20. The Role of Atomic and Molecular Processes in Magnetic Fusion Plasmas

    Plasma edge physics (plasmas with temperatures in the 1 to 100 eV range, near solid surfaces) has become a key issue in controlled nuclear fusion research. As for the physics of the fully ionized hot plasma core, appropriate dimensionless parameters have been identified: present fusion research acts like wind-channel experiments on downsized models, with respect to future fusion reactors. This is not longer possible for the plasma edge region due to dominant effects from atomic and surface processes. Integrated computational models comprising the physics of the plasma flow near boundaries, the atomic and molecular processes and the particle-surface interactions are the only tool to evaluate present experimental results (LHD, JT60, Tore Supra, JET,...) with respect to their relevance for future fusion power experiments (ITER) or a reactor.In particular proton and electron collisions with the hydrogenic molecules H2, O2, T2, DT, and their ions, play a key role in cooling and attenuating the magnetically confined plasma, before it hits exposed target surfaces. The surface released molecules travel in a bath of electrons and hydrogenic ions, with plasma temperatures (in the relevant region) in the 1 to 20 eV range, and typical (plasma) scale lengths are in the 1 to 10 cm range.Sample calculations with current fusion plasma edge codes, as e.g. used by the international design team for the ITER prototypical fusion reactor, applied to the tokamak with the highest divertor collisionality today (Alcator-C-Mod), are used to demonstrate these issues