WorldWideScience
 
 
1

Towards a molecular-level theory of carbohydrate processivity in glycoside hydrolases.  

Science.gov (United States)

Polysaccharide depolymerization in nature is primarily accomplished by processive glycoside hydrolases (GHs), which abstract single carbohydrate chains from polymer crystals and cleave glycosidic linkages without dissociating after each catalytic event. Understanding the molecular-level features and structural aspects of processivity is of importance due to the prevalence of processive GHs in biomass-degrading enzyme cocktails. Here, we describe recent advances towards the development of a molecular-level theory of processivity for cellulolytic and chitinolytic enzymes, including the development of novel methods for measuring rates of key steps in processive action and insights gained from structural and computational studies. Overall, we present a framework for developing structure-function relationships in processive GHs and outline additional progress towards developing a fundamental understanding of these industrially important enzymes. PMID:24863902

Beckham, Gregg T; Ståhlberg, Jerry; Knott, Brandon C; Himmel, Michael E; Crowley, Michael F; Sandgren, Mats; Sørlie, Morten; Payne, Christina M

2014-06-01

2

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

Energy Technology Data Exchange (ETDEWEB)

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.

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

1999-10-31

3

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

Directory of Open Access Journals (Sweden)

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.

Ilko Bald

2014-09-01

4

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

International Nuclear Information System (INIS)

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 ?-electrons of the aromatic rings in the interaction provides extra stabilization to the flat adsorption configurations

5

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

Science.gov (United States)

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

Shuai, Zhigang; Peng, Qian

2014-04-01

6

Supercritical Fluid Processing of Polymer Thin Films: An X-ray Study of Molecular-Level Porosity  

International Nuclear Information System (INIS)

This paper reviews our recent experimental results that address the effects of solvent density inhomogeneities in supercritical carbon dioxide (scCO2) on polymer thin film processing. The key phenomenon is excess sorption of CO2 molecules into polymer thin films even when the bulk miscibility with CO2 is very poor. We have found that the amount of the excess sorption is attributed to the large density fluctuations in scCO2 near the critical point. Further, taking advantage of the vitrification process of polymer chains through quick evaporation of CO2, we can preserve the 'expanded' structures as they are. The resultant films have large degree of molecular-level porosity that is very useful in producing coatings with low dielectric constants, enhanced adhesion, and metallization properties. These characteristics can be achieved in an environmentally 'green' manner, without organic solvents, and are not specific to any class of polymers

7

Supercritical fluid processing of polymer thin films: an X-ray study of molecular-level porosity.  

Science.gov (United States)

This paper reviews our recent experimental results that address the effects of solvent density inhomogeneities in supercritical carbon dioxide (scCO(2)) on polymer thin film processing. The key phenomenon is excess sorption of CO(2) molecules into polymer thin films even when the bulk miscibility with CO(2) is very poor. We have found that the amount of the excess sorption is attributed to the large density fluctuations in scCO(2) near the critical point. Further, taking advantage of the vitrification process of polymer chains through quick evaporation of CO(2), we can preserve the "expanded" structures as they are. The resultant films have large degree of molecular-level porosity that is very useful in producing coatings with low dielectric constants, enhanced adhesion, and metallization properties. These characteristics can be achieved in an environmentally "green" manner, without organic solvents, and are not specific to any class of polymers. PMID:17239334

Koga, Tadanori; Jerome, J; Rafailovich, M H; Chu, B; Douglas, J; Satija, S

2006-12-21

8

Photodissociation processes in molecular beams  

International Nuclear Information System (INIS)

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

9

Photodissociation processes in molecular beams  

Energy Technology Data Exchange (ETDEWEB)

A description is presented of a study of the photodissociation dynamics of molecules in a molecular beam. Photo-fragmentation translational spectroscopy has been utilized to observe the photodissociation dynamics of ozone. Using a supersonic molecular beam and a 10 nanosecond pulsed laser at lambda = 266 nm, the velocities of the fragment products are measured by the method of time of flight. The resolution of the time of flight spectrum of ozone is sufficiently high that the electronic and vibrational states are clearly resolved and identified. Above the threshold (lambda < 310 nm), the quantum yield for the production of O(/sup 1/D) has been estimated in the past to be unity for the process O/sub 3/ (/sup 1/A/sub 1/) + h..nu..)lambda < 300 nm) ..-->.. O/sub 3/(/sup 1/B/sub 2/) ..-->.. O/sub 2/(/sup 1/..delta../sub g/) + O(/sup 1/D). However a small production of O/sub 2/ (/sup 3/..sigma../sub g//sup -/) + O(/sup 3/P) has been observed in this study. The O/sub 2/(/sup 1/..delta../sub g/) product yields four vibrational states (v = 0, 1, 2, 3) which yields a vibrational temperature of 2700/sup 0/K along with narrow energy distributions of rotational levels. These energy distributions are compared with photodissociation models along with the polarization dependence of the dissociative process which was also measured. 143 references.

Carlson, L.R.

1979-05-01

10

Molecular Processes in Biological Thermosensation  

Directory of Open Access Journals (Sweden)

Full Text Available Since thermal gradients are almost everywhere, thermosensation could represent one of the oldest sensory transduction processes that evolved in organisms. There are many examples of temperature changes affecting the physiology of living cells. Almost all classes of biological macromolecules in a cell (nucleic acids, lipids, proteins can present a target of the temperature-related stimuli. This review discusses some features of different classes of temperature-sensing molecules as well as molecular and biological processes that involve thermosensation. Biochemical, structural, and thermodynamic approaches are applied in the paper to organize the existing knowledge on molecular mechanisms of thermosensation. Special attention is paid to the fact that thermosensitive function cannot be assigned to any particular functional group or spatial structure but is rather of universal nature. For instance, the complex of thermodynamic, structural, and functional features of hemoglobin family proteins suggests their possible accessory role as “molecular thermometers”.

G. M. Artmann

2008-05-01

11

Theory of atomic and molecular collision processes  

International Nuclear Information System (INIS)

This research is primarily involved with the development of theoretical methods and models for describing atomic and molecular collision processes. Current projects include quantum mechanical reaction scattering and reaction dynamics in polyatomic molecular systems

12

The Accuracy of Molecular Processes  

Science.gov (United States)

Recombination is arguably one of the most fundamental mechanisms driving genetic diversity during evolution. Recombination takes place in one way or another from viruses such as HIV and polio, to bacteria, and finally to man. In both prokaryotes and eukaryotes, homologous recombination is assisted by enzymes, recombinases, that promote the exchange of strands between two segments of DNA, thereby creating new genetic combinations. In bacteria, homologous recombination takes place as a pathway for the repair of DNA lesions and also during horizontal or lateral gene transfer processes, in which cells take in exogenous pieces of DNA. This allows bacteria to evolve rapidly by acquiring large sequences of DNA, a process which would take too long by gene duplications and single mutations. I will survey recent results on the fidelity of homologous recombination as catalyzed by the bacterial recombinase RecA. These results show discrimination up to the level of single base mismatches, during the initial stages of the recombination process. A cascaded kinetic proofreading process is proposed to explain this high discrimination. Kinetic proofreading ideas are also reviewed.

Stavans, Joel

13

Dynamical processes in atomic and molecular physics  

CERN Document Server

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

Ogurtsov, Gennadi

2012-01-01

14

Processing TES Level-2 Data  

Science.gov (United States)

TES Level 2 Subsystem is a set of computer programs that performs functions complementary to those of the program summarized in the immediately preceding article. TES Level-2 data pertain to retrieved species (or temperature) profiles, and errors thereof. Geolocation, quality, and other data (e.g., surface characteristics for nadir observations) are also included. The subsystem processes gridded meteorological information and extracts parameters that can be interpolated to the appropriate latitude, longitude, and pressure level based on the date and time. Radiances are simulated using the aforementioned meteorological information for initial guesses, and spectroscopic-parameter tables are generated. At each step of the retrieval, a nonlinear-least-squares- solving routine is run over multiple iterations, retrieving a subset of atmospheric constituents, and error analysis is performed. Scientific TES Level-2 data products are written in a format known as Hierarchical Data Format Earth Observing System 5 (HDF-EOS 5) for public distribution.

Poosti, Sassaneh; Akopyan, Sirvard; Sakurai, Regina; Yun, Hyejung; Saha, Pranjit; Strickland, Irina; Croft, Kevin; Smith, Weldon; Hoffman, Rodney; Koffend, John; Benenyan, Gerard; Nair, Hari; Sarkissian, Edwin; McDuffie, James; Monarrez, Ruth; Ho,David; Chan, Benny; Lampel, Michael

2006-01-01

15

Atomic and molecular processes in fusion plasmas  

Energy Technology Data Exchange (ETDEWEB)

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)

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

1997-01-01

16

Designing an university-level module on molecular imaging chemistry  

International Nuclear Information System (INIS)

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 radiopharious 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 application

17

Humidity level In psychrometric processes  

International Nuclear Information System (INIS)

When a thermal engineer needs to control, rather than merely moderate humidity, he must focus on the moisture level as a separate variable - not simply an addition of temperature control. Controlling humidity generally demands a correct psychrometric approach dedicated to that purpose [1].Analysis of the humidity level in psychrometric thermal processes leads to relevant data for theory and practice [2]. This paper presents: (1) the summer climatic curve for the Skopje region, (2) selected results of investigation on farm dryers made outside laboratories. The first purpose of such activity was to examine relations between weather conditions and drying conditions. The estimation of weather condition for the warmest season of the year was realized by a summer climatic curve. In the science of drying, basic drying conditions are temperature, relative humidity and velocity of air, thickness of dried product and dryer construction. The second purpose was to realize correct prediction of drying rates for various psychrometrics drying processes and local products. Test runs with the dryer were carried out over a period of 24 h, using fruits and vegetables as experimental material. Air flow rate through the dryer of 150 m3/h, overall drying rate of 0.04 kg/h and air temperature of 65 oC were reached. Three types of solar dryers, were exploited in the research.

18

Understanding diseases at a molecular level  

Energy Technology Data Exchange (ETDEWEB)

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.'

Rosev, Tatjana K [Los Alamos National Laboratory

2008-01-01

19

1985 bibliography of atomic and molecular processes  

International Nuclear Information System (INIS)

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

20

1982 bibliography of atomic and molecular processes  

International Nuclear Information System (INIS)

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

 
 
 
 
21

1980 bibliography of atomic and molecular processes  

International Nuclear Information System (INIS)

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

22

1979 bibliography of atomic and molecular processes  

International Nuclear Information System (INIS)

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

23

Bibliography of atomic and molecular processes, 1983  

International Nuclear Information System (INIS)

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

24

1978 bibliography of atomic and molecular processes  

International Nuclear Information System (INIS)

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

25

Bibliography of atomic and molecular processes, 1983  

Energy Technology Data Exchange (ETDEWEB)

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.

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

26

1984 Bibliography of atomic and molecular processes  

Energy Technology Data Exchange (ETDEWEB)

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.

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

27

1985 bibliography of atomic and molecular processes  

Energy Technology Data Exchange (ETDEWEB)

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.

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

28

The auditory corticocollicular system: molecular and circuit-level considerations.  

Science.gov (United States)

We live in a world imbued with a rich mixture of complex sounds. Successful acoustic communication requires the ability to extract meaning from those sounds, even when degraded. One strategy used by the auditory system is to harness high-level contextual cues to modulate the perception of incoming sounds. An ideal substrate for this process is the massive set of top-down projections emanating from virtually every level of the auditory system. In this review, we provide a molecular and circuit-level description of one of the largest of these pathways: the auditory corticocollicular pathway. While its functional role remains to be fully elucidated, activation of this projection system can rapidly and profoundly change the tuning of neurons in the inferior colliculus. Several specific issues are reviewed. First, we describe the complex heterogeneous anatomical organization of the corticocollicular pathway, with particular emphasis on the topography of the pathway. We also review the laminar origin of the corticocollicular projection and discuss known physiological and morphological differences between subsets of corticocollicular cells. Finally, we discuss recent findings about the molecular micro-organization of the inferior colliculus and how it interfaces with corticocollicular termination patterns. Given the assortment of molecular tools now available to the investigator, it is hoped that his review will help guide future research on the role of this pathway in normal hearing. PMID:24911237

Stebbings, Kevin A; Lesicko, Alexandria M H; Llano, Daniel A

2014-08-01

29

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  

Energy Technology Data Exchange (ETDEWEB)

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.

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

30

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  

International Nuclear Information System (INIS)

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.

31

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  

Science.gov (United States)

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.

Bulienkov, N. A.

2011-07-01

32

Reasoning across Ontologically Distinct Levels: Students' Understandings of Molecular Genetics  

Science.gov (United States)

In this article we apply a novel analytical framework to explore students' difficulties in understanding molecular genetics--a domain that is particularly challenging to learn. Our analytical framework posits that reasoning in molecular genetics entails mapping across ontologically distinct levels--an information level containing the genetic…

Duncan, Ravit Golan; Reiser, Brian J.

2007-01-01

33

Switching Faraday rotation on a molecular level  

Science.gov (United States)

In this work we present measurements of the switching of the Faraday effect in metal-organic compounds. Faraday rotation is the rotation of the plane of polarization of linearly polarized light under the influence of a magnetic field in the direction of propagation of the light. It is the magnetic equivalent of circular birefringence and is related to magnetic circular dichroism via the Kramers-Kronig transformation. The Faraday effect is used in optical isolators and magnetic sensors. Faraday rotation and magnetic circular dichroism spectra have been calculated and measured for various nanoparticles, nanocomposites, magnetic fluids and metal-organic complexes. These measurements and calculations indicate that it is possible to change the magneto-optical response by changing the state of the molecule, such as a change in protonation or oxidation state. The molecular environment also influences the magneto-optical spectra of metal-organic complexes and organic molecules. Thus it is possible to change the Faraday rotation spectrum by modifying the molecular environment or the molecule itself. We have measured the reversible switching of the magneto-optical response by these principles. This easily induced reversible switching opens the possibility of new devices such as switchable optical isolators.

Vandendriessche, Stefaan; Brullot, Ward; Verbiest, Thierry

2012-06-01

34

Molecular-level understanding of the carbonisation of polysaccharides.  

Science.gov (United States)

Understanding of both the textural and functionality changes occurring during (mesoporous) polysaccharide carbonisation at the molecular level provides a deeper insight into the whole spectrum of material properties, from chemical activity to pore shape and surface energy, which is crucial for the successful application of carbonaceous materials in adsorption, catalysis and chromatography. Obtained information will help to identify the most appropriate applications of the carbonaceous material generated during torrefaction and different types of pyrolysis processes and therefore will be important for the development of cost- and energy-efficient zero-waste biorefineries. The presented approach is informative and semi-quantitative with the potential to be extended to the formation of other biomass-derived carbonaceous materials. PMID:23740856

Shuttleworth, Peter S; Budarin, Vitaliy; White, Robin J; Gun'ko, Vladimir M; Luque, Rafael; Clark, James H

2013-07-01

35

First excess levels of vector processes  

Directory of Open Access Journals (Sweden)

Full Text Available This paper analyzes the behavior of a point process marked by a two-dimensional renewal process with dependent components about some fixed (two-dimensional level. The compound process evolves until one of its marks hits (i.e. reaches or exceeds its associated level for the first time. The author targets a joint transformation of the first excess level, first passage time, and the index of the point process which labels the first passage time. The cases when both marks are either discrete or continuous or mixed are treated. For each of them, an explicit and compact formula is derived. Various applications to stochastic models are discussed.

Jewgeni H. Dshalalow

1994-01-01

36

Practical ?-Ray Level for Low Molecular Weight Chitosan  

International Nuclear Information System (INIS)

The present work proposes a practical level of ?-Ray to lower the molecular weigh of chitosan irradiated in solid state and water. The molecular weight reduction is up to 80% at ?-ray amount of 50 kGy. The same level of reduction can be achieved by only 20 kGy in the presence of initiator (K2S2O8 or H2O2). The structure is significantly changed in the case of chitosan-acetic acid solution or chitosan dispersed in water with 2% aq. K2S2O8 solution

37

Features, Events, and Processes: system Level  

Energy Technology Data Exchange (ETDEWEB)

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).

D. McGregor

2004-10-15

38

Features, Events, and Processes: system Level  

International Nuclear Information System (INIS)

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)

39

User-Level Process Migration Mechanism  

Directory of Open Access Journals (Sweden)

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.

Dr. Narayan A. Joshi

2013-02-01

40

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

DEFF Research Database (Denmark)

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

 
 
 
 
41

Molecular Simulation of Fundamental Processes in Nanoparticle - Polymer - Nanoparticle Systems Under Tensile Load  

Directory of Open Access Journals (Sweden)

Full Text Available We demonstrate molecular modeling of polymer (polyacrylate association to ZnO nanoparticles by means of a recently developed molecule-by-molecule association approach. Upon multiple acrylate association steps, potential sites for connecting ZnO particles are elaborated and explored under tensile loading from molecular dynamics simulation. This offers molecular level insights into processes that account for elastic and plastic deformation, creep and self-healing in ZnO-polymer composite materials

Dirk Zahn

2013-08-01

42

Molecular simulation of non-equilibrium methane hydrate decomposition process  

Energy Technology Data Exchange (ETDEWEB)

Graphical abstract: Highlights: > Decomposition of methane hydrate is studied with molecular dynamics simulations. > Simulations are performed under adiabatic conditions (no thermostats). > The effects of heat and mass transfer during the decomposition are observed. > Temperature gradients are established as the hydrate decomposes. > Intrinsic reaction kinetics picture of hydrate dissociation is revisited. - Abstract: We recently performed constant energy molecular dynamics simulations of the endothermic decomposition of methane hydrate in contact with water to study phenomenologically the role of mass and heat transfer in the decomposition rate [S. Alavi, J.A. Ripmeester, J. Chem. Phys. 132 (2010) 144703]. We observed that with the progress of the decomposition front temperature gradients are established between the remaining solid hydrate and the solution phases. In this work, we provide further quantitative macroscopic and molecular level analysis of the methane hydrate decomposition process with an emphasis on elucidating microscopic details and how they affect the predicted rate of methane hydrate decomposition in natural methane hydrate reservoirs. A quantitative criterion is used to characterize the decomposition of the hydrate phase at different times. Hydrate dissociation occurs in a stepwise fashion with rows of sI cages parallel to the interface decomposing simultaneously. The correlations between decomposition times of subsequent layers of the hydrate phase are discussed.

Bagherzadeh, S.Alireza; Englezos, Peter [Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, V6T 1Z3 (Canada); Alavi, Saman, E-mail: saman.alavi@nrc-cnrc.gc.ca [Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Dr., Ottawa, Ontario, K1A 0R6 (Canada); Ripmeester, John A., E-mail: john.ripmeester@nrc-cnrc.gc.ca [Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Dr., Ottawa, Ontario, K1A 0R6 (Canada)

2012-01-15

43

Molecular simulation of non-equilibrium methane hydrate decomposition process  

International Nuclear Information System (INIS)

Graphical abstract: Highlights: ? Decomposition of methane hydrate is studied with molecular dynamics simulations. ? Simulations are performed under adiabatic conditions (no thermostats). ? The effects of heat and mass transfer during the decomposition are observed. ? Temperature gradients are established as the hydrate decomposes. ? Intrinsic reaction kinetics picture of hydrate dissociation is revisited. - Abstract: We recently performed constant energy molecular dynamics simulations of the endothermic decomposition of methane hydrate in contact with water to study phenomenologically the role of mass and heat transfer in the decomposition rate [S. Alavi, J.A. Ripmeester, J. Chem. Phys. 132 (2010) 144703]. We observed that with the progress of the decomposition front temperature gradients are established between the remaining solid hydrate and the solution phases. In this work, we provide further quantitative macroscopic and molecular level analysis of the methane hydrate decomposition process with an emphasis on elucidating microscopic details and how they affect the predicted rate of methane hydrate decomposition in natural methane hydrate reservoirs. A quantitative criterion is used to characterize the decomposition of the hydrate phase at different times. Hydrate dissociation occurs in a stepwise fashion with rows of sI cages parallel to the interface decomposing simultaneously. The correlations between decomposition times of subsequent layers of the hydrate phase are discussed.

44

A Process Calculus for Molecular Interaction Maps  

Directory of Open Access Journals (Sweden)

Full Text Available 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 a formal definition of the syntax and semantics of the MIM calculus, and we study properties of the formalism. A case study is also presented to show the use of the calculus for modeling biomolecular networks.

Roberto Barbuti

2009-11-01

45

Processing EOS MLS Level-2 Data  

Science.gov (United States)

A computer program performs level-2 processing of thermal-microwave-radiance data from observations of the limb of the Earth by the Earth Observing System (EOS) Microwave Limb Sounder (MLS). The purpose of the processing is to estimate the composition and temperature of the atmosphere versus altitude from .8 to .90 km. "Level-2" as used here is a specialists f term signifying both vertical profiles of geophysical parameters along the measurement track of the instrument and processing performed by this or other software to generate such profiles. Designed to be flexible, the program is controlled via a configuration file that defines all aspects of processing, including contents of state and measurement vectors, configurations of forward models, measurement and calibration data to be read, and the manner of inverting the models to obtain the desired estimates. The program can operate in a parallel form in which one instance of the program acts a master, coordinating the work of multiple slave instances on a cluster of computers, each slave operating on a portion of the data. Optionally, the configuration file can be made to instruct the software to produce files of simulated radiances based on state vectors formed from sets of geophysical data-product files taken as input.

Snyder, W. Van; Wu, Dong; Read, William; Jiang, Jonathan; Wagner, Paul; Livesey, Nathaniel; Schwartz, Michael; Filipiak, Mark; Pumphrey, Hugh; Shippony, Zvi

2006-01-01

46

Actinide geochemistry: From the molecular level to the real system  

Science.gov (United States)

Geochemical processes leading to either mobilization or retention of radionuclides in an aquifer system are significantly influenced by their interaction with rock, sediment and colloid surfaces. Therefore, a sound safety assessment of nuclear waste disposal requires the elucidation and quantification of those processes. State-of-the-art analytical techniques as e.g. laser- and X-ray spectroscopy are increasingly applied to study solid-liquid interface reactions to obtain molecular level speciation insight. We have studied the sorption of trivalent lanthanides and actinides onto aluminium oxides, hydroxides and purified clay minerals by the time-resolved laser fluorescence spectroscopy and X-ray-absorption spectroscopy. Chemical constitution and structure of surface bound actinides are proposed based on spectroscopic information. Open questions still remain with regard to the exact nature of mineral surface ligands and the mineral/water interface. Similarities of spectroscopic data obtained for M(III) sorbed onto ?-alumina, and clay minerals suggest the formation of very comparable inner-sphere surface complexes such as tbnd S-O-An(III)(OH) x(2 - x) (H 2O) 5 - x at pH > 5. Those speciation data are found consistent with those predicted by surface complexation modelling. The applicability of data obtained for pure mineral phases to actinide sorption onto heterogeneously composed natural clay rock is examined by experiments and by geochemical modelling. Good agreement of experiment and model calculations is found for U(VI) and trivalent actinide/lanthanide sorption to natural clay rock. The agreement of spectroscopy, geochemical modelling and batch experiments with natural rock samples and purified minerals increases the reliability in model predictions. The assessment of colloid borne actinide migration observed in various laboratory and field studies calls for detailed information on actinide-colloid interaction. Kinetic stabilization of colloid bound actinides can be due to inclusion into inorganic colloid matrix or by macromolecular rearrangement in case of organic, humic/fulvic like colloids. Only a combination of spectroscopy, microscopy and classical batch sorption experiments can help to elucidate the actinide-colloid interaction mechanisms and thus contribute to the assessment of colloids for radionuclide migration.

Geckeis, Horst; Rabung, Thomas

2008-12-01

47

Capillary leveling of stepped films with inhomogeneous molecular mobility  

CERN Document Server

A homogeneous thin polymer film with a stepped height profile levels due to the presence of Laplace pressure gradients. Here we report on studies of polymeric samples with precisely controlled, spatially inhomogeneous molecular weight distributions. The viscosity of a polymer melt strongly depends on the chain length distribution; thus, we learn about thin-film hydrodynamics with viscosity gradients. These gradients are achieved by stacking two films with different molecular weights atop one another. After a sufficient time these samples can be well described as having one dimensional viscosity gradients in the plane of the film, with a uniform viscosity normal to the film. We develop a hydrodynamic model that accurately predicts the shape of the experimentally observed self-similar profiles. The model allows for the extraction of a capillary velocity, the ratio of the surface tension and the viscosity, in the system. The results are in excellent agreement with capillary velocity measurements of uniform mono-...

McGraw, Joshua D; Bäumchen, Oliver; Raphaël, Elie; Dalnoki-Veress, Kari

2013-01-01

48

Finding Novel Molecular Connections between Developmental Processes and Disease  

Science.gov (United States)

Identifying molecular connections between developmental processes and disease can lead to new hypotheses about health risks at all stages of life. Here we introduce a new approach to identifying significant connections between gene sets and disease genes, and apply it to several gene sets related to human development. To overcome the limits of incomplete and imperfect information linking genes to disease, we pool genes within disease subtrees in the MeSH taxonomy, and we demonstrate that such pooling improves the power and accuracy of our approach. Significance is assessed through permutation. We created a web-based visualization tool to facilitate multi-scale exploration of this large collection of significant connections (http://gda.cs.tufts.edu/development). High-level analysis of the results reveals expected connections between tissue-specific developmental processes and diseases linked to those tissues, and widespread connections to developmental disorders and cancers. Yet interesting new hypotheses may be derived from examining the unexpected connections. We highlight and discuss the implications of three such connections, linking dementia with bone development, polycystic ovary syndrome with cardiovascular development, and retinopathy of prematurity with lung development. Our results provide additional evidence that plays a key role in the early pathogenesis of polycystic ovary syndrome. Our evidence also suggests that the VEGF pathway and downstream NFKB signaling may explain the complex relationship between bronchopulmonary dysplasia and retinopathy of prematurity, and may form a bridge between two currently-competing hypotheses about the molecular origins of bronchopulmonary dysplasia. Further data exploration and similar queries about other gene sets may generate a variety of new information about the molecular relationships between additional diseases. PMID:24874013

Park, Jisoo; Wick, Heather C.; Kee, Daniel E.; Noto, Keith; Maron, Jill L.; Slonim, Donna K.

2014-01-01

49

Improving Molecular Level Chemical Speciation of Organic Aerosols  

Science.gov (United States)

A substantial fraction of fine mode aerosols are organic with the majority formed in the atmosphere through oxidation of gas phase compounds emitted from a variety of natural and man-made sources. As a result, organic aerosols are comprised of thousands of individual organic species whose complexity increases exponentially with carbon number and degree of atmospheric oxidation. Chemical characterization of individual compounds present in this complex mixture provides information on sources and transformation processes that are critical for apportioning organic carbon from an often convoluted mixture of sources and to constrain oxidation mechanisms needed for atmospheric models. These compounds also affect the physical and optical properties of the aerosol but the vast majority remain unidentified and missing from published mass spectral libraries because of difficulties in separating and identifying them. We have developed improved methodologies for chemical identification in order to better understand complex environmental mixtures. Our approach has been to combine two-dimensional gas chromatography with high resolution time of flight mass spectrometry (GC×GC-HRTOFMS) and both traditional electron ionization (EI) and vacuum ultraviolet (VUV) photoionization. GC×GC provides improved separation of individual compounds over traditional one dimensional GC and minimizes co-elution of peaks resulting in mass spectra that are virtually free of interferences. VUV ionization is a ';soft' ionization technique that reduces fragmentation and enhances the abundance of the parent or molecular ion, which when combined with high resolution mass spectrometry can provide molecular formulas for chromatographic peaks. We demonstrate our methodology by applying it to identify more than 500 individual compounds in aerosol filter samples collected at Blodgett Forest, a rural site in the Sierra Nevada Mountains. Using the EI NIST mass spectral library and molecular formulas determined from the high resolution VUV analysis we characterized the observed peaks into those that were: (i) confidently identified by EI and confirmed by VUV (154 compounds), (ii) not matched by EI but assigned molecular formulas from VUV (230), (iii) EI matched but not confirmed by VUV (32), and (iv) not matched by EI and no molecular formula obtained from VUV (92). By combining the molecular formula information with both gas chromatography retention information and the EI mass fragmentation patterns it is possible to characterize previously unidentified compounds in chemically relevant functional group classes. Temporal patterns of all these tracers together provide a new and more complete lens through which to study SOA formation and transformation processes than has previously been possible.

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

2013-12-01

50

Hydrodynamical processes in the Draco molecular cloud  

International Nuclear Information System (INIS)

IRAS 100 micron images of the Draco cloud show several cloud components with cometary plumes of material extending 7-10 pc. The brightest plumes are very uniform in thickness but often terminate in large amorphous regions. The structure is consistent with low Reynolds number hydrodynamics and is suggestive of a molecular cloud shedding material in a plume as it falls onto the galactic plane from the halo region. A subsequent study of the 100 micron images from the entire IRAS survey has revealed a total of 14 additional cometlike objects with /b II/ greater then 15 deg. 42 references

51

Optically and thermally induced molecular switching processes at metal surfaces  

International Nuclear Information System (INIS)

Using light to control the switching of functional properties of surface-bound species is an attractive strategy for the development of new technologies with possible applications in molecular electronics and functional surfaces and interfaces. Molecular switches are promising systems for such a route, since they possess the ability to undergo reversible changes between different molecular states and accordingly molecular properties by excitation with light or other external stimuli. In this review, recent experiments on photo- and thermally induced molecular switching processes at noble metal surfaces utilizing two-photon photoemission and surface vibrational spectroscopies are reported. The investigated molecular switches can either undergo a trans-cis isomerization or a ring opening-closure reaction. Two approaches concerning the connection of the switches to the surface are applied: physisorbed switches, i.e. molecules in direct contact with the substrate, and surface-decoupled switches incorporated in self-assembled monolayers. Elementary processes in molecular switches at surfaces, such as excitation mechanisms in photoisomerization and kinetic parameters for thermally driven reactions, which are essential for a microscopic understanding of molecular switching at surfaces, are presented. This in turn is needed for designing an appropriate adsorbate-substrate system with the desired switchable functionality controlled by external stimuli.external stimuli.

52

Genomic Signal Processing: Predicting Basic Molecular Biological Principles  

Science.gov (United States)

Advances in high-throughput technologies enable acquisition of different types of molecular biological data, monitoring the flow of biological information as DNA is transcribed to RNA, and RNA is translated to proteins, on a genomic scale. Future discovery in biology and medicine will come from the mathematical modeling of these data, which hold the key to fundamental understanding of life on the molecular level, as well as answers to questions regarding diagnosis, treatment and drug development. Recently we described data-driven models for genome-scale molecular biological data, which use singular value decomposition (SVD) and the comparative generalized SVD (GSVD). Now we describe an integrative data-driven model, which uses pseudoinverse projection (1). We also demonstrate the predictive power of these matrix algebra models (2). The integrative pseudoinverse projection model formulates any number of genome-scale molecular biological data sets in terms of one chosen set of data samples, or of profiles extracted mathematically from data samples, designated the ``basis'' set. The mathematical variables of this integrative model, the pseudoinverse correlation patterns that are uncovered in the data, represent independent processes and corresponding cellular states (such as observed genome-wide effects of known regulators or transcription factors, the biological components of the cellular machinery that generate the genomic signals, and measured samples in which these regulators or transcription factors are over- or underactive). Reconstruction of the data in the basis simulates experimental observation of only the cellular states manifest in the data that correspond to those of the basis. Classification of the data samples according to their reconstruction in the basis, rather than their overall measured profiles, maps the cellular states of the data onto those of the basis, and gives a global picture of the correlations and possibly also causal coordination of these two sets of states. Mapping genome-scale protein binding data using pseudoinverse projection onto patterns of RNA expression data that had been extracted by SVD and GSVD, a novel correlation between DNA replication initiation and RNA transcription during the cell cycle in yeast, that might be due to a previously unknown mechanism of regulation, is predicted. (1) Alter & Golub, Proc. Natl. Acad. Sci. USA 101, 16577 (2004). (2) Alter, Golub, Brown & Botstein, Miami Nat. Biotechnol. Winter Symp. 2004 (www.med.miami.edu/mnbws/alter-.pdf)

Alter, Orly

2005-03-01

53

An approach of molecular orbital calculations to process plasmas  

International Nuclear Information System (INIS)

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.)

54

Process for separating high molecular mixtures. [Solvent extraction  

Energy Technology Data Exchange (ETDEWEB)

A process is described for separating a high-molecular mixture, the constituents of which are totally miscible at the temperature of the process into portions having different properties. The mixture, together with a quantity of a low-molecular treating agent, is subjected to temperature and pressure conditions at which the treating agent is in its para-critical state. The temperature is above the critical temperature of the low molecular treating agent, and at least a portion of the mixture is dissolved in the treating agent, thereby forming a liquid phase containing a treating agent and dissolved high-molecular substances. The pressure is then reduced under conditions causing a decrease in the density of the treating agent in the liquid phase, thereby causing the precipitation of a portion of the dissolved high-molecular substances from the liquid phase to form a separate heavier phase. The resulting phases are separated with the reduced pressure being sufficient to prevent all of the dissolved high-molecular substances from being precipitated, and the temperature is below the paracritical temperature range for the high molecular mixture.

van Dijck, W.J.D.

1942-05-05

55

Extracting Dwell Time Sequences from Processive Molecular Motor Data  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Processive molecular motors, such as kinesin, myosin, or dynein, convert chemical energy into mechanical energy by hydrolyzing ATP. The mechanical energy is used for moving in discrete steps along the cytoskeleton and carrying a molecular load. Single-molecule recordings of motor position along a substrate polymer appear as a stochastic staircase. Recordings of other single molecules, such as F1-ATPase, RNA polymerase, or topoisomerase, have the same appearance. We present a maximum likelihoo...

Milescu, Lorin S.; Yildiz, Ahmet; Selvin, Paul R.; Sachs, Frederick

2006-01-01

56

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

International Nuclear Information System (INIS)

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

57

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

Science.gov (United States)

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)].

Mayer, Bernd; Köauthler, Gottfried; Rasmussen, Steen

1997-04-01

58

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

Energy Technology Data Exchange (ETDEWEB)

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} {ital 1997} {ital The American Physical Society}

Mayer, B.; Kohler, G., [Institut fuer Theoretische Chemie und Strahlenchemie, Universitaet Wien, UZAII, Althanstrasse 14, A-1090 Wien (Austria); Rasmussen, S., [Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico 87501 (United States)]|[TSA-DO/SA MS-M997 and CNLS MS-B258, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

1997-04-01

59

Molecular epidemiology biomarkers-Sample collection and processing considerations  

International Nuclear Information System (INIS)

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 centurymiology of the 21st century

60

Enhancement of Signaling Processes on Membrane through Molecular Crowding  

CERN Document Server

We investigated the influences of molecular crowding on biochemical reaction processes on two-dimensional surfaces, using the model of signal-transduction processes on biomembranes. We performed simulations of the two-dimensional cell-based model, which describes the reactions and diffusions of the receptors, signaling proteins, target proteins, and crowders, on the cell membrane. The signaling proteins are activated by receptors and induce target proteins to unbind from the membrane. We found that the reaction rates of two-dimensional systems consistently exhibit a maximum at a high volume fraction of molecules, such that two molecules in the vicinity cannot easily exchange their positions. We further demonstrated that molecular crowding influences the hierarchical molecular distributions throughout the reaction process. The signaling proteins tend to surround the receptors, and the target proteins tend to become distributed around the signaling protein-receptor clusters. This distribution accelerates the re...

Fujii, Masashi; Awazu, Akinori

2012-01-01

 
 
 
 
61

Orbital Energy Levels in Molecular Hydrogen. A Simple Approach.  

Science.gov (United States)

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)

Willis, Christopher J.

1988-01-01

62

1978 bibliography of atomic and molecular processes. [Bibliography  

Energy Technology Data Exchange (ETDEWEB)

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.

1980-03-01

63

1978-1981 bibliography of atomic and molecular processes  

Energy Technology Data Exchange (ETDEWEB)

This annotated bibliography lists 10,676 works on atomic and molecular processes reported in publications dated 1978 to 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 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.

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

1982-10-01

64

Selective vibrational pumping of a molecular beam by a stimulated Raman process  

International Nuclear Information System (INIS)

Stimulated Raman process is used to selectively pump a highly excited vibrational state in a molecular beam. Theoretical evaluation shows that continuous lasers with power of less than 1 W can efficiently pump a single rotational-vibrational level of many simple molecules. Characteristics of the selectively pumped molecular beam and operational conditions are discussed theoretically. The experiment on a Na2 beam is found to agree with theoretical predictions. A flux of 4 x 10 to the 7th/s in the v = 31, J = 5 excited level has been obtained with use of two CW dye lasers with powers of 80 and 300 mW. 33 references

65

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

Energy Technology Data Exchange (ETDEWEB)

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.

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

2009-10-01

66

Processing TES Level-1B Data  

Science.gov (United States)

TES L1B Subsystem is a computer program that performs several functions for the Tropospheric Emission Spectrometer (TES). The term "L1B" (an abbreviation of "level 1B"), refers to data, specific to the TES, on radiometric calibrated spectral radiances and their corresponding noise equivalent spectral radiances (NESRs), plus ancillary geolocation, quality, and engineering data. The functions performed by TES L1B Subsystem include shear analysis, monitoring of signal levels, detection of ice build-up, and phase correction and radiometric and spectral calibration of TES target data. Also, the program computes NESRs for target spectra, writes scientific TES level-1B data to hierarchical- data-format (HDF) files for public distribution, computes brightness temperatures, and quantifies interpixel signal variability for the purpose of first-order cloud and heterogeneous land screening by the level-2 software summarized in the immediately following article. This program uses an in-house-developed algorithm, called "NUSRT," to correct instrument line-shape factors.

DeBaca, Richard C.; Sarkissian, Edwin; Madatyan, Mariyetta; Shepard, Douglas; Gluck, Scott; Apolinski, Mark; McDuffie, James; Tremblay, Dennis

2006-01-01

67

Manipulating the conduction process of a molecular resonant tunneling diode  

International Nuclear Information System (INIS)

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)

68

Information processing at single neuron level  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

Vidybida, A. K.

2007-01-01

69

Low-level nitrate waste process development  

International Nuclear Information System (INIS)

A denitrification technology development program has been conducted for four years at the Rocky Flats Plant and has identified several promising denitrification methods. DOE sites were first surveyed to determine nitrate waste generation rates, inventory and regulatory concern. The need for processes to handle this waste category was evident, both from the survey results and comments of site operators. The denitrification methods identified are classified as thermal, aqueous and biological. Thermal processes were demonstrated to destroy the nitrates with the creation of less than 500 ppm NO/sub x/ as a by-product. Studies were performed on a molten salt destructor, high temperature fluid wall (HTFW) reactor, and also by Mound using their glass furnace. A preliminary design and cost estimate report has been prepared for a one million kilogram per year process for denitrification using the HTFW reactor. An aqueous process consisting of formic acid and sulfuric acid reflux was developed which converts the nitrate to other forms, but results in slightly elevated NO/sub x/ emissions. Biodenitrification was developed at Oak Ridge and is in production use there. Results and conclusions on the program are discussed

70

Cisplatin and platinum drugs at the molecular level. (Review).  

Science.gov (United States)

Over twenty years of intensive work toward improvement of cisplatin, and with hundreds of platinum drugs tested, has resulted in the introduction of the widely used carboplatin and of oxaliplatin used only for a very narrow spectrum of cancers. A number of interesting platinum compounds including the orally administered platinum drug JM216, nedaplatin, the sterically hindered platinum(II) complex ZD0473, the trinuclear platinum complex BBR3464, and the liposomal forms Lipoplatin and SPI-77 are under clinical evaluation. This review summarizes the molecular mechanisms of platinum compounds for DNA damage, DNA repair and induction of apoptosis via activation or modulation of signaling pathways and explores the basis of platinum resistance. Cisplatin, carboplatin, oxaliplatin and most other platinum compounds induce damage to tumors via induction of apoptosis; this is mediated by activation of signal transduction leading to the death receptor mechanisms as well as mitochondrial pathways. Apoptosis is responsible for the characteristic nephrotoxicity, ototoxicity and most other toxicities of the drugs. The major limitation in the clinical applications of cisplatin has been the development of cisplatin resistance by tumors. Mechanisms explaining cisplatin resistance include the reduction in cisplatin accumulation inside cancer cells because of barriers across the cell membrane, the faster repair of cisplatin adducts, the modulation of apoptotic pathways in various cells, the upregulation in transcription factors, the loss of p53 and other protein functions and a higher concentration of glutathione and metallothioneins in some type of tumors. A number of experimental strategies to overcome cisplatin resistance are at the preclinical or clinical level such as introduction of the bax gene, inhibition of the JNK pathway, introduction of a functional p53 gene, treatment of tumors with aldose reductase inhibitors and others. Particularly important are combinations of platinum drug treatments with other drugs, radiation and the emerging gene therapy regimens. PMID:14534679

Boulikas, Teni; Vougiouka, Maria

2003-01-01

71

Visual displays that directly interface and provide read-outs of molecular states via molecular graphics processing units.  

Science.gov (United States)

The monitoring of molecular systems usually requires sophisticated technologies to interpret nanoscale events into electronic-decipherable signals. We demonstrate a new method for obtaining read-outs of molecular states that uses graphics processing units made from molecular circuits. Because they are made from molecules, the units are able to directly interact with molecular systems. We developed deoxyribozyme-based graphics processing units able to monitor nucleic acids and output alphanumerical read-outs via a fluorescent display. Using this design we created a molecular 7-segment display, a molecular calculator able to add and multiply small numbers, and a molecular automaton able to diagnose Ebola and Marburg virus sequences. These molecular graphics processing units provide insight for the construction of autonomous biosensing devices, and are essential components for the development of molecular computing platforms devoid of electronics. PMID:25044570

Poje, Julia E; Kastratovic, Tamara; Macdonald, Andrew R; Guillermo, Ana C; Troetti, Steven E; Jabado, Omar J; Fanning, M Leigh; Stefanovic, Darko; Macdonald, Joanne

2014-08-25

72

Advances Towards Synthetic Machines at the Molecular and Nanoscale Level  

Directory of Open Access Journals (Sweden)

Full Text Available The fabrication of increasingly smaller machines to the nanometer scale can be achieved by either a “top-down” or “bottom-up” approach. While the former is reaching its limits of resolution, the latter is showing promise for the assembly of molecular components, in a comparable approach to natural systems, to produce functioning ensembles in a controlled and predetermined manner. In this review we focus on recent progress in molecular systems that act as molecular machine prototypes such as switches, motors, vehicles and logic operators.

Kristina Konstas

2010-06-01

73

Atomic and molecular processes in JT-60U divertor plasmas  

Energy Technology Data Exchange (ETDEWEB)

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)

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

1997-01-01

74

Amino-nitro-azobenzene dimers as a prototype for a molecular-level machine  

International Nuclear Information System (INIS)

Low-temperature scanning tunnelling microscope measurements of an X-shaped dimer, consisting of two amino-nitro-azobenzene molecules, on a Au(111)-surface are presented. Electron-induced manipulation switches either the upper- or the lower-lying molecule. These reversible switching processes are based on the cis-trans isomerization of the azobenzene molecules. The switching of the upper molecule moves the lower-lying molecule in a controlled way. Thus mechanical work is performed. This proof-of-principle shows the ability of azobenzene molecules to act as a molecular-level machine

75

High-level waste processing and disposal  

International Nuclear Information System (INIS)

Without reprocessing, spent LWR fuel itself is generally considered an acceptable waste form. With reprocessing, borosilicate glass canisters, have now gained general acceptance for waste immobilization. The current first choice for disposal is emplacement in an engineered structure in a mined cavern at a depth of 500-1000 meters. A variety of rock types are being investigated including basalt, clay, granite, salt, shale, and volcanic tuff. This paper gives specific coverage to the national high level waste disposal plans for France, the Federal Republic of Germany, Japan and the United States. The French nuclear program assumes prompt reprocessing of its spent fuels, and France has already constructed the AVM. Two larger borosilicate glass plants are planned for a new French reprocessing plant at La Hague. France plans to hold the glass canisters in near-surface storage for a forty to sixty year cooling period and then to place them into a mined repository. The FRG and Japan also plan reprocessing for their LWR fuels. Both are currently having some fuel reprocessed by France, but both are also planning reprocessing plants which will include waste vitrification facilities. West Germany is now constructing the PAMELA Plant at Mol, Belgium to vitrify high level reprocessing wastes at the shutdown Eurochemic Plant. Japan is now operating a vitrification mockup test facility and plans a pilot plant facility at the Tokai reprocessing plant by 1990. Both countries have active geologic repository programs. The United State program assumes little LWR fuel reprocessing and is thus primarily aimed at direct disposal of spent fuel into mined repositories. However, the US have two borosilicate glass plants under construction to vitrify existing reprocessing wastes

76

Molecular-Level Design of Heterogeneous Chiral Catalysis  

Energy Technology Data Exchange (ETDEWEB)

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.

Francisco Zaera

2012-03-21

77

Secondary ionization process in laser induced breakdown of molecular gases  

International Nuclear Information System (INIS)

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

78

Processing of lumpy molybdenum waste by fluorination with molecular fluorine  

International Nuclear Information System (INIS)

A fluoride technology of processing molybdenum boats waste used in production of nuclear fuel pellets based on uranium dioxide at the final stage of their sintering in a reducing atmosphere is proposed based on the results of thermodynamic calculations and experimental studies on bulky molybdenum fluorination kinetics. The technology comprises the following three stages: mechanical or chemical removal of the molybdenum boat surface layer contaminated with uranium oxides, fluorination of molybdenum waste by molecular fluorine, processing of MoF6 by the method of low-temperature vacuum sublimation, reduction to metal of MoF6 by hydrogen

79

Molecular and Supramolecular Information Processing From Molecular Switches to Unconventional Computing  

CERN Document Server

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.

Katz, Evgeny

2012-01-01

80

Molecular-level Design of Heterogeneous Chiral Catalysts  

Energy Technology Data Exchange (ETDEWEB)

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.

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

 
 
 
 
81

Biotin Sensing at the Molecular Level1–3  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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...

Beckett, Dorothy

2009-01-01

82

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

Science.gov (United States)

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

Volinsky, Roman; Kinnunen, Paavo K J

2013-06-01

83

Entendendo o Processo Molecular da Tumorigênese / Understanding the Molecular Process of Tumorigenesis  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: Portuguese Abstract in portuguese Nos últimos 25 anos, o reconhecimento dos mecanismos genético-moleculares implicados na gênese e na progressão do câncer tem permitido obter novos métodos de diagnóstico e de acompanhamento, redirecionando de forma drástica a terapêutica do paciente com neoplasia. Alguns marcadores moleculares já es [...] tão sendo utilizados na rotina e deverão prover testes sensíveis e específicos para o diagnóstico precoce, estadiamento e acompanhamento do paciente com câncer. As características moleculares de cada tumor deverão permitir predição do seu comportamento, ajudando a delinear estratégias terapêuticas mais efetivas. Apresentamos de forma didática os principais mecanismos controladores do ciclo celular e do crescimento, definindo a importância de oncogenes erroneamente ativados e de genes supressores tumorais perdidos ou não-funcionantes, dos genes envolvidos na programação e manutenção da vida celular e de outros genes que atuam no processo de tumorigênese. Os mecanismos de progressão tumoral, invasão e metastatização à distância são revistos enfatizando-se a aplicação prática do conhecimento a respeito de tais mecanismos. Lembramos o papel da instabilidade genética e dos fenômenos epigenéticos na definição fenotípica do câncer, sugerindo as aplicações da genética molecular na terapia gênica do câncer. Abstract in english Over the past 25 years, knowledge of the genetic-molecular mechanisms involved in the genesis and progression of cancer have helped to obtain new diagnostic and follow up methods that have drastically redirected the therapeutics used in patients with neoplasia. Some molecular markers are already bei [...] ng routinely used and should provide sensitive and specific tests for early diagnosis, staging and follow up of cancer patients. The molecular characteristics of each tumor should help in predicting its behavior and outlining more effective therapeutic strategies. We have used a didactic manner of presenting the main mechanisms that control the growth and cellular cycle, defined the importance of erroneously activated oncogenes and tumor suppressor genes that are lost or non-functioning, genes involved in programming and maintaining cell life as well as other genes that participate in the tumorigenic process. The mechanisms of tumor progression, invasion and metastasis are reviewed placing an emphasis on the practical application of the knowledge related to these mechanisms. The role of genetic instability and epigenetic changes in the definition of cancer phenotype have been underscored, suggesting the application of molecular genetics in the gene therapy of cancer.

Laura Sterian, Ward.

84

UV processing of ices across the Rosette molecular cloud  

Science.gov (United States)

During star-formation, materials in the general cloud medium are subjected to numerous chemical and physical processes that are driven mostly by thermal and energetic radiation. In part because of Spitzer, significant progress has been made towards understanding the various effects of these radiation processes on the ices and organics as they form and cycle through the dense and diffuse regions of molecular clouds and subsequently become incorporated into (proto)stellar environments (i.e planets, comets, etc.). However, to date the majority of the focus has been directed at clouds (such as Taurus-Auriga) that are NOT analogous to the molecular cloud from which the solar nebula originated. Rather, the Sun formed in a high mass star-forming cloud where a number of supernova events occurred, resulting in intense UV radiation throughout the cloud complex, such as the Rosette Nebula. We propose to take low resolution spectra from 5 to 22 microns along the line of sight toward 13 sources in 8 embedded clusters in the Rosette molecular cloud. The clusters are all deeply embedded, indicative of a similar formation time but have a range of luminosities and are spread out across the cloud at different distances from the neighboring HII region, NGC 2244. We will also take high resolution spectra from 10 to 20 microns toward the 5 brightest and most embedded sources to examine the CO_2 line profile in detail. This will allow us to determine the mixture of different ices and thereby the temperature and radiation processing history in each region. These observations will reveal how the ice composition in each cluster envelope varies with environment, both locally from the embedded sources and globally due to the heating and UV radiation from NGC 2244. Differences in gas phase chemistry have already been observed at millimeter wavelengths and we will use these mid-infrared data to obtain a more complete picture of the chemistry.

Keane, Jacqueline; Bergin, Edwin; Bonnell, Ian; Lada, Elizabeth; Williams, Jonathan

2008-03-01

85

High Speed Data Processing for Imaging MS-Based Molecular Histology Using Graphical Processing Units  

Science.gov (United States)

Imaging MS enables the distributions of hundreds of biomolecular ions to be determined directly from tissue samples. The application of multivariate methods, to identify pixels possessing correlated MS profiles, is referred to as molecular histology as tissues can be annotated on the basis of the MS profiles. The application of imaging MS-based molecular histology to larger tissue series, for clinical applications, requires significantly increased computational capacity in order to efficiently analyze the very large, highly dimensional datasets. Such datasets are highly suited to processing using graphical processor units, a very cost-effective solution for high speed processing. Here we demonstrate up to 13× speed improvements for imaging MS-based molecular histology using off-the-shelf components, and demonstrate equivalence with CPU based calculations. It is then discussed how imaging MS investigations may be designed to fully exploit the high speed of graphical processor units.

Jones, Emrys A.; van Zeijl, René J. M.; Andrén, Per E.; Deelder, André M.; Wolters, Lex; McDonnell, Liam A.

2012-04-01

86

Levels of processing: the evolution of a framework  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english Although the levels of processing framework have evolved over its nearly 40 years of existence, the essence of the idea has not changed from the original. The original article published in 1972 suggests that in the encoding stage of a stimulus, there is a series of processing hierarchies ranging fro [...] m the shallowest level (perceptual processing-the subject initially perceives the physical and sensory characteristics of the stimulus) to the deepest level (semantic processing-related to pattern recognition and extraction of meaning). The depth processing is associated with high levels of retention and long-term memory traces. After extensive research and criticism, the authors added several concepts that aided in a better understanding of levels of processing framework and the items that subjects can recall such as transfer-appropriate processing and robust encoding. However, there are still some gaps in this framework that call for new scientific investigations, ranging from experimental paradigms with lists of words with healthy or pathological conditions subject to neuroimaging studies to confirm, refute or improve the framework. The aim of this article is to review the publications (articles and book chapters) dating from the original article to the present day to better understand the mnemonic process in terms of levels of processing and to highlight some of its contributions.

Roberta, Ekuni; Leonardo José, Vaz; Orlando Francisco Amodeo, Bueno.

2011-12-01

87

Levels of processing: the evolution of a framework  

Directory of Open Access Journals (Sweden)

Full Text Available Although the levels of processing framework have evolved over its nearly 40 years of existence, the essence of the idea has not changed from the original. The original article published in 1972 suggests that in the encoding stage of a stimulus, there is a series of processing hierarchies ranging from the shallowest level (perceptual processing—the subject initially perceives the physical and sensory characteristics of the stimulus to the deepest level (semantic processing—related to pattern recognition and extraction of meaning. The depth processing is associated with high levels of retention and long-term memory traces. After extensive research and criticism, the authors added several concepts that aided in a better understanding of levels of processing framework and the items that subjects can recall such as transfer-appropriate processing and robust encoding. However, there are still some gaps in this framework that call for new scientific investigations, ranging from experimental paradigms with lists of words with healthy or pathological conditions subject to neuroimaging studies to confirm, refute or improve the framework. The aim of this article is to review the publications (articles and book chapters dating from the original article to the present day to better understand the mnemonic process in terms of levels of processing and to highlight some of its contributions.

Orlando Francisco Amodeo Bueno

2011-07-01

88

Levels of processing: the evolution of a framework  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english Although the levels of processing framework have evolved over its nearly 40 years of existence, the essence of the idea has not changed from the original. The original article published in 1972 suggests that in the encoding stage of a stimulus, there is a series of processing hierarchies ranging fro [...] m the shallowest level (perceptual processing-the subject initially perceives the physical and sensory characteristics of the stimulus) to the deepest level (semantic processing-related to pattern recognition and extraction of meaning). The depth processing is associated with high levels of retention and long-term memory traces. After extensive research and criticism, the authors added several concepts that aided in a better understanding of levels of processing framework and the items that subjects can recall such as transfer-appropriate processing and robust encoding. However, there are still some gaps in this framework that call for new scientific investigations, ranging from experimental paradigms with lists of words with healthy or pathological conditions subject to neuroimaging studies to confirm, refute or improve the framework. The aim of this article is to review the publications (articles and book chapters) dating from the original article to the present day to better understand the mnemonic process in terms of levels of processing and to highlight some of its contributions.

Roberta, Ekuni; Leonardo José, Vaz; Orlando Francisco Amodeo, Bueno.

89

Charge transfer processes: the role of optimized molecular orbitals.  

Science.gov (United States)

The influence of the molecular orbitals on charge transfer (CT) reactions is analyzed through wave function-based calculations. Characteristic CT processes in the organic radical 2,5-di-tert-butyl-6-oxophenalenoxyl linked with tetrathiafulvalene and the inorganic crystalline material LaMnO3 show that changes in the inner shells must be explicitly taken into account. Such electronic reorganization can lead to a reduction of the CT vertical transition energy up to 66%. A state-specific approach accessible through an adapted CASSCF (complete active space self-consistent field) methodology is capable of reaching good agreement with the experimental spectroscopy of CT processes. A partitioning of the relaxation energy in terms of valence- and inner-shells is offered and sheds light on their relative importance. This work paves the way to the intimate description of redox reactions using quantum chemistry methods. PMID:24781811

Meyer, Benjamin; Domingo, Alex; Krah, Tim; Robert, Vincent

2014-08-01

90

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

Science.gov (United States)

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.

2003-01-01

91

Simulation of deacidification process by molecular distillation of deodorizer distillate  

Scientific Electronic Library Online (English)

Full Text Available SciELO Argentina | Language: English Abstract in english A computer program has been developed to simulate the deacidification of sunflower deodorizer distillate. The developed mathematical model is based on momentum, mass and energy balances. The Langmuir-Knudsen constitutive equation was used in order to represent the kinetics of evaporation and condens [...] ation. Physical and transport properties have been evaluated using correlations, which are functions of temperature and composition. The obtained partial differential equation system was solved by means of the Crank-Nicholson technique, and the calculation programs employed were developed and debugged using Matlab 7.1. The mathematical model was used to analyze the phenomena that take place during the molecular distillation process, and it also allowed studying the influence of operating variables on the performance of the process. In this investigation, we analyzed the influence of the operating temperature on purity and yield of the components. Trials at three evaporating temperatures (110 ºC, 130 ºC, and 140 ºC) were carried out in a KDL4 (UIC) molecular distillation apparatus to verify the model.

M. A., Marttinello; I., Leone; M., Pramparo.

2008-12-01

92

Simulation of deacidification process by molecular distillation of deodorizer distillate  

Scientific Electronic Library Online (English)

Full Text Available SciELO Argentina | Language: English Abstract in english A computer program has been developed to simulate the deacidification of sunflower deodorizer distillate. The developed mathematical model is based on momentum, mass and energy balances. The Langmuir-Knudsen constitutive equation was used in order to represent the kinetics of evaporation and condens [...] ation. Physical and transport properties have been evaluated using correlations, which are functions of temperature and composition. The obtained partial differential equation system was solved by means of the Crank-Nicholson technique, and the calculation programs employed were developed and debugged using Matlab 7.1. The mathematical model was used to analyze the phenomena that take place during the molecular distillation process, and it also allowed studying the influence of operating variables on the performance of the process. In this investigation, we analyzed the influence of the operating temperature on purity and yield of the components. Trials at three evaporating temperatures (110 ºC, 130 ºC, and 140 ºC) were carried out in a KDL4 (UIC) molecular distillation apparatus to verify the model.

M. A., Marttinello; I., Leone; M., Pramparo.

93

The Molecular Level: Tools for Structural Biology Education and Training  

Science.gov (United States)

This website from Professor Gale Rhodes of the Chemistry Department at the University of Southern Maine offers teachers and students a variety of useful tools and other resources related to structural biology. New biochemistry students will appreciate the site tutorials including Bioinformatics for Beginners, Tutorial for RasMol, and Tutorial for Deep View (Swiss-PdbViewer). Professors looking for tips on creating more dynamic classroom environments will want to peruse the User's Manual for Student-Led Discussion. Other site offerings include a Biochemistry Topics List; A Glossary of Terms from Crystallography, NMR, and Homology Modeling; and a section on Stereo Viewing. If for no other reason, you will want to stop by this website to read Professor Rhodes' Molecular Graphics Manifesto.

Rhodes, Gale

2005-12-16

94

Space Based Multi-level Process Flow and Logistics Analysis  

Directory of Open Access Journals (Sweden)

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.

Zhou Qiu-Zhong

2013-01-01

95

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

Science.gov (United States)

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

Hu, Hai-Bao; Chen, Li-Bin; Bao, Lu-Yao; Huang, Su-He

2014-07-01

96

Transitons of Markovian Process Through a Given Level  

Directory of Open Access Journals (Sweden)

Full Text Available This paper is a free continuation of [l] where properties of Markovian process were also dealt with. It may be necessary to determine the count of transitions through a given level and the mean time during that the random process persists over or below a chosen level. Traffic load estimations and predictions in dynamically controlled broadband networks may serve as an example of practical applications. Unlike of [l] where as many changes in the state of random process as possible shall be caught up, now we are only interested in those transitions which cross a chosen level.

Gustav Cepciansky

2003-01-01

97

Managing the high level waste nuclear regulatory commission licensing process  

International Nuclear Information System (INIS)

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

98

High level waste management at the Idaho Chemical Processing Plant  

International Nuclear Information System (INIS)

This paper summarizes past and current high-level waste management practices at the Idaho Chemical Processing Plant (ICPP); options for long-term waste management of existing and future waste calcine are also emphasized

99

Communication: Molecular-level insights into asymmetric triblock copolymers: Network and phase development  

Science.gov (United States)

Molecularly asymmetric triblock copolymers progressively grown from a parent diblock copolymer can be used to elucidate the phase and property transformation from diblock to network-forming triblock copolymer. In this study, we use several theoretical formalisms and simulation methods to examine the molecular-level characteristics accompanying this transformation, and show that reported macroscopic-level transitions correspond to the onset of an equilibrium network. Midblock conformational fractions and copolymer morphologies are provided as functions of copolymer composition and temperature.

Tallury, Syamal S.; Mineart, Kenneth P.; Woloszczuk, Sebastian; Williams, David N.; Thompson, Russell B.; Pasquinelli, Melissa A.; Banaszak, Michal; Spontak, Richard J.

2014-09-01

100

High-Level Waste System Process Interface Description  

Energy Technology Data Exchange (ETDEWEB)

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.

d' Entremont, P.D.

1999-01-14

 
 
 
 
101

Exploring the Impact of and Perceptions about Interactive, Self-Explaining Environments in Molecular- Level Animations  

Directory of Open Access Journals (Sweden)

Full Text Available This mixed-method study investigates the effects of interactivity in animations of a molecular-level process and explores perceptions aboutthe animated learning tool used. Treatments were based on principlesof cognitive psychology designed to study the main effects of treatment and spatial ability and their interaction. Results with students (n=189 showed that science majors scored higher than non-science majors in retention measures (i.e., structure and function but not in transfer. Significant main effects were found for treatment in function questions and spatial ability in structure questions. There was a significant interaction between treatment and spatial ability in structure questions. Additionally, in this study participants believed the key and the motion of ions and molecules were the most helpful parts of the animation. This study shows that students perceive the animations as being supportive of their learning, suggesting that animations do have a role in scienceclassrooms.

David A. Falvo

2011-01-01

102

Molecular chaperone GroEL/ES: unfolding and refolding processes.  

Science.gov (United States)

Molecular chaperones are a special class of heat shock proteins (Hsp) that assist the folding and formation of the quaternary structure of other proteins both in vivo and in vitro. However, some chaperones are complex oligomeric proteins, and one of the intriguing questions is how the chaperones fold. The representatives of the Escherichia coli chaperone system GroEL (Hsp60) and GroES (Hsp10) have been studied most intensively. GroEL consists of 14 identical subunits combined into two interacting ring-like structures of seven subunits each, while the co-chaperone GroES interacting with GroEL consists of seven identical subunits combined into a dome-like oligomeric structure. In spite of their complex quaternary structure, GroEL and GroES fold well both in vivo and in vitro. However, the specific oligomerization of GroEL subunits is dependent on ligands and external conditions. This review analyzes the literature and our own data on the study of unfolding (denaturation) and refolding (renaturation) processes of these molecular chaperones and the effect of ligands and solvent composition. Such analysis seems to be useful for understanding the folding mechanism not only of the GroEL/GroES complex, but also of other oligomeric protein complexes. PMID:24490731

Ryabova, N A; Marchenkov, V V; Marchenkova, S Yu; Kotova, N V; Semisotnov, G V

2013-12-01

103

Effect of vacuum processing on outgassing within an orbiting molecular shield  

Science.gov (United States)

The limiting hydrogen number density in an orbiting molecular shield is highly dependent on the outgassing rates from the materials of construction for the shield, experimental apparatus, and other hardware contained within the shield. Ordinary degassing temperatures used for ultrahigh vacuum studies (less than 450 C) are not sufficient to process metals so that the contribution to the number density within the shield due to outgassing is less than the theoretically attainable level (approximately 200 per cu. cm). Pure aluminum and type 347 stainless steel were studied as candidate shield materials. Measurements of their hydrogen concentration and diffusion coefficients were made, and the effects of high temperature vacuum processing (greater than 600 C) on their resulting outgassing rates was determined. The densities in a molecular shield due to the outgassing from either metal were substantially less ( 0.003) than the density due to the ambient atomic hydrogen flux at an orbital altitude of 500 km.

Outlaw, R. A.

1982-01-01

104

Quantum control of molecular processes. 2. rev. and enl. ed.  

Energy Technology Data Exchange (ETDEWEB)

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 physicists, physical chemists, materials scientists and nanotechnologists. The authors are among the cofounders of the field of coherent control. They have published extensively on this and related subjects in chemical physics, and have received numerous awards and worldwide recognition for their research contributions. (orig.)

Shapiro, Moshe [British Columbia Univ., Vancouver, BC (Canada). Dept. of Chemistry; Brumer, Paul [Toronto Univ., ON (Canada). Dept. of Chemistry

2012-07-01

105

Solution processed molecular floating gate for flexible flash memories  

Science.gov (United States)

Solution processed fullerene (C60) molecular floating gate layer has been employed in low voltage nonvolatile memory device on flexible substrates. We systematically studied the charge trapping mechanism of the fullerene floating gate for both p-type pentacene and n-type copper hexadecafluorophthalocyanine (F16CuPc) semiconductor in a transistor based flash memory architecture. The devices based on pentacene as semiconductor exhibited both hole and electron trapping ability, whereas devices with F16CuPc trapped electrons alone due to abundant electron density. All the devices exhibited large memory window, long charge retention time, good endurance property and excellent flexibility. The obtained results have great potential for application in large area flexible electronic devices.

Zhou, Ye; Han, Su-Ting; Yan, Yan; Huang, Long-Biao; Zhou, Li; Huang, Jing; Roy, V. A. L.

2013-10-01

106

Quantum control of molecular processes. 2. rev. and enl. ed.  

International Nuclear Information System (INIS)

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 physicists, physical chemists, materials scientists and nanotechnologists. The authors are among the cofounders of the field of coherent control. They have published extensively on this and related subjects in chemical physics, and have received numerous awards and worldwide recognition for their research contributions. (orig.)

107

Graphics processing units accelerated semiclassical initial value representation molecular dynamics  

International Nuclear Information System (INIS)

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

108

The Algorithm Theoretical Basis Document for Level 1A Processing  

Science.gov (United States)

The first process of the Geoscience Laser Altimeter System (GLAS) Science Algorithm Software converts the Level 0 data into the Level 1A Data Products. The Level 1A Data Products are the time ordered instrument data converted from counts to engineering units. This document defines the equations that convert the raw instrument data into engineering units. Required scale factors, bias values, and coefficients are defined in this document. Additionally, required quality assurance and browse products are defined in this document.

Jester, Peggy L.; Hancock, David W., III

2012-01-01

109

Molecular Surveillance of Viral Processes Using Silicon Nitride Membranes  

Directory of Open Access Journals (Sweden)

Full Text Available 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 layers concentrated rotavirus particles similarly to affinity-coated carbon films. However, affinity-coated SiN membranes outperformed glow-discharged conventional carbon films 5-fold as indicated by the number of viral particles quantified in EM images. In addition, we were able to recapitulate viral uncoating and transcription mechanisms directed onto the microchip surfaces. EM images of these processes revealed the production of RNA transcripts emerging from active rotavirus complexes. These results were confirmed by the functional incorporation of radiolabeled nucleotides into the nascent RNA transcripts. Collectively, we demonstrate new uses for SiN membranes to perform molecular surveillance on life processes in real-time.

Deborah F. Kelly

2013-03-01

110

Fine-tuning molecular energy levels by nonresonant laser pulses  

CERN Document Server

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

Lemeshko, Mikhail

2010-01-01

111

High Level Waste (HLW) Feed Process Control Strategy  

Energy Technology Data Exchange (ETDEWEB)

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.

STAEHR, T.W.

2000-06-14

112

Document authentication at molecular levels using desorption atmospheric pressure chemical ionization mass spectrometry imaging.  

Science.gov (United States)

Molecular images of documents were obtained by sequentially scanning the surface of the document using desorption atmospheric pressure chemical ionization mass spectrometry (DAPCI-MS), which was operated in either a gasless, solvent-free or methanol vapor-assisted mode. The decay process of the ink used for handwriting was monitored by following the signal intensities recorded by DAPCI-MS. Handwritings made using four types of inks on four kinds of paper surfaces were tested. By studying the dynamic decay of the inks, DAPCI-MS imaging differentiated a 10-min old from two 4 h old samples. Non-destructive forensic analysis of forged signatures either handwritten or computer-assisted was achieved according to the difference of the contour in DAPCI images, which was attributed to the strength personalized by different writers. Distinction of the order of writing/stamping on documents and detection of illegal printings were accomplished with a spatial resolution of about 140 µm. A Matlab® written program was developed to facilitate the visualization of the similarity between signature images obtained by DAPCI-MS. The experimental results show that DAPCI-MS imaging provides rich information at the molecular level and thus can be used for the reliable document analysis in forensic applications. PMID:24078245

Li, Ming; Jia, Bin; Ding, Liying; Hong, Feng; Ouyang, Yongzhong; Chen, Rui; Zhou, Shumin; Chen, Huanwen; Fang, Xiang

2013-09-01

113

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

Science.gov (United States)

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

Norlén, L

2014-09-01

114

Extracting dwell time sequences from processive molecular motor data.  

Science.gov (United States)

Processive molecular motors, such as kinesin, myosin, or dynein, convert chemical energy into mechanical energy by hydrolyzing ATP. The mechanical energy is used for moving in discrete steps along the cytoskeleton and carrying a molecular load. Single-molecule recordings of motor position along a substrate polymer appear as a stochastic staircase. Recordings of other single molecules, such as F1-ATPase, RNA polymerase, or topoisomerase, have the same appearance. We present a maximum likelihood algorithm that extracts the dwell time sequence from noisy data, and estimates state transition probabilities and the distribution of the motor step size. The algorithm can handle models with uniform or alternating step sizes, and reversible or irreversible kinetics. A periodic Markov model describes the repetitive chemistry of the motor, and a Kalman filter allows one to include models with variable step size and to correct for baseline drift. The data are optimized recursively and globally over single or multiple data sets, making the results objective over the full scale of the data. Local binary algorithms, such as the t-test, do not represent the behavior of the whole data set. Our method is model-based, and allows rapid testing of different models by comparing the likelihood scores. From data obtained with current technology, steps as small as 8 nm can be resolved and analyzed with our method. The kinetic consequences of the extracted dwell sequence can be further analyzed in detail. We show results from analyzing simulated and experimental kinesin and myosin motor data. The algorithm is implemented in the free QuB software. PMID:16905607

Milescu, Lorin S; Yildiz, Ahmet; Selvin, Paul R; Sachs, Frederick

2006-11-01

115

Levels of processing and Eye Movements: A Stimulus driven approach  

DEFF Research Database (Denmark)

The aim of this research is to investigate the explication of levels of attention through eye movement parameters. Previous research from disparate fields have suggested that eye movements are related to cognitive processing, however, the exact nature of the relationship is unclear. Since eye movements can be controlled either by bottom up stimulus properties or by top down cognitive control, studies have compared eye movements in real world tasks and searched for indicators of cognitive load or level of attention when task demands increase. Extracting the effects of cognitive processing on eye movements from the effect of the changing nature of the stimulus is difficult. Characterising and confirming the parameters of levels of processing in eye movements requires measures with the explicit intention of systematically varying task demands while also taking account of individual differences. This series of studies attempts to provide explanatory information for previous findings that saccade amplitude and fixation duration are indicative of levels of processing and to isolate top down influences on eye movements with a stimulus driven approach. This approach involves developing measures suitable for studying individual differences in attention in large sample groups, using stimulus pairs which are similar in terms of bottom up properties but different in terms of higher level processing. These methods are presented in study 1, stimuli are developed and tested in Study 2. Study 3 uses these stimuli to investigate individual differences in levels of processing within the normal population using existing constructs and tests of cognitive style. Study 4 investigates these stimuli and the eye movements of a clinical group with known interruption to the dorsal stream of processing, and subsequent isolated difficulty with certain aspects of visual cognition. Results are presented in terms of the development of methods for assessing and tracking individual differences in cognition and subjectiveattentional states in real time through eye movement analysis.

Mulvey, Fiona Bríd

2014-01-01

116

Communication: Highest occupied molecular orbital-lowest unoccupied molecular orbital gaps of doped silicon clusters from core level spectroscopy.  

Science.gov (United States)

A method to determine band gaps of size-selected and isolated nanoparticles by combination of valence band and core-level photoionization spectroscopy is presented. This approach is widely applicable and provides a convenient alternative to current standard techniques for the determination of band gaps by optical or photoelectron spectroscopy. A first application to vanadium doped silicon clusters confirms a striking size-dependence of their highest occupied-lowest unoccupied molecular orbital gaps. PMID:21280677

Lau, J T; Vogel, M; Langenberg, A; Hirsch, K; Rittmann, J; Zamudio-Bayer, V; Möller, T; von Issendorff, B

2011-01-28

117

Viscous origin of ionic liquids at the molecular level: A quantum chemical insight  

Science.gov (United States)

The viscosity of selected families of ionic liquids has been assessed at the molecular level as a function of the intermolecular interactions using Density Functional Theory together with Atoms-in-a-Molecule and Natural Bond Orbitals approaches. Large ion clusters were studied, with the energetics and topology of interactions being related with experimental viscosity data to infer nanoscopic mechanisms controlling the viscous behavior. The reported results exhibit important information on the molecular basis controlling viscosity, which would allow advancing in the development of low-viscous ionic liquids, through a judicious selection of ion pairs considering their interactions and molecular structure.

García, Gregorio; Atilhan, Mert; Aparicio, Santiago

2014-08-01

118

[Molecular genetic bases of adaptation processes and approaches to their analysis].  

Science.gov (United States)

Great interest in studying the molecular genetic bases of the adaptation processes is explained by their importance in understanding evolutionary changes, in the development ofintraspecific and interspecific genetic diversity, and in the creation of approaches and programs for maintaining and restoring the population. The article examines the sources and conditions for generating adaptive genetic variability and contribution of neutral and adaptive genetic variability to the population structure of the species; methods for identifying the adaptive genetic variability on the genome level are also described. Considerable attention is paid to the potential of new technologies of genome analysis, including next-generation sequencing and some accompanying methods. In conclusion, the important role of the joint use of genomics and proteomics approaches in understanding the molecular genetic bases of adaptation is emphasized. PMID:23662427

Salmenkova, E A

2013-01-01

119

Why do we need three levels to understand the molecular optical response?  

Science.gov (United States)

Traditionally, the nonlinear optical response at the molecular level has been modeled using the two-level approximation, under the assumption that the behavior of the exact sum-over-states (SOS) expressions for the molecular polarizabilities is well represented by the contribution of only two levels. We show how, a rigorous application of the Thomas-Kuhn sum-rules over the SOS expression for the diagonal component of the first-hyperpolarziability proves that the two-level approximation is unphysical. In addition, we indicate how the contributions of potentially infinite number of states to the SOS expressions for the first-hyperpolarizability are well represented by the contributions of a generic three-level system. This explains why the analysis of the three-level model in conjugation with the sum rules has lead to successful paradigms for the optimization of organic chromophores.

Perez-Moreno, Javier; Clays, Koen; Kuzyk, Mark G.

2011-10-01

120

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

Directory of Open Access Journals (Sweden)

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.

Shigemura Masahiko

2012-07-01

 
 
 
 
121

Polarization-induced renormalization of molecular levels at metallic and semiconducting surfaces  

Digital Repository Infrastructure Vision for European Research (DRIVER)

On the basis of first-principles G0W0 calculations we systematically study how the electronic levels of a benzene molecule are renormalized by substrate polarization when physisorbed on different metallic and semiconducting surfaces. The polarization-induced reduction in the energy gap between occupied and unoccupied molecular levels is found to scale with the substrate density of states at the Fermi level (for metals) and substrate band gap (for semiconductors). These conclusions are further...

Garci?a Lastra, Juan Maria; Rostgaard, Carsten; Rubio, A.; Thygesen, Kristian Sommer

2010-01-01

122

Vibrational spectroscopy for probing molecular-level interactions in organic films mimicking biointerfaces.  

Science.gov (United States)

Investigation into nanostructured organic films has served many purposes, including the design of functionalized surfaces that may be applied in biomedical devices and tissue engineering and for studying physiological processes depending on the interaction with cell membranes. Of particular relevance are Langmuir monolayers, Langmuir-Blodgett (LB) and layer-by-layer (LbL) films used to simulate biological interfaces. In this review, we shall focus on the use of vibrational spectroscopy methods to probe molecular-level interactions at biomimetic interfaces, with special emphasis on three surface-specific techniques, namely sum frequency generation (SFG), polarization-modulated infrared reflection absorption spectroscopy (PM-IRRAS) and surface-enhanced Raman scattering (SERS). The two types of systems selected for exemplifying the potential of the methods are the cell membrane models and the functionalized surfaces with biomolecules. Examples will be given on how SFG and PM-IRRAS can be combined to determine the effects from biomolecules on cell membrane models, which include determination of the orientation and preservation of secondary structure. Crucial information for the action of biomolecules on model membranes has also been obtained with PM-IRRAS, as is the case of chitosan removing proteins from the membrane. SERS will be shown as promising for enabling detection limits down to the single-molecule level. The strengths and limitations of these methods will also be discussed, in addition to the prospects for the near future. PMID:24530000

Volpati, Diogo; Aoki, Pedro H B; Alessio, Priscila; Pavinatto, Felippe J; Miranda, Paulo B; Constantino, Carlos J L; Oliveira, Osvaldo N

2014-05-01

123

Free energy calculations using dual-level Born-Oppenheimer molecular dynamics  

International Nuclear Information System (INIS)

We describe an efficient and accurate method to compute free energy changes in complex chemical systems that cannot be described through classical molecular dynamics simulations, examples of which are chemical and photochemical reactions in solution, enzymes, interfaces, etc. It is based on the use of dual-level Born-Oppenheimer molecular dynamics simulations. A low-level quantum mechanical method is employed to calculate the potential of mean force through the umbrella sampling technique. Then, a high-level quantum mechanical method is used to estimate a free energy correction on selected points of the reaction coordinate using perturbation theory. The precision of the results is comparable to that of ab initio molecular dynamics methods such as the Car-Parrinello approach but the computational cost is much lower, roughly by two to three orders of magnitude. The method is illustrated by discussing the association free energy of simple organometallic compounds, although the field of application is very broad.

124

Process Analysis and Level Measurement of Textbooks Use by Teachers  

Science.gov (United States)

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

Kong, Fanzhe; Shi, Ningzhong

2009-01-01

125

High-Level waste process and product data annotated bibliography  

International Nuclear Information System (INIS)

The objective of this document is to provide information on available issued documents that will assist interested parties in finding available data on high-level waste and transuranic waste feed compositions, properties, behavior in candidate processing operations, and behavior on candidate product glasses made from those wastes. This initial compilation is only a partial list of available references

126

Molecular processes affecting the macroscopic tribological behavior of surfaces  

International Nuclear Information System (INIS)

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)

127

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

DEFF Research Database (Denmark)

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

Harper, Peter Mathias; Gani, Rafiqul

2001-01-01

128

Effect of the bread-making process on zearalenone levels.  

Science.gov (United States)

The effects of the bread-making process including fermentation with Saccharomyces cerevisiae and lactic acid bacteria (Lactobacillus casei, Lactobacillus rhamnosus, Lactobacillus acidophilus and Lactobacillus fermentum) and baking at 200°C on zearalenone (ZEA) levels were investigated. Standard solutions of ZEA were added to flour and then loaves of bread were prepared. Sourdough and three types of yeast including active dry yeast, instant dry yeast and compressed yeast were used for the fermentation of dough. ZEA levels in flour, dough and bread were determined by HPLC with fluorescence detection after extraction and clean-up on an immunoaffinity column. The highest reduction in levels of ZEA was found in the first fermentation (first proof), while the lowest reduction was observed in the baking stage. In addition, the results showed that compressed yeast had the maximum reduction potential on ZEA levels even at the baking stage. PMID:25291600

Heidari, Sara; Milani, Jafar; Nazari, Seyed Saman Seyed Jafar

2014-12-01

129

Level 0 and Level 1 data processing for a type of hyperspectral imager  

Science.gov (United States)

Hyper-spectral imaging (HSI) is a kind of optical remote sensor that can simultaneously obtain spatial and spectral information of ground targets. We are now designing a data processing system for a type of space-borne push-broom HSI, which has 128 spectral channels covering the spectral range from 400nm to 2500nm. With its large amount of spectral channels, the HSI collects large volume of spectral imaging data need to be efficiently and accurately processed and calibrated. In this paper, the detailed Level 0 and Level 1 data processing steps for the HSI were presented. The Level 0 processing refers to a set of tasks performed on the data downlinked from the spacecraft, including decoding to extract science data, separating the science data into files corresponding to different tasks (e.g. ground imaging, dark imaging, and onboard calibration), checking data integrity and instrument settings, data format conversion, and Level 0 files creation. The Level 1 processing performs several steps on Level 0 data. Firstly, it corrects the image artifacts (mostly the SWIR smear effect), subtracts the dark background, and performs the bad pixel replacement according to the prelaunch measurement; then it performs radiometric and spectral calibration based on the ground calibration results and onboard calibration collection. The detailed algorithms for bad pixel replacement, radiometric and spectral calibration were presented. After processing, the digital numbers downlinked from the spacecraft can be converted into at-sensor absolute spectral radiance of ground targets, thus providing accurate quantified spectral imaging data for various applications.

Li, Xiaohui; Yan, Changxiang

2009-11-01

130

Optimal degradation processes control by two-level policies  

International Nuclear Information System (INIS)

Two-level control policies are applied to various types of Markov processes describing degrading parameters of system units. To estimate the system operation cost an expectation of losses per unit time is evaluated. It is assumed that the degradation process is observable, and a monitoring system can signal about future failures. Firstly, semi-Markov processes are considered. A death process is proposed for a unit subjected to corrosion. A Markov chain are used for the problem of fatigue crack growth. The control problem is studied mainly in a steady-state regime for units of multiple use when the cost function is performed as the ratio of expectations. The cost function as the expectation of losses per unit time for single units is also studied, and the majorizing property of this cost function is shown

131

Separation processes for high-level radioactive waste treatment  

International Nuclear Information System (INIS)

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

132

Commercial low level waste processing in a competitive market  

International Nuclear Information System (INIS)

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

133

Mixing Processes in High-Level Waste Tanks - Final Report  

International Nuclear Information System (INIS)

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

134

Progress on molecular imaging  

International Nuclear Information System (INIS)

Molecular imaging is a new era of medical imaging,which can non-invasively monitor biological processes at the cellular and molecular level in vivo, including molecular imaging of nuclear medicine, magnetic resonance molecular imaging, ultrasound molecular imaging,optical molecular imaging and molecular imaging with X-ray. Recently, with the development of multi-subjects amalgamation, multimodal molecular imaging technology has been applied in clinical imaging, such as PET-CT and PET-MRI. We believe that with development of molecular probe and multi-modal imaging, more and more molecular imaging techniques will be applied in clinical diagnosis and treatment. (authors)

135

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

Energy Technology Data Exchange (ETDEWEB)

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.

D.L. McGregor

2000-12-20

136

Multi-Level Filter for Infrared Image Processing  

Science.gov (United States)

This paper presents a new multi-level filter algorithm and its corresponding VLSI architecture for infrared image processing. The algorithm eliminates the phenomena of splitting targets by inserting Gaussian pyramid processing. Owning three filter paths, the proposed filter VLSI architecture can enhance small targets with different size in infrared images. This architecture has been implemented using SMIC 0.35?m 4-layer CMOS technology. The test result shows that the filter chip not only effectively suppresses background, eliminates noise and enhances small targets in an infrared image, but also meets infrared image real-time processing requirement(5M ˜ 10M pixels/s). The implemented filter chip consists of 60,284 gates and 8K SRAM, operates at 50MHz.

Zhaoqing, Zheng; Tianxu, Zhang; Xubang, Shen

2006-12-01

137

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

International Nuclear Information System (INIS)

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

138

Vision-based level control for beverage-filling processes  

Science.gov (United States)

This paper presents a vision-based on-line level control system which is used in beverage filling machines. Motivation for the development of this sensor system was the need for an intelligent filling valve, which can provide constant filling levels for all container/product combinations (i.e. juice, milk, beer, water, etc. in glass or PET bottles with various transparency and shape) by using a non-tactile and completely sterile measurement method. The sensor concept being presented in this paper is based on several CCD-cameras imaging the moving containers from the outside. The stationary lighting system illuminating the bottles is located within the filler circle. The field of view covers between 5 and 8 bottles depending on the bottle diameter and the filler partitioning. Each filling element's number is identified by the signals of an angular encoder. The electro-pneumatic filling valves can be opened and closed by computer control The cameras continuously monitor the final stages of the filling process, i.e. after the filling height has reached the upper half of the bottle. The sensor system measures the current filling height and derives the filling speed. Based on static a priori- knowledge and dynamic process knowledge the sensor system generates a best estimate of the particular time when the single valve is to be closed. After every new level measurement the system updates the closing time. The measurement process continues until the result of the next level calculation would be available after the estimated closing time would have been passed. The vision-based filling valve control enables the filling machine to adapt the filling time of each valve to the individual bottle shape. Herewith a standard deviation between 2 and 4 mm (depending on the slew rate in the bottle neck) can be accomplished, even at filling speed > 70.000 bottles per hour. 0

Ley, Dietmar; Braune, Ingolf

1994-11-01

139

Free-electron laser induced processes in thin molecular ice.  

Science.gov (United States)

Intermolecular reactions in and on icy films on silicate and carbonaceous grains constitute a major route for the formation of new molecular constituents in interstellar molecular clouds. In more diffuse regions and in protoplanetary discs, energetic radiation can trigger reaction routes far from thermal equilibrium. As an analog of interstellar ice-covered dust grains, highly-oriented pyrolytic graphite (HOPG) covered with D2O, NO, and H atoms is irradiated by ultrashort XUV pulses and the desorbing ionic and neutral products are analysed. The yields of several products show a nonlinear intensity dependence and thus enable the elucidation of reaction dynamics by two-pulse correlated desorption. PMID:25302398

Siemer, Björn; Roling, Sebastian; Frigge, Robert; Hoger, Tim; Mitzner, Rolf; Zacharias, Helmut

2014-01-01

140

Driving ordering processes in molecular-dynamics simulations.  

Science.gov (United States)

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

Dittmar, Harro; Kusalik, Peter G

2014-05-16

 
 
 
 
141

Driving Ordering Processes in Molecular-Dynamics Simulations  

Science.gov (United States)

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.

Dittmar, Harro; Kusalik, Peter G.

2014-05-01

142

Defense Waste Processing Facility: a remote process for solidification of Savannah River Plant high level waste  

International Nuclear Information System (INIS)

The Department of Energy is proposing that a Defense Waste Processing Facility be built at the Savannah River Plant (SRP) to remotely process and immobilize high level radioactive waste produced at the site. Research, development, and design of the facility is being provided by a multidisciplined task force of personnel from the Du Pont Company which designed, built and has operated SRP since 1950. This remotely operated facility will immobilize 28 million gallons of high level waste now stored in tanks, plus the waste to be generated from continued reprocessing operations. Borosilicate glass has been selected as the reference waste form for the immobilization process

143

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

Energy Technology Data Exchange (ETDEWEB)

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.

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

144

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

International Nuclear Information System (INIS)

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 ?-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)

145

An algebraic approach for simultaneous solution of process and molecular design problems  

Directory of Open Access Journals (Sweden)

Full Text Available The property integration framework has allowed for simultaneous representation of processes and products from a properties perspective and thereby established a link between molecular and process design problems. The simultaneous approach involves solving two reverse problems. The first reverse problem identifies the property targets corresponding to the desired process performance. The second reverse problem is the reverse of a property prediction problem, which identifies the molecular structures that match the targets identified in the first problem. Group Contribution Methods (GCM are used to form molecular property operators that will be used to track properties. Earlier contributions in this area have worked to include higher order estimation of GCM for solving the molecular design problem. In this work, the accuracy of the property prediction is further enhanced by improving the techniques to enumerate higher order groups. Incorporation of these higher order enumeration techniques increases the efficiency of property prediction and thus the application range of the group contribution methods in molecular design problems. Successful tracking of properties is the key in applying the reverse problem formulation for integrated process and product design problems. An algebraic technique has been developed for solving process and molecular design problems simultaneously. Since both process and molecular property operators target the same optimum process performance, the set of inequality expressions can be solved simultaneously to identify the molecules that meet the desired process performance. Since this approach is based on an algebraic algorithm, any number of properties can be tracked simultaneously.

S. Bommareddy

2010-09-01

146

Bias-dependent molecular-level structure of electrical double layer in ionic liquid on graphite  

Energy Technology Data Exchange (ETDEWEB)

Bias-dependent structure of electrochemical double layers at liquid-solid interfaces underpin a multitude of phenomena in virtually all areas of scientific enquiry ranging from energy storage and conversion systems, biology, to geophysics and geochemistry. Here we report the bias-evolution of the electric double layer structure of an ionic liquid on highly ordered pyrolytic graphite as a model system for carbon-based electrodes for electrochemical supercapacitors measured by atomic force microscopy. Matching the observed structures to molecular dynamics simulations allows us to resolve steric effects due to cation and anion layers. We observe reconfiguration under applied bias and the orientational transitions in the Stern layer. The synergy between molecular dynamics simulation and experiment provides a comprehensive picture of structural phenomena and long- and short range interactions. This insight will improve understanding of the mechanism of charge storage in electrochemical capacitors on a molecular level which can be used to enhance their electrochemical performance.

Black, Jennifer M [ORNL; Walters, Deron [Asylum Research, Santa Barbara, CA; Labuda, Aleksander [Asylum Research, Santa Barbara, CA; Feng, Guang [ORNL; Hillesheim, Patrick C [ORNL; Dai, Sheng [ORNL; Cummings, Peter T [ORNL; Kalinin, Sergei V [ORNL; Proksch, Roger [Asylum Research, Santa Barbara, CA; Balke, Nina [ORNL

2013-01-01

147

Pyrochemical Processing for Low-Level Waste Production in PEACER  

International Nuclear Information System (INIS)

A pyrochemical partitioning process has been conceptually designed so that the transmutation of spent LWR fuels in PEACER can produce mainly low-level waste (Class C waste) for near-surface burial. Chloride salt technology developed for IFR has been employed as the baseline. Electrorefining, reductive extraction and salt recycling steps are used to construct overall flowsheet in order to support PEACER operation. The decontamination factor for transuranic elements was estimated based on both thermodynamic models and reported experimental data. It is expected that overall decontamination factor can be as high as 105 for transuranic elements. Final wastes from pyrochemical processing for PEACER are noble metals, alkaline earth metal, and lanthanides. The final wastes are stabilized by mixing with zeolite and glass-frits such that concentration limit for class C waste can be met. The volume of Class C waste is estimated to be small enough to make PEACER concept valuable for densely populated countries. (authors)

148

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

Science.gov (United States)

The pectinolytic species Pseudomonas viridiflava has a wide host range among plants, causing foliar and stem necrotic lesions and basal stem and root rots. However, little is known about the molecular evolution of this species. In this study we investigated the intraspecies genetic variation of P. viridiflava amongst local (Cretan), as well as international isolates of the pathogen. The genetic and phenotypic variability were investigated by molecular fingerprinting (rep-PCR) and partial sequencing of three housekeeping genes (gyrB, rpoD and rpoB), and by biochemical and pathogenicity profiling. The biochemical tests and pathogenicity profiling did not reveal any variability among the isolates studied. However, the molecular fingerprinting patterns and housekeeping gene sequences clearly differentiated them. In a broader phylogenetic comparison of housekeeping gene sequences deposited in GenBank, significant genetic variability at the molecular level was found between isolates of P. viridiflava originated from different host species as well as among isolates from the same host. Our results provide a basis for more comprehensive understanding of the biology, sources and shifts in genetic diversity and evolution of P. viridiflava populations and should support the development of molecular identification tools and epidemiological studies in diseases caused by this species. PMID:22558343

Sarris, Panagiotis F; Trantas, Emmanouil A; Mpalantinaki, Evaggelia; Ververidis, Filippos; Goumas, Dimitrios E

2012-01-01

149

Study on Removal of Organics of Different Molecular Weight by Coagulation-Membrane Filtration Process  

Directory of Open Access Journals (Sweden)

Full Text Available This paper compares the difference in membrane flux between direct membrane filtration and coagulation-membrane filtration, and investigates the removal of organics of different molecular weight by coagulation-membrane filtration process, in turn studies the fouling removal mechanism of coagulation process. The results indicate that for COD removal from raw water, coagulation is effective mainly on the organics of molecular weight higher than 10 kDa, and membrane filtration is effective mainly on the organics of molecular weight between 30 kDa and 100 kDa and higher than 100 kDa; as for UV254 removal, coagulation is effective mainly on the organics of high molecular weight, and membrane filtration is effective mainly on the organics of molecular weight between 1 kDa and 100 kDa. Therefore, it proves that the high molecular organics are mainly responsible for the membrane fouling.

Lin Yang

2010-02-01

150

Role of contact formation process in transport properties of molecular junctions: conductance of Au/BDT/Au molecular wires  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We report theoretical investigations on the role of contact formation process and its resulting structures to quantum transport in molecular wires and show that these processes critically control charge conduction. It was found, for Au(111)/1,4-benzenedithiol(BDT)/Au(111) junctions, the hydrogen atom in the thiol groups is energetically non-dissociative after the contact formation. The calculated conductances and junction breakdown forces of H-non-dissociative Au/BDT/Au devi...

Ning, Zhanyu; Ji, Wei; Guo, Hong

2009-01-01

151

Molecular dump processes induced by chirped laser pulses.  

Science.gov (United States)

We focus on the applications of shaped-dump laser pulses in the femtosecond regime. Calculations on a model system show that a wealth of information on molecular properties can be obtained from spectroscopy with such pulses. Systematic parameter scans are presented for linearly chirped pulses and for colored double pulses, revealing the dynamical properties of the system. For characterization of the system, quantum control fitness landscapes prove to be a powerful tool. PMID:19044763

Marquetand, Philipp; Nuernberger, Patrick; Brixner, Tobias; Engel, Volker

2008-08-21

152

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

Energy Technology Data Exchange (ETDEWEB)

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.

Henderson, Michael A.; Lyubinetsky, Igor

2013-06-12

153

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

Directory of Open Access Journals (Sweden)

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.

Moreno Víctor

2008-12-01

154

EOS MLS Level 1B Data Processing Software. Version 3  

Science.gov (United States)

This software is an improvement on Version 2, which was described in EOS MLS Level 1B Data Processing, Version 2.2, NASA Tech Briefs, Vol. 33, No. 5 (May 2009), p. 34. It accepts the EOS MLS Level 0 science/engineering data, and the EOS Aura spacecraft ephemeris/attitude data, and produces calibrated instrument radiances and associated engineering and diagnostic data. This version makes the code more robust, improves calibration, provides more diagnostics outputs, defines the Galactic core more finely, and fixes the equator crossing. The Level 1 processing software manages several different tasks. It qualifies each data quantity using instrument configuration and checksum data, as well as data transmission quality flags. Statistical tests are applied for data quality and reasonableness. The instrument engineering data (e.g., voltages, currents, temperatures, and encoder angles) is calibrated by the software, and the filter channel space reference measurements are interpolated onto the times of each limb measurement with the interpolates being differenced from the measurements. Filter channel calibration target measurements are interpolated onto the times of each limb measurement, and are used to compute radiometric gain. The total signal power is determined and analyzed by each digital autocorrelator spectrometer (DACS) during each data integration. The software converts each DACS data integration from an autocorrelation measurement in the time domain into a spectral measurement in the frequency domain, and estimates separately the spectrally, smoothly varying and spectrally averaged components of the limb port signal arising from antenna emission and scattering effects. Limb radiances are also calibrated.

Perun, Vincent S.; Jarnot, Robert F.; Wagner, Paul A.; Cofield, Richard E., IV; Nguyen, Honghanh T.; Vuu, Christina

2011-01-01

155

Variational calculation of energy levels in {ital {bar p}}He{sup +} molecular systems  

Energy Technology Data Exchange (ETDEWEB)

A variational calculation is presented of energy levels for the nonrelativistic Hamiltonian of the metastable antiprotonic helium atom {ital {bar p}}{sup 3,4}He{sup +}. This calculation is based on a molecular expansion of the wave function. We estimate the precision of the results to be about 10{sup {minus}7} a.u. {copyright} {ital 1996 The American Physical Society.}

Korobov, V.I. [Joint Institute for Nuclear Research, Dubna (Russia)

1996-09-01

156

Molecular electronic level alignment at weakly coupled organic film/metal interfaces.  

Science.gov (United States)

Electronic level alignment at interfaces of molecular materials with inorganic semiconductors and metals controls many interfacial phenomena. How the intrinsic properties of the interacting systems define the electronic structure of their interface remains one of the most important problems in molecular electronics and nanotechnology that can be solved through a combination of surface science experimental techniques and theoretical modeling. In this article, we address this fundamental problem through experimental and computational studies of molecular electronic level alignment of thin films of C6F6 on noble metal surfaces. The unoccupied electronic structure of C6F6 is characterized with single molecule resolution using low-temperature scanning tunneling microscopy-based constant-current distance-voltage spectroscopy. The experiments are performed on several noble metal surfaces with different work functions and distinct surface-normal projected band structures. In parallel, the electronic structures of the quantum wells (QWs) formed by the lowest unoccupied molecular orbital state of the C6F6 monolayer and multilayer films and their alignment with respect to the vacuum level of the metallic substrates are calculated by solving the Schrödinger equation for a semiempirical one-dimensional (1D) potential of the combined system using input from density functional theory. Our analysis shows that the level alignment for C6F6 molecules bound through weak van der Waals interactions to noble metal surfaces is primarily defined by the image potential of metal, the electron affinity of the molecule, and the molecule surface distance. We expect the same factors to determine the interfacial electronic structure for a broad range of molecule/metal interfaces. PMID:25303040

Zhao, Jin; Feng, Min; Dougherty, Daniel Barker; Sun, Hao; Petek, Hrvoje

2014-10-28

157

Characterization of Amyloid Structures at the Molecular Level by Solid State Nuclear Magnetic Resonance Spectroscopy  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Solid state nuclear magnetic resonance (NMR) spectroscopy is particularly useful in structural studies of amyloid fibrils because solid state NMR techniques have unique capabilities as site-specific, molecular-level structural probes of noncrystalline materials. These techniques provide experimental data that strongly constrain the secondary, tertiary, and quaternary structures of amyloid fibrils, permitting the development of experimentally-based structural models. Examples of techniques tha...

Tycko, Robert

2006-01-01

158

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

Directory of Open Access Journals (Sweden)

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

Carmen Silva

2004-11-01

159

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

Scientific Electronic Library Online (English)

Full Text Available SciELO Chile | Language: Spanish Abstract in spanish 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 difere [...] nciación 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 sociales Abstract in english A 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 empowerme [...] nt 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

Carmen, Silva; María Loreto, Martínez.

2004-11-01

160

SENTINEL-2 image quality and level 1 processing  

Science.gov (United States)

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

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

2009-08-01

 
 
 
 
161

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

CERN Document Server

The proton nuclear spin-lattice relaxation rate 1/T1 has been measured as a function of temperature and magnetic field (up to 15 T) in the molecular magnetic ring 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.

Julien, M H; Lascialfari, A; Borsa, F; Horvatic, M; Caneschi, A; Gatteschi, Dante

1999-01-01

162

Influence of polyvinylpyrrolidone with different molecular weight on silver nanoconfiguration in polyol process  

International Nuclear Information System (INIS)

This paper researches the influence of different molecular weight polyvinylpyrrolidone on silver nanoconfiguration in polyol process. The silver nanoparticles are characterized by scanning electron microscopy and X-ray diffraction. Their optical properties are studied by UV-Vis spectrophotometer. The results indicate that under of silver nanoparticles different morphology will be made by different molecular weight polyvinylpyrrolidone under the same experimental conditions; the yield of silver nanowires is the largest when the molecular weight of polyvinylpyrrolidone is 1.0 x 104, and silver nanowires will reduce and silver nanocubes will increase when the molecular weight of polyvinylpyrrolidone increases. (authors)

163

Applying CLIPS to control of molecular beam epitaxy processing  

Science.gov (United States)

A key element of U.S. industrial competitiveness in the 1990's will be the exploitation of advanced technologies which involve low-volume, high-profit manufacturing. The demands of such manufacture limit participation to a few major entities in the U.S. and elsewhere, and offset the lower manufacturing costs of other countries which have, for example, captured much of the consumer electronics market. One such technology is thin-film epitaxy, a technology which encompasses several techniques such as Molecular Beam Epitaxy (MBE), Chemical Beam Epitaxy (CBE), and Vapor-Phase Epitaxy (VPE). Molecular Beam Epitaxy (MBE) is a technology for creating a variety of electronic and electro-optical materials. Compared to standard microelectronic production techniques (including gaseous diffusion, ion implantation, and chemical vapor deposition), MBE is much more exact, though much slower. Although newer than the standard technologies, MBE is the technology of choice for fabrication of ultraprecise materials for cutting-edge microelectronic devices and for research into the properties of new materials.

Rabeau, Arthur A.; Bensaoula, Abdelhak; Jamison, Keith D.; Horton, Charles; Ignatiev, Alex; Glover, John R.

1990-01-01

164

Molecular neural network devices based on non-linear dynamic media: basic primitive information processing operations.  

Science.gov (United States)

Basic primitive image-processing operations performed by molecular and biomolecular dynamic media functioning in the oscillating mode are discussed. These operations have rather high computational complexity and can be considered as simulations of human vision capabilities. PMID:8573697

Rambidi, N G; Maximychev, A V

1995-01-01

165

Tectonic processes modelling for high-level radioactive waste disposal  

International Nuclear Information System (INIS)

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

166

Elementary processes, transport and kinetics of molecular plasmas  

International Nuclear Information System (INIS)

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 modells 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

167

EOS MLS Level 2 Data Processing Software Version 3  

Science.gov (United States)

This software accepts the EOS MLS calibrated measurements of microwave radiances products and operational meteorological data, and produces a set of estimates of atmospheric temperature and composition. This version has been designed to be as flexible as possible. The software is controlled by a Level 2 Configuration File that controls all aspects of the software: defining the contents of state and measurement vectors, defining the configurations of the various forward models available, reading appropriate a priori spectroscopic and calibration data, performing retrievals, post-processing results, computing diagnostics, and outputting results in appropriate files. In production mode, the software operates in a parallel form, with one instance of the program acting as a master, coordinating the work of multiple slave instances on a cluster of computers, each computing the results for individual chunks of data. In addition, to do conventional retrieval calculations and producing geophysical products, the Level 2 Configuration File can instruct the software to produce files of simulated radiances based on a state vector formed from a set of geophysical product files taken as input. Combining both the retrieval and simulation tasks in a single piece of software makes it far easier to ensure that identical forward model algorithms and parameters are used in both tasks. This also dramatically reduces the complexity of the code maintenance effort.

Livesey, Nathaniel J.; VanSnyder, Livesey W.; Read, William G.; Schwartz, Michael J.; Lambert, Alyn; Santee, Michelle L.; Nguyen, Honghanh T.; Froidevaux, Lucien; wang, Shuhui; Manney, Gloria L.; Wu, Dong L.; Wagner, Paul A.; Vuu, Christina; Pumphrey, Hugh C.

2011-01-01

168

The dissolution of polyols in salt solutions and ionic liquids at molecular level: ions, counter ions, and hofmeister effects.  

Science.gov (United States)

The dissolving process of polyols in salt solutions (TBAF, TBAC, TBAB, TBAI, TMAF) and imidazolium-based ionic liquids ([C2 mim][OAc], [C2 mim][Et2 PO4 ], [C2 mim][EtSO4 ], [C2 mim][SCN]) is exemplarily studied by IR spectroscopy. Vibrational bands and their shifts in the OH stretch region reveal crucial information for the dissolved polyol interacting with the anions of the salt solutions and ionic liquids. The well-chosen set of ionic solutions confirms the linear relation between the OH-stretch frequencies and the solubility capacity of the salt solutions. Likewise, it also provides an explanation of the dissolving process at molecular level. Notably, the solubility capacities of the anions in the salt solutions follow the well-known Hofmeister series. This phenomenon can be understood on the basis of the disruption power of the anions and the specific size ratio of the anion/cation combinations. PMID:23843268

Papanyan, Zakar; Roth, Christian; Wittler, Kai; Reimann, Sebastian; Ludwig, Ralf

2013-11-11

169

In-situ growth monitoring of molecular beam epitaxy processes  

Science.gov (United States)

The strong collaboration between Arizona State University and General Electric Corp. has resulted in a comprehensive program to develop intelligent, in-situ sensors for monitoring and control of semiconductor thin film growth by Molecular Beam Epitaxy (MBE). An intimate collaboration with a commercial MBE manufacturer (DCA Instruments) has resulted in a new ultra-stable substrate manipulator which is compatible with in-situ optical measurements. Another long time collaboration with an ellipsometer manufacturer (Woollam Co.) has generated a new prototype high speed in-situ spectroscopic ellipsometer. Both the manipulator and the ellipsometer have become commercial products. Adaptation of spectroscopic ellipsometry to real time MBE growth monitoring and development of advanced computer algorithms have enabled the tracking of epitaxial layer thickness, temperature and alloy composition. Temperature dependent (from room temperature to 650 deg C) optical constants of GaAs have been measured and verified. Work is continuing on obtaining optical constants for AlGaAs compound semiconductors.

Maracas, George N.; Sohie, Guy R.

1993-09-01

170

A surface-anchored molecular four-level conductance switch based on single proton transfer  

Science.gov (United States)

The development of a variety of nanoscale applications requires the fabrication and control of atomic or molecular switches that can be reversibly operated by light, a short-range force, electric current or other external stimuli. For such molecules to be used as electronic components, they should be directly coupled to a metallic support and the switching unit should be easily connected to other molecular species without suppressing switching performance. Here, we show that a free-base tetraphenyl-porphyrin molecule, which is anchored to a silver surface, can function as a molecular conductance switch. The saddle-shaped molecule has two hydrogen atoms in its inner cavity that can be flipped between two states with different local conductance levels using the electron current through the tip of a scanning tunnelling microscope. Moreover, by deliberately removing one of the hydrogens, a four-level conductance switch can be created. The resulting device, which could be controllably integrated into the surrounding nanoscale environment, relies on the transfer of a single proton and therefore contains the smallest possible atomistic switching unit.

Auwärter, Willi; Seufert, Knud; Bischoff, Felix; Ecija, David; Vijayaraghavan, Saranyan; Joshi, Sushobhan; Klappenberger, Florian; Samudrala, Niveditha; Barth, Johannes V.

2012-01-01

171

Predicting the residual aluminum level in water treatment process  

Directory of Open Access Journals (Sweden)

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

J. Tomperi

2012-06-01

172

Predicting the residual aluminum level in water treatment process  

Directory of Open Access Journals (Sweden)

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

J. Tomperi

2013-06-01

173

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

International Nuclear Information System (INIS)

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)

174

Molecular Modeling of Environmentally Important Processes: Reduction Potentials  

Science.gov (United States)

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

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

2004-01-01

175

Atomic and molecular surface and volume processes in the analysis of negative hydrogen discharges  

International Nuclear Information System (INIS)

The principal source of negative ion generation in hydrogen discharges is now recognized to be low-energy electron attachment to H2(? prime prime) molecules excited to the middle portion of the vibrational spectrum. Electron excitation processes are generally taken to be the principal source of H2(? prime prime) generation, with high-energy excitations through the singlet spectrum being the principal excitation process populating the active portion of the vibrational spectrum. A description of the collisional re-excitation from level ? prime prime, to level ? prime prime, requires 15 times 15 matrix of cross sections linking all initial and final levels. These cross sections have been evaluated and incorporated into the modelling code. An additional source of vibrational excitation may be derived from recombination of H2+ and H3+ ions on the surfaces of the discharge. In this case the molecular ions will impinge with kinetic energies given by the plasma potential, 1--10 eV. In this paper we report the evaluation of H2(? prime prime) resulting from the surface recombination process. The use of low-work-function materials for the discharge surfaces makes possible two additional source of negative ions: the direct formation of negative ions by hydrogen atoms rebounding from the surface, and the dissociation of H2- ions formed in the surface selvage. A recent paper has demonstrated the efficacy of Ba surfaces as an active medium for H- formation. Here we shall extend our discussion to H2+, H3+ collisions on Ba surfaces and inventory the generation of H, H2(? prime prime), and H- rebounding from these surfaces. 16 refs., 4 figs

176

Molecular simulation of dioleoylphosphatidylcholine lipid bilayers at differing levels of hydration.  

Science.gov (United States)

The structure and dynamics of the lipid and water components of dioleoylphosphatidylcholine bilayers at various levels of hydration were studied using molecular dynamics (MD) simulations. Equilibration of these systems proceeded by use of a hybrid MD and configurational-bias Monte Carlo technique using one atmosphere of pressure normal to the membrane and a set point for the lateral area derived from experimental Bragg spacings, combined with experimentally derived specific volumes for each of the system components. Membrane surface tensions were observed to be of the order of tens of dyn/cm. The transbilayer molecular fragment peak positions at low hydration were found to agree with experimental neutron and x-ray scattering profiles and previously published simulations. For hydration levels of 5.4, 11.4, and 16 waters/lipid, molecular fragment distributions and order parameters for the headgroup, lipid chains, and water were quantified. Spin-lattice relaxation rates and lateral self-diffusion coefficients of water agreed well with results from experimental nuclear magnetic resonance studies. Relaxation rates of the choline segments and chemical shift anisotropies for the phosphate and carbonyls were computed. Headgroup orientation, as measured by the P-N vector, showed enhanced alignment with the membrane surface at low hydration. The sign of the membrane dipole potential reversed at low hydration, with the membrane interior negative relative to the interlamellar region. Calculation of the number of water molecules in the headgroup hydration shell, as a function of hydration level, supports the hypothesis that the break point in the curve of Bragg spacing versus hydration level near 12 waters/lipid, observed experimentally by Hristova and White (1988. Biophys. J. 74:2419-2433), marks the completion of the first hydration shell. PMID:11720971

Mashl, R J; Scott, H L; Subramaniam, S; Jakobsson, E

2001-12-01

177

Reconsolidation and extinction are dissociable and mutually exclusive processes: behavioral and molecular evidence.  

Science.gov (United States)

Memory persistence is critically influenced by retrieval. In rats, a single presentation of a conditioned fear stimulus induces memory reconsolidation and fear memory persistence, while repeated fear cue presentations result in loss of fear through extinction. These two opposite behavioral outcomes are operationally linked by the number of cue presentations at memory retrieval. However, the behavioral properties and mechanistic determinants of the transition have not yet been explored; in particular, whether reconsolidation and extinction processes coexist or are mutually exclusive, depending on the exposure to non-reinforced retrieval events. We characterized both behaviorally and molecularly the transition from reconsolidation to extinction of conditioned fear and showed that an increase in calcineurin (CaN) in the basolateral amygdala (BLA) supports the shift from fear maintenance to fear inhibition. Gradually increasing the extent of retrieval induces a gradual decrease in freezing responses to the conditioned stimulus and a gradual increase in amygdala CaN level. This newly synthesized CaN is required for the extinction, but not the reconsolidation, of conditioned fear. During the transition from reconsolidation to extinction, we have revealed an insensitive state of the fear memory where NMDA-type glutamate receptor agonist and antagonist drugs are unable either to modulate CaN levels in the BLA or alter the reconsolidation or extinction processes. Together, our data indicate both that reconsolidation and extinction are mutually exclusive processes and also reveal the presence of a transitional, or "limbo," state of the original memory between these two alternative outcomes of fear memory retrieval, when neither process is engaged. PMID:24523532

Merlo, Emiliano; Milton, Amy L; Goozée, Zara Y; Theobald, David E; Everitt, Barry J

2014-02-12

178

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

Directory of Open Access Journals (Sweden)

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.

Derbenev I.V.

2011-01-01

179

The Defense Waste Processing Facility: an innovative process for high-level waste immobilization  

International Nuclear Information System (INIS)

The Defense Waste Processing Facility (DWPF), under construction at the Department of Energy's Savannah River Plant (SRP), will process defense high-level radioactive waste so that it can be disposed of safely. The DWPF will immobilize the high activity fraction of the waste in borosilicate glass cast in stainless steel canisters which can be handled, stored, transported and disposed of in a geologic repository. The low-activity fraction of the waste, which represents about 90% of the high-level waste HLW volume, will be decontaminated and disposed of on the SRP site. After decontamination the canister will be welded shut by an upset resistance welding technique. In this process a slightly oversized plug is pressed into the canister opening. At the same time a large current is passed through the canister and plug. The higher resistance of the canister/plug interface causes the heat which welds the plug in place. This process provides a high quality, reliable weld by a process easily operated remotely

180

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

Directory of Open Access Journals (Sweden)

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

Peiqiang Yu

2007-01-01

 
 
 
 
181

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

Energy Technology Data Exchange (ETDEWEB)

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

Yu,P.

2007-01-01

182

An algebraic approach for simultaneous solution of process and molecular design problems  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english The property integration framework has allowed for simultaneous representation of processes and products from a properties perspective and thereby established a link between molecular and process design problems. The simultaneous approach involves solving two reverse problems. The first reverse prob [...] lem identifies the property targets corresponding to the desired process performance. The second reverse problem is the reverse of a property prediction problem, which identifies the molecular structures that match the targets identified in the first problem. Group Contribution Methods (GCM) are used to form molecular property operators that will be used to track properties. Earlier contributions in this area have worked to include higher order estimation of GCM for solving the molecular design problem. In this work, the accuracy of the property prediction is further enhanced by improving the techniques to enumerate higher order groups. Incorporation of these higher order enumeration techniques increases the efficiency of property prediction and thus the application range of the group contribution methods in molecular design problems. Successful tracking of properties is the key in applying the reverse problem formulation for integrated process and product design problems. An algebraic technique has been developed for solving process and molecular design problems simultaneously. Since both process and molecular property operators target the same optimum process performance, the set of inequality expressions can be solved simultaneously to identify the molecules that meet the desired process performance. Since this approach is based on an algebraic algorithm, any number of properties can be tracked simultaneously.

S., Bommareddy; N. G., Chemmangattuvalappil; C. C., Solvason; M. R., Eden.

183

Molecular-level methods for monitoring soil organic matter responses to global climate change.  

Science.gov (United States)

Soil organic matter (SOM) is one of the most complex natural mixtures on earth. It plays a critical role in many ecosystem functions and is directly responsible for sustaining life on our planet. However, due to its chemical heterogeneity, SOM composition at molecular-level is still not completely clear. Consequently, the response of SOM to global climate change is difficult to predict. Here we highlight applications of two complementary molecular-level methods (biomarkers and nuclear magnetic resonance (NMR)) for ascertaining SOM responses to various environmental changes. Biomarker methods that measure highly specific molecules determine the source and decomposition stage of SOM components. However, biomarkers only make up a small fraction of SOM components because much of SOM is non-extractable. By comparison, (13)C solid-state NMR allows measurement of SOM in its entirety with little or no pretreatment but suffers from poor resolution (due to overlapping of SOM components) and insensitivity, and thus subtle changes in SOM composition may not always be detected. Alternatively, (1)H solution-state NMR methods offer an added benefit of improved resolution and sensitivity but can only analyze SOM components that are fully soluble (humic type molecules) in an NMR compatible solvent. We discuss how these complementary methods have been employed to monitor SOM responses to: soil warming in a temperate forest, elevated atmospheric CO(2) and nitrogen fertilization in a temperate forest, and permafrost thawing in the Canadian High Arctic. These molecular-level methods allow some novel and important observations of soil dynamics and ecosystem function in a changing climate. PMID:21416081

Feng, Xiaojuan; Simpson, Myrna J

2011-05-01

184

Coarse-grained Molecular-level Analysis of Polyurea Properties and Shock-mitigation Potential  

Science.gov (United States)

Several experimental investigations reported in the open literature clearly established that polyurea (PU), an elastic copolymer, has an unusually high ability to attenuate and disperse shock waves. This behavior of PU is normally attributed to its unique nanometer-scale two-phase microstructure consisting of (high glass-transition temperature, T g) hydrogen-bonded discrete, hard domains dispersed within a (low T g) contiguous soft matrix. However, details regarding the mechanism(s) responsible for the superior shock-wave mitigation capacity of PU are still elusive. In the present study, molecular-level computational methods and tools are used to help us identify and characterize these mechanism(s). Because the shock-wave front structure and propagation involve coordinated motion of a large number of atoms and nano-second to micro-second characteristic times, these phenomena cannot be readily analyzed using all-atom molecular-level modeling and simulation techniques. To overcome this problem, all-atom PU microstructure is coarse-grained by introducing larger particles (beads), which account for the collective degrees of freedom of the constituent atoms, the associated force-field functions determined and parameterized using all-atom computational results, and the resulting coarse-grained model analyzed using conventional molecular-level computational methods and tools. The results thus obtained revealed that a combination of different deformation mechanisms (primarily shock-induced ordering and crystallization of hard domains and coordinated shuffle-like lateral motion of the soft-matrix segments) is most likely responsible for the superior ability of PU to attenuate/disperse shock waves.

Grujicic, M.; Snipes, J. S.; Ramaswami, S.; Yavari, R.; Runt, J.; Tarter, J.; Dillon, G.

2013-07-01

185

Efficient inverted polymer solar cells with thermal-evaporated and solution-processed small molecular electron extraction layer  

Science.gov (United States)

Efficient inverted polymer solar cell is reported upon by integrating with a small molecular 1,3,5-tri(phenyl-2-benzimi-dazolyl)-benzene (TPBi) electron extraction layer (EEL) at low processing temperature with thermal-evaporation and solution-process, resulting in the power conversion efficiencies of 3.70% and 3.47%, respectively. The potential of TPBi as an efficient EEL is associated with its suitable electronic energy level for electron extraction and hole blocking from the active layer to the indium tin oxide cathode.

Sun, Fu-Zhou; Shi, Ai-Li; Xu, Zai-Quan; Wei, Huai-Xin; Li, Yan-Qing; Lee, Shuit-Tong; Tang, Jian-Xin

2013-04-01

186

Molecular level studies on binding modes of labeling molecules with polyalanine peptides  

Science.gov (United States)

In this work, the binding modes of typical labeling molecules (thioflavin T (ThT), Congo red (CR) and copper(ii) phthalocyanine tetrasulfonic acid tetrasodium salt (PcCu(SO3Na)4)) on pentaalanine, which is a model peptide segment of amyloid peptides, have been resolved at the molecular level by using scanning tunneling microscopy (STM). In the STM images, ThT molecules are predominantly adsorbed parallel to the peptide strands and two binding modes could be identified. It was found that ThT molecules are preferentially binding on top of the peptide strand, and the mode of intercalated between neighboring peptides also exists. The parallel binding mode of CR molecules can be observed with pentaalanine peptides. Besides the binding modes of labeling molecules, the CR and PcCu(SO3Na)4 display different adsorption affinity with the pentaalanine peptides. The results could be beneficial for obtaining molecular level insight of the interactions between labeling molecules and peptides.In this work, the binding modes of typical labeling molecules (thioflavin T (ThT), Congo red (CR) and copper(ii) phthalocyanine tetrasulfonic acid tetrasodium salt (PcCu(SO3Na)4)) on pentaalanine, which is a model peptide segment of amyloid peptides, have been resolved at the molecular level by using scanning tunneling microscopy (STM). In the STM images, ThT molecules are predominantly adsorbed parallel to the peptide strands and two binding modes could be identified. It was found that ThT molecules are preferentially binding on top of the peptide strand, and the mode of intercalated between neighboring peptides also exists. The parallel binding mode of CR molecules can be observed with pentaalanine peptides. Besides the binding modes of labeling molecules, the CR and PcCu(SO3Na)4 display different adsorption affinity with the pentaalanine peptides. The results could be beneficial for obtaining molecular level insight of the interactions between labeling molecules and peptides. Electronic supplementary information (ESI) available. See DOI: 10.1039/c0nr00782j

Mao, Xiaobo; Wang, Chenxuan; Ma, Xiaojing; Zhang, Min; Liu, Lei; Zhang, Lan; Niu, Lin; Zeng, Qindao; Yang, Yanlian; Wang, Chen

2011-04-01

187

Hanford low-level waste process chemistry testing data package  

Energy Technology Data Exchange (ETDEWEB)

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 principle{close_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 & 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).

Smith, H.D.; Tracey, E.M.; Darab, J.G.; Smith, P.A.

1996-03-01

188

Hanford low-level waste process chemistry testing data package  

International Nuclear Information System (INIS)

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)

189

Coffee husk composting: An investigation of the process using molecular and non-molecular tools  

Science.gov (United States)

Various parameters were measured during a 90-day composting process of coffee husk with cow dung (Pile 1), with fruit/vegetable wastes (Pile 2) and coffee husk alone (Pile 3). Samples were collected on days 0, 32 and 90 for chemical and microbiological analyses. C/N ratios of Piles 1 and 2 decreased significantly over the 90 days. The highest bacterial counts at the start of the process and highest actinobacterial counts at the end of the process (Piles 1 and 2) indicated microbial succession with concomitant production of compost relevant enzymes. Denaturing gradient gel electrophoresis of rDNA and COMPOCHIP microarray analysis indicated distinctive community shifts during the composting process, with day 0 samples clustering separately from the 32 and 90-day samples. This study, using a multi-parameter approach, has revealed differences in quality and species diversity of the three composts. PMID:24369846

Shemekite, Fekadu; Gómez-Brandón, María; Franke-Whittle, Ingrid H.; Praehauser, Barbara; Insam, Heribert; Assefa, Fassil

2014-01-01

190

Wood–water interactions : Linking molecular level mechanisms with macroscopic performance  

DEFF Research Database (Denmark)

Predicting the performance of wood for decades ahead is important when using the material for structural purposes. The performance is closely related to the hierarchical material structure of wood and the dependent interaction with water in the structure. Accurately predicting wood performance therefore requires an understanding of material structure from molecular to macroscopic level as well as of the impact of water molecules. The objective of this work is to investigate the performance of wood in terms of mechanical response of the material and effect of water. To understand the latter, one must first know in which parts of the wood structure, water is located. If parts of the water in wood are held in capillaries in the wood structure, these water molecules interact with the material differently than those held within wood cell walls. In this study, the occurrence of capillary water in wood is investigated at high levels of relative humidity (RH), where capillary water might be present. Three different techniques are employed in overlapping RH regimes. The three techniques give similar results and show that the amount of capillary water is insignificant up to at least 99.5 % RH. Thus, for wood in equilibrium with surrounding climate in the RH range 0-99.5 %, water is only significantly present within cell walls. A structural model of a wood cell is developed in this study using Finite Element Method for predicting the mechanical performance of wood. The starting point for the model is the physical behaviour on the molecular level since water interferes with wood at this level. The elastic material properties of the wood cell wall are explained by the organisation of wood constituents and their properties. The effect of water as well as temperature is incorporated by considering the amount of hydrogen bonds between wood constituents and the stiffness of these bonds. The mechanical response of wood includes a substantial time-dependent response, which previously has been explained by sliding between wood constituents on the molecular level. In this study, this is incorporated in the model as time-dependent shearing of the material planes of the cell wall. The calculated results of the model is verified against various experimental results from literature as well as from measurements presented in this work. It is shown that the structural model is able to describe a diverse range of mechanical responses of wood cells in both elastic and time-dependent domains. Furthermore, comparison of results from experiments and model suggests that the mechanical response of wood tissue, i.e. the hierarchical level above single wood cells, is a sum of responses from both wood cells and intercellular layer, i.e. the middle lamella.

Engelund, Emil Tang

2011-01-01

191

Molecular orbital state due to halo neutrons in heavy ion nuclear reaction and its resonance level  

International Nuclear Information System (INIS)

For the systems involving weakly bound, exotic nuclei, the distinctive features of CRC effects are expected, and the formation of nucleonic molecular orbitals may become the dominant effect. The energy level spacing of weakly bound nucleon states may be much smaller, and furthermore, the tails of wave functions extend to far outside the core nuclei. In 11Be + 10Be system, the radioactive nuclei 11Be have two weakly bound valence neutron states (halo states). The neutron wave functions in the states of 11Be extend to far outside the nuclei for the weakly bound states and for the sharp resonance state, respectively. Moreover, the energy spacing of these states is very small. The core excitation energy of 10Be is much higher than the Coulomb barrier. The CRC calculation and the molecular orbital analysis for this system by employing the channels of 11Be states were carried out. The procedure is explained. The results are shown, and the sharp rise and big enhancement of the subbarrier fusion cross section of the CRC calculation were observed. Such CRC effects reflect the formation of a covalent molecular orbital. The behavior of the fine structure depends on the choice of parameters of the bare potential. (K.I.)

192

Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Members of the forkhead gene family act as transcription regulators in biological processes including development and metabolism. The evolution of forkhead genes has not been widely examined and selection pressures at the molecular level influencing subfamily evolution and differentiation have not been explored. Here, in silico methods were used to examine selection pressures acting on the coding sequence of five multi-species FOX protein subfamily clusters; FoxA, FoxD, FoxI, FoxO and FoxP. Results Application of site models, which estimate overall selection pressures on individual codons throughout the phylogeny, showed that the amino acid changes observed were either neutral or under negative selection. Branch-site models, which allow estimated selection pressures along specified lineages to vary as compared to the remaining phylogeny, identified positive selection along branches leading to the FoxA3 and Protostomia clades in the FoxA cluster and the branch leading to the FoxO3 clade in the FoxO cluster. Residues that may differentiate paralogs were identified in the FoxA and FoxO clusters and residues that differentiate orthologs were identified in the FoxA cluster. Neutral amino acid changes were identified in the forkhead domain of the FoxA, FoxD and FoxP clusters while positive selection was identified in the forkhead domain of the Protostomia lineage of the FoxA cluster. A series of residues under strong negative selection adjacent to the N- and C-termini of the forkhead domain were identified in all clusters analyzed suggesting a new method for refinement of domain boundaries. Extrapolation of domains among cluster members in conjunction with selection pressure information allowed prediction of residue function in the FoxA, FoxO and FoxP clusters and exclusion of known domain function in residues of the FoxA and FoxI clusters. Conclusion Consideration of selection pressures observed in conjunction with known functional information allowed prediction of residue function and refinement of domain boundaries. Identification of residues that differentiate orthologs and paralogs provided insight into the development and functional consequences of paralogs and forkhead subfamily composition differences among species. Overall we found that after gene duplication of forkhead family members, rapid differentiation and subsequent fixation of amino acid changes through negative selection has occurred.

Rannala Bruce

2008-09-01

193

Tank farm processing of high-level waste for the Defense Waste Processing Facility  

International Nuclear Information System (INIS)

The high-level radioactive waste that has accumulated at the Savannah River Plant is stored in large, underground steel tanks. Programs to remove the waste from the storage tanks and immobilize the radioactivity in borosilicate glass in the Defense Waste Processing Facility (DWPF) are currently in the construction phase. Much of the processing of the waste prior to vitrification is accomplished in the waste storage areas (tank farms). Tank farm processing includes resuspension and washing of the insoluble (sludge) waste, dissolution and decontamination of soluble (salt) waste, and waste transfer between the tanks and operations areas. The overall program for handling the waste in the tank farms, the research program that supports it, and the major concerns with implementing the program are described

194

Molecular-level understanding of protein adsorption at the interface between water and a strongly interacting uncharged solid surface.  

Science.gov (United States)

Although protein adsorption on solids is of immense relevance, experimental limitations mean there is still a remarkable lack of understanding of the adsorption mechanism, particularly at a molecular level. By subjecting 240+ molecular dynamics simulations of two peptide/water/solid surface systems to statistical analysis, a generalized molecular level mechanism for peptide adsorption has been identified for uncharged surfaces that interact strongly with the solution phase. This mechanism is composed of three phases: (1) biased diffusion of the peptide from the bulk phase toward the surface; (2) anchoring of the peptide to the water/solid interface via interaction of a hydrophilic group with the water adjacent to the surface or a strongly interacting hydrophobic group with the surface; and (3) lockdown of the peptide on the surface via a slow, stepwise and largely sequential adsorption of its residues, which we term 'statistical zippering'. The adsorption mechanism is dictated by the existence of water layers adjacent to the solid and orientational ordering therein. By extending the solid into the solution by ~8 Å and endowing it with a charged character, the water layers ensure the peptide feels the effect of the solid at a range well beyond the dispersion force that arises from it, thus inducing biased diffusion from afar. The charging of the interface also facilitates anchoring of the peptide near the surface via one of its hydrophilic groups, allowing it time it would otherwise not have to rearrange and lockdown. Finally, the slowness of the lockdown process is dictated by the need for the peptide groups to replace adjacent tightly bound interfacial water. PMID:24506166

Penna, Matthew J; Mijajlovic, Milan; Biggs, Mark J

2014-04-01

195

New tools for the study of chromosome segregation and aneuploidy at the molecular level  

Energy Technology Data Exchange (ETDEWEB)

The molecular mechanisms which allow the correct distribution of chromosomes during cell division are not yet well known. The centromere, because of its possible involvement in the attachment of sister chromatids and its participation in the formation of the kinetochore, may play an important role in these mechanisms. Trisomy 21 (down syndrome, DS) provides a good model for studying aneuploidy resulting from the dysfunction of the chromosome distribution process. A possible means of analyzing the mechanisms leading to non-disjunction (NDJ) could be to determine the origin of the supernumerary chromosome 21 and to attempt to find some structural or physical characteristics of the potentially responsible centromere. This could be performed by using molecular tools which allow each of the two parental chromosomes 21 to be distinguished. Possible markers suitable for this purpose are DNA fragments that exhibit length polymorphisms. We present here some examples of such molecular tools, and discuss ways to use them in order to study the parental origin and the meiotic stage of nondisjunction, and we propose an hypothesis suggesting a possible cause of nondisjunction in human chromosomes.

Charlieu, J.P.; Marcais, B.; Laurent, A.M.; Roizes, G. [Institut de Biologie, Montpellier (France)

1993-12-31

196

Dynamics of molecular processes by NMR in liquid crystalline solvents  

Energy Technology Data Exchange (ETDEWEB)

The effect of dynamic processes on the lineshapes of NMR spectra in liquid crystalline solutions is discussed. The discussion includes dynamic /sup 1/H spectra of s-trioxane, cyclooctatetraene and bullvalene undergoing, respectively, ring inversion, bond shift and bond rearrangement. Also discussed are dynamic deuteron spectra using the examples of cyclohexane-d/sub 12/ and p-dioxane-d/sub 8/ undergoing ring inversion. Finally the formalism required to simulate dynamic NMR spectra in liquid crystalline solution is reviewed and the possible factorization of the problem by symmetry considerations is discussed.

Luz, Z. (Weizmann Inst. of Science, Rehovoth (Israel). Dept. of Isotopes)

1983-01-01

197

Dynamics of molecular processes by NMR in liquid crystalline solvents  

International Nuclear Information System (INIS)

The effect of dynamic processes on the lineshapes of NMR spectra in liquid crystalline solutions is discussed. The discussion includes dynamic 1H spectra of s-trioxane, cyclooctatetraene and bullvalene undergoing, respectively, ring inversion, bond shift and bond rearrangement. Also discussed are dynamic deuteron spectra using the examples of cyclohexane-d12 and p-dioxane-d8 undergoing ring inversion. Finally the formalism required to simulate dynamic NMR spectra in liquid crystalline solution is reviewed and the possible factorization of the problem by symmetry considerations is discussed

198

Reconstructing the free-energy landscape associated to molecular motors processivity  

CERN Document Server

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.

Alamilla, J Lopez

2012-01-01

199

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

Science.gov (United States)

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.

Valentini, Paolo; Norman, Paul; Zhang, Chonglin; Schwartzentruber, Thomas E.

2014-05-01

200

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

Energy Technology Data Exchange (ETDEWEB)

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 N{sub 2}; (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 N{sub 2} bond determines the strength of the rovibrational coupling. Although neglecting N{sub 2} 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 N{sub 2} dissociation.

Valentini, Paolo, E-mail: vale0142@umn.edu; Norman, Paul, E-mail: norma198@umn.edu; Zhang, Chonglin, E-mail: zhang993@umn.edu; Schwartzentruber, Thomas E., E-mail: schwart@aem.umn.edu [Department of Aerospace Engineering and Mechanics, College of Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (United States)

2014-05-15

 
 
 
 
201

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

International Nuclear Information System (INIS)

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

202

Feasibility analysis of studying dissociative recombination processes of molecular ions at HIRFL-CSR  

International Nuclear Information System (INIS)

In the present paper, it is introduced the scientific background and the current status of the high precision spectroscopy of the molecular ions at cooler storage ring. The advantages to study the dissociative recombination (DR) processes using cooler storage ring CSRe are discussed. The physics design, the main parameters of the injection beam line and the injection of the molecular ions into the CSRe and the key techniques are described in detail. With a new injection beam line, HIRFL-CSRe will be reconstructed to a multi-discipline research platform, offering good opportunities for the study of DR processes of molecular ions, especially for that of the molecular ions of m > 70 amu with much improved resolution. (authors)

203

Computer Insight into the Molecular Level of Heart Failure. What is the Role of NCX?  

Directory of Open Access Journals (Sweden)

Full Text Available Though congestive heart failure is a leading cause of death in our population, the pathophysiological mechanisms at molecular level remain to be elucidated. This paper discusses the contribution of NCX to the pathological pattern of intracellular calcium regulation and contraction on the basis of computer simulations of a virtual cell. The model comprises calcium handling mechanisms, troponin control and acto-myosin interactions. The contribution of NCX was studied by changing its activity and turning it off for some simulations.It was found that NCX helps to support diastolic function by reducing the Ca2 level during the diastole. At the same time there is a reduction in peak Cai and hence contraction. However, increased NCX activity does not seem to improve calcium handling and contraction crucially, as has been suggested by some authors.

M. Fischer

2008-01-01

204

The McClelland approximation and the distribution of ?-electron molecular orbital energy levels  

Directory of Open Access Journals (Sweden)

Full Text Available The total ?-electron energy E of a conjugated hydrocarbon with n carbon atoms and m carbon–carbon bonds can be approximately calculated by means of the McClelland formula E = g SQRT(2mr, where g is an empirical ?tting constant, g ? 0.9. It was claimed that the good quality of the McClelland approximation is a consequence of the fact that the ?-electron molecular orbital energy levels are distributed in a nearly uniform manner. It will now be shown that the McClelland approximation does not depend on the nature of the distribution of energy levels, i.e., that it is compatible with a large variety of such distributions.

IVAN GUTMAN

2007-10-01

205

Correlation of plasma trough levels of imatinib with molecular response in patients with chronic myeloid leukemia.  

Science.gov (United States)

Abstract The present study looked at the correlation between mean trough Imatinib plasma levels and molecular response in 131 CML patients on imatinib. Patients receiving Glivec versus generic Imatinib were also compared. A ROC curve was constructed to estimate a threshold level that correlates with a favourable response. Patients were grouped into Responders (bcr/abl ration by RQ-PCR less than 1) and Non Responders (ration ? 1). The mean trough imatinib plasma level in the responders was significantly higher than in the non responders (p = 0.001). The area under ROC curve was 0.733, with best sensitivity (51.85%) and specificity (89.42%) at a plasma threshold of 0.988 g/ml [1.675 M]. Levels in the patients on Glivec versus generic drug (p > 0.05) were comparable. Trough Imatinib plasma levels may be a marker for suboptimal response and may identify patients in whom increase of drug dose or change in therapy may be indicated. PMID:24446903

Malhotra, Hemant; Sharma, Pratibha; Bhargava, Shipra; Rathore, Om Singh; Malhotra, Bharti; Kumar, Madhu

2014-11-01

206

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

International Nuclear Information System (INIS)

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

207

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

CERN Document Server

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...

Erdmann, Thorsten; Schwarz, Ulrich S

2013-01-01

208

Cross sections for hydrogen muonic atomic processes in two-level approximation of the adiabatic framework  

International Nuclear Information System (INIS)

The phase-shifts and cross sections have been calculated in a broad collision energy range (0.001 ? ? ? 50 eV) for the elastic scattering, isotopic exchange and spin-flip hydrogen muonic atomic processes. The so-called ''simple approach'' to the three-body problem with the Coulomb interaction in the adiabatic two-level approximation has been applied. The comparison of the obtained values with available results of the multichannel approximation shows that the accuracy of our calculations is about 10%. The presented set of the phases and cross sections together with corrections for the electron screening and molecular structure enables one to investigate kinetics of the muon-catalyzed fusion in any mixtures of hydrogen isotopes

209

Molecular Insights into Poly(ADP-ribose Recognition and Processing  

Directory of Open Access Journals (Sweden)

Full Text Available Poly(ADP-ribosylation is a post-translational protein modification involved in the regulation of important cellular functions including DNA repair, transcription, mitosis and apoptosis. The amount of poly(ADP-ribosylation (PAR in cells reflects the balance of synthesis, mediated by the PARP protein family, and degradation, which is catalyzed by a glycohydrolase, PARG. Many of the proteins mediating PAR metabolism possess specialised high affinity PAR-binding modules that allow the efficient sensing or processing of the PAR signal. The identification of four such PAR-binding modules and the characterization of a number of proteins utilising these elements during the last decade has provided important insights into how PAR regulates different cellular activities. The macrodomain represents a unique PAR-binding module which is, in some instances, known to possess enzymatic activity on ADP-ribose derivatives (in addition to PAR-binding. The most recently discovered example for this is the PARG protein, and several available PARG structures have provided an understanding into how the PARG macrodomain evolved into a major enzyme that maintains PAR homeostasis in living cells.

Ivan Ahel

2012-12-01

210

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

International Nuclear Information System (INIS)

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 mulof 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)

211

Dynamical image-charge effect in molecular tunnel junctions : Beyond energy level alignment  

DEFF Research Database (Denmark)

When an electron tunnels between two metal contacts it temporarily induces an image charge (IC) in the electrodes which acts back on the tunneling electron. It is usually assumed that the IC forms instantaneously such that a static model for the image potential applies. Here we investigate how the finite IC formation time affects charge transport through a molecule suspended between two electrodes. For a single-level model, an analytical treatment shows that the conductance is suppressed by a factor Z(2), where Z is the quasiparticle renormalization factor, compared to the static IC approximation. We show that Z can be expressed either in terms of the plasma frequency of the electrode or as the overlap between electrode wave functions corresponding to an empty and filled level, respectively. First-principles GW calculations for benzene-diamine connected to gold electrodes show that the dynamical corrections can reduce the conductance by more than a factor of two when compared to static GW or density functional theory where the molecular energy levels have been shifted to match the exact quasiparticle levels.

Jin, Chengjun; Thygesen, Kristian Sommer

2014-01-01

212

Dynamical image-charge effect in molecular tunnel junctions: Beyond energy level alignment  

Science.gov (United States)

When an electron tunnels between two metal contacts it temporarily induces an image charge (IC) in the electrodes which acts back on the tunneling electron. It is usually assumed that the IC forms instantaneously such that a static model for the image potential applies. Here we investigate how the finite IC formation time affects charge transport through a molecule suspended between two electrodes. For a single-level model, an analytical treatment shows that the conductance is suppressed by a factor Z2, where Z is the quasiparticle renormalization factor, compared to the static IC approximation. We show that Z can be expressed either in terms of the plasma frequency of the electrode or as the overlap between electrode wave functions corresponding to an empty and filled level, respectively. First-principles GW calculations for benzene-diamine connected to gold electrodes show that the dynamical corrections can reduce the conductance by more than a factor of two when compared to static GW or density functional theory where the molecular energy levels have been shifted to match the exact quasiparticle levels.

Jin, Chengjun; Thygesen, Kristian S.

2014-01-01

213

Evaluation of the degradation effect on the processability of high molecular weight polypropylene  

Energy Technology Data Exchange (ETDEWEB)

One way to improve the processability of high molecular weight and melt strength of Polypropylene (PP) is reducing its molecular weight by chain scission with increase of flow index. Nevertheless, the more significant occurrence of chain scission in its structure, further improved its processability is at expense of physical properties. It is well known that the high energy radiation creates free radicals in the polymer chains that subsequently stabilize forming structures. These structures composed by low molecular weight chains and by grafted, branched and crosslinked chains modify the physical and chemical properties of the polymer, depending of their distribution. The low molecular weight chains become from the degradation process by high energy irradiation, which decreases the melt strength and improves its processability. So, this work has the objective to evaluate the degradation of the high molecular weight PP using different irradiation doses. Two kinds of PP samples were utilized. The first one, without additive, presented a flow index of 1.9 g/10 min, and the second, additivated with 0.2 wt % of antioxidant phenolic, Irganox 1010, with a flow index of 0.9 g/10 min. These samples were irradiated with doses of 12.5 and 20.0 kGy. The results of flow index and melt strength obtained with these two kinds of samples showed the antioxidant and the radiation action. (author)

Shinzato, Rodrigo; Otaguro, Harumi; Lima, Luis F.C.P.; Parra, Duclerc F.; Lugao, Ademar B. [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil). Centro de Quimica e Meio Ambiente], E-mail: rodrigo.shinzato@gmail.com, E-mail: ablugao@ipen.br; Artel, Beatriz W.H. [Empresa Brasileira de Radiacao Ltda. (EMBRARAD), Cotia, SP (Brazil)

2007-07-01

214

Correlating molecular spectroscopy and molecular chemometrics to explore carbohydrate functional groups and utilization of coproducts from biofuel and biobrewing processing.  

Science.gov (United States)

Dried distillers grains with solubles (DDGS) was coproducts from bioethanol and biobrewing industry. It was an excellent resource of protein and energy feedstuff in China. Conventional studies often focus on traditional nutritional profiles. To data, there is little research on molecular structure-nutrition interaction of carbohydrate in coproducts. In this study, five kinds of corn-grain based DDGS and two kinds of barley-grain based DDGS were collected from different manufactures in the north of China. They were coded as "1, 2, 3, 4, 5, 6, and 7", respectively. The primary purposes of this project were to investigate the molecular structure-nutrition interaction of carbohydrate in coproducts, in terms of (1) carbohydrate-related chemical composition and nutrient profiles, (2) predicted values for energy in coproducts for animal, and (3) in situ digestion of dry matter. The result showed that acid detergent fiber content in corn DDGS and barley DDGS had negative correlation with structural carbohydrate peak area, cellulose compounds, and carbohydrate component peaks (first, second, and total peak area), which were measured with molecular spectroscopy. The correlation between carbohydrate peak area (second and total) and digestible fiber (tdNDF) were negative. There were no correlation between carbohydrate spectral intensities and energy values, carbohydrate subfractions partitioned by CNCPS system, and in situ rumen degradation. The results indicate that carbohydrate spectral profiles (functional groups) are associated with the carbohydrate nutritive values in coproducts from biofuel and biobrewing processing. PMID:24738876

Chen, Limei; Zhang, Xuewei; Yu, Peiqiang

2014-06-01

215

Process for solidifying high-level nuclear waste  

International Nuclear Information System (INIS)

The addition of a small amount of reducing agent to a mixture of a high-level radioactive waste calcine and glass frit before the mixture is melted will produce a more homogeneous glass which is leach-resistant and suitable for long-term storage of high-level radioactive waste products

216

Fast analysis of molecular dynamics trajectories with graphics processing units-Radial distribution function histogramming  

International Nuclear Information System (INIS)

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 the GPU's memory hierarchy and dynamic load balancing to allow high performance on heterogeneous configurations of GPUs. Several versions of the RDF algorithm are presented, utilizing the specific hardware features found on different generations of GPUs. We take advantage of larger shared memory and atomic memory operations available on state-of-the-art GPUs to accelerate the code significantly. The use of atomic memory operations allows the fast, limited-capacity on-chip memory to be used much more efficiently, resulting in a fivefold increase in performance compared to the version of the algorithm without atomic operations. The ultimate version of the algorithm running in parallel on four NVIDIA GeForce GTX 480 (Fermi) GPUs was found to be 92 times faster than a multithreaded implementation running on an Intel Xeon 5550 CPU. On this multi-GPU hardware, the RDF between two selections of 1,000,000 atoms each can be calculated in 26.9 s per frame. The multi-GPU RDF algorithms described here are implemented in VMD, a widely used and freely available software package for molecular dynamics visualization and analysis.

217

Multiple functions of aromatic-carbohydrate interactions in a processive cellulase examined with molecular simulation.  

Science.gov (United States)

Proteins employ aromatic residues for carbohydrate binding in a wide range of biological functions. Glycoside hydrolases, which are ubiquitous in nature, typically exhibit tunnels, clefts, or pockets lined with aromatic residues for processing carbohydrates. Mutation of these aromatic residues often results in significant activity differences on insoluble and soluble substrates. However, the thermodynamic basis and molecular level role of these aromatic residues remain unknown. Here, we calculate the relative ligand binding free energy by mutating tryptophans in the Trichoderma reesei family 6 cellulase (Cel6A) to alanine. Removal of aromatic residues near the catalytic site has little impact on the ligand binding free energy, suggesting that aromatic residues immediately upstream of the active site are not directly involved in binding, but play a role in the glucopyranose ring distortion necessary for catalysis. Removal of aromatic residues at the entrance and exit of the Cel6A tunnel, however, dramatically impacts the binding affinity, suggesting that these residues play a role in chain acquisition and product stabilization, respectively. The roles suggested from differences in binding affinity are confirmed by molecular dynamics and normal mode analysis. Surprisingly, our results illustrate that aromatic-carbohydrate interactions vary dramatically depending on the position in the enzyme tunnel. As aromatic-carbohydrate interactions are present in all carbohydrate-active enzymes, these results have implications for understanding protein structure-function relationships in carbohydrate metabolism and recognition, carbon turnover in nature, and protein engineering strategies for biomass utilization. Generally, these results suggest that nature employs aromatic-carbohydrate interactions with a wide range of binding affinities for diverse functions. PMID:21965672

Payne, Christina M; Bomble, Yannick J; Taylor, Courtney B; McCabe, Clare; Himmel, Michael E; Crowley, Michael F; Beckham, Gregg T

2011-11-25

218

High-level waste processing and conditioning: vitrification  

International Nuclear Information System (INIS)

The vitrification process used to treat fission product solutions at the Marcoule Vitrification Plant is described. The type of waste processed is characterized by its very high activity and the long lifetimes of some of the emitters that it contains. The performance obtained with this process is given together with the future developments envisaged. The storage of glasses is described as well as their behavior with time

219

Level dependence of spatial processing in the primate auditory cortex.  

Science.gov (United States)

Sound localization in both humans and monkeys is tolerant to changes in sound levels. The underlying neural mechanism, however, is not well understood. This study reports the level dependence of individual neurons' spatial receptive fields (SRFs) in the primary auditory cortex (A1) and the adjacent caudal field in awake marmoset monkeys. We found that most neurons' excitatory SRF components were spatially confined in response to broadband noise stimuli delivered from the upper frontal sound field. Approximately half the recorded neurons exhibited little change in spatial tuning width over a ~20-dB change in sound level, whereas the remaining neurons showed either expansion or contraction in their tuning widths. Increased sound levels did not alter the percent distribution of tuning width for neurons collected in either cortical field. The population-averaged responses remained tuned between 30- and 80-dB sound pressure levels for neuronal groups preferring contralateral, midline, and ipsilateral locations. We further investigated the spatial extent and level dependence of the suppressive component of SRFs using a pair of sequentially presented stimuli. Forward suppression was observed when the stimuli were delivered from "far" locations, distant to the excitatory center of an SRF. In contrast to spatially confined excitation, the strength of suppression typically increased with stimulus level at both the excitatory center and far regions of an SRF. These findings indicate that although the spatial tuning of individual neurons varied with stimulus levels, their ensemble responses were level tolerant. Widespread spatial suppression may play an important role in limiting the sizes of SRFs at high sound levels in the auditory cortex. PMID:22592309

Zhou, Yi; Wang, Xiaoqin

2012-08-01

220

Molecular analysis of low-level fluoroquinolone resistance in clinical isolates of Moraxella catarrhalis.  

Science.gov (United States)

We investigated antimicrobial susceptibility and the molecular mechanism underlying low-level resistance to fluoroquinolones in 70 non-duplicate clinical isolates of Moraxella catarrhalis. The isolates were collected in a general hospital in Tokyo, Japan, between January and October 2013 from 38 men and 32 women; most of the isolates (48 out of 70, 68.5%) were obtained from post-nasal drips of children. The antimicrobial susceptibility of M. catarrhalis isolates was determined with an Etest, and low-level fluoroquinolone-resistant isolates were subtyped by PFGE. Mutations in the gyrA and parC genes were determined by PCR and sequencing. PCR products of the gyrA and parC genes from the low-level fluoroquinolone-resistant isolates were transformed into a fluoroquinolone-susceptible strain. Among the 70 isolates, five (7.1%) exhibited elevated fluoroquinolone MICs (levofloxacin, 1.0 mg l(-1); ciprofloxacin, 0.5 mg l(-1)) and different PFGE patterns. The patients from whom these five isolates were isolated had not undergone treatment with fluoroquinolones for the past 6 months. Each of the five low-level fluoroquinolone-resistant isolates had a gyrA gene mutation resulting in a Thr-to-Ile substitution at aa 80 (T80I) in the GyrA protein, while no changes were detected in the parC gene. A transformant carrying the gyrA gene containing the T80I substitution, which corresponded to Ser83 in Escherichia coli, displayed an elevated fluoroquinolone MIC and contained the T80I alteration in GyrA. Thus, our findings reveal that the low-level resistance to fluoroquinolones in M. catarrhalis is due to an amino acid substitution of Thr80 to Ile in GyrA. This is the first evidence of low-level fluoroquinolone resistance in M. catarrhalis. PMID:24850882

Yamada, Kageto; Saito, Ryoichi

2014-08-01

 
 
 
 
221

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

Energy Technology Data Exchange (ETDEWEB)

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.

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

1982-10-01

222

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

International Nuclear Information System (INIS)

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

223

Organization of Lipids in the Tear Film: A Molecular-Level View  

Science.gov (United States)

Biophysical properties of the tear film lipid layer are studied at the molecular level employing coarse grain molecular dynamics (MD) simulations with a realistic model of the human tear film. In this model, polar lipids are chosen to reflect the current knowledge on the lipidome of the tear film whereas typical Meibomian-origin lipids are included in the thick non-polar lipids subphase. Simulation conditions mimic those experienced by the real human tear film during blinks. Namely, thermodynamic equilibrium simulations at different lateral compressions are performed to model varying surface pressure, and the dynamics of the system during a blink is studied by non-equilibrium MD simulations. Polar lipids separate their non-polar counterparts from water by forming a monomolecular layer whereas the non-polar molecules establish a thick outermost lipid layer. Under lateral compression, the polar layer undulates and a sorting of polar lipids occurs. Moreover, formation of three-dimensional aggregates of polar lipids in both non-polar and water subphases is observed. We suggest that these three-dimensional structures are abundant under dynamic conditions caused by the action of eye lids and that they act as reservoirs of polar lipids, thus increasing stability of the tear film. PMID:24651175

Wizert, Alicja; Iskander, D. Robert; Cwiklik, Lukasz

2014-01-01

224

Control of molecular organization and energy level alignment by an electronically nanopatterned boron nitride template.  

Science.gov (United States)

Suitable templates to steer the formation of nanostructure arrays on surfaces are indispensable in nanoscience. Recently, atomically thin sp(2)-bonded layers such as graphene or boron nitride (BN) grown on metal supports have attracted considerable interest due to their potential geometric corrugation guiding the positioning of atoms, metallic clusters or molecules. Here, we demonstrate three specific functions of a geometrically smooth, but electronically corrugated, sp(2)/metal interface, namely, BN/Cu(111), qualifying it as a unique nanoscale template. As functional adsorbates we employed free-base porphine (2H-P), a prototype tetrapyrrole compound, and tetracyanoquinodimethane (TCNQ), a well-known electron acceptor. (i) The electronic moirons of the BN/Cu(111) interface trap both 2H-P and TCNQ, steering self-organized growth of arrays with extended molecular assemblies. (ii) We report an effective decoupling of the trapped molecules from the underlying metal support by the BN, which allows for a direct visualization of frontier orbitals by scanning tunneling microscopy (STM). (iii) The lateral molecular positioning in the superstructured surface determines the energetic level alignment; i.e., the energy of the frontier orbitals, and the electronic gap are tunable. PMID:24328081

Joshi, Sushobhan; Bischoff, Felix; Koitz, Ralph; Ecija, David; Seufert, Knud; Seitsonen, Ari Paavo; Hutter, Jürg; Diller, Katharina; Urgel, José I; Sachdev, Hermann; Barth, Johannes V; Auwärter, Willi

2014-01-28

225

Low-level radioactive waste regulatory constraints affecting radwaste processing  

International Nuclear Information System (INIS)

Utilities frequently find that regulatory constraints strongly affect their choice of technology for processing LLRW from nuclear power plants. It is the purpose of the present study to identify such constraints and assess their impact on utilities' LLRW processing choices. The term regulatory constraint is used in this report to encompass regulations, rules, and procedures that effectively control any or all phases of LLRW managerial activity. These constraints may be issued by agencies of federal, state, or local governments, and, in some cases, non-governmental organizations. The phases of LLRW to which these constraints may be addressed are disposal, processing (including effluent control), storage and transportation

226

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

International Nuclear Information System (INIS)

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.

227

Acid-Base Interactions at the Molecular Level: Adhesion and Friction Studies with Interfacial Force Microscopy  

Energy Technology Data Exchange (ETDEWEB)

To examine the forces of acid-base adhesive interactions at the molecular level, we utilize the scanning probe Interracial Force Microscope (IFM). Unlike cantilever-based atomic force microscopes, the EM is a non-compliant, mechanically stable probe that provides a complete adhesive profile without jump-to-contact. In this way, we are able to quantitatively measure the work of adhesion and bond energies at well-defined, nanometer-scale single asperity contacts. In particular, we will discuss the displacement-controlled adhesive forces between self-assembled monolayer of functionalized alkanethiols strongly bound to a gold substrate and a similarly functionalized tip. We also discuss a method utilizing decoupled lateral and normal force sensors to simultaneously observe the onset of both friction and chemical bond formation. Measurements show that friction can be directly attributed to bond formation and rupture well before repulsive contact.

Burns, A.R.; Carpick, R.W.; Houston, J.E.; Michalske, T.A.

1998-12-09

228

Molecular characterization of high-level gentamicin-resistant Enterococcus faecalis from chicken meat in Korea.  

Science.gov (United States)

Because the intrinsically antimicrobial-resistant Enterococcus has acquired high-level aminoglycoside resistance genes, treating enterococcal infections is difficult. In this study, of the 101 food-borne Enterococcus faecalis isolates collected from retail chicken meat between 2003 and 2010, 11 high-level gentamicin-resistant (HLGR) E. faecalis isolates (MICs>2,048 ?g/mL) were found. Molecular characterization was performed to determine the basis of this resistance. All HLGR E. faecalis isolates encoded aac(6')-Ie-aph(2?)-Ia and harbored at least 3 virulence traits in the asa1, esp, gelE, efaA, ace, and cylA genes. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were performed to characterize their molecular epidemiology. A total of 8 sequence types (STs), including 3 novel STs, were identified (ST35, ST82, ST116, ST202, ST300, ST403, ST407, and ST420). ST82, which is associated with amyloid arthropathy in poultry, was the most prevalent ST among HLGR E. faecalis isolates (4 out of 11 isolates, 36.4%); all other STs were identified in the isolates as well. The STs of food-borne HLGR E. faecalis in this study have been confirmed as corresponding to clinical isolates in the MLST database (DB), except for ST300 and the new STs. Three out of 11 isolates belonged to CC116, including ST116, ST407, and ST420. This study characterized HLGR E. faecalis isolates and provided evidence for the spread of HLGR E. faecalis with virulence factors to chicken sources in Korea. The emergence of food-borne HLGR E. faecalis suggests that chicken could be a potential source of transmission of antimicrobial resistance and virulence factors. PMID:23685465

Choi, Jong-Mi; Woo, Gun-Jo

2013-07-01

229

Low-level radioactive waste processing at nuclear power plants  

International Nuclear Information System (INIS)

The Solid Radwaste Processing Source Book is presented as a supplement to the Liquid Radwaste Source Book released in 1990 and updated in 1991. The publication is the result of an industry-wide survey, and is intended as a resource for technical and managerial decisions involving of the processing of solid radioactive waste including ''wet'' and ''dry'' active waste as found at both Pressurized and Boiling Water Reactor sites. In addition to information on processes, vendors, volumes, and in-plant management activities, technology under consideration for future use and computer applications are listed. Together with key personnel and contact information contained in the Liquid Source Books, the collected data will be of great use when seeking specific, unbiased experience on which to base decisions related to so processing, disposal policy, or potential economic and regulatory impact

230

DIGITAL SIGNAL PROCESSING IN LIQUID LEVELS MEASURING SYSTEM  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The result of our diploma thesis presents a possible method for digital processing an analog signal in liquid measurement process with an ultrasonic measurement system. This measuring system is constituted of an ultrasonic sensor in conjunction with a digital signal processor (DSP - Digital signal processor) and specially designed software. DSP is placed on the measuring circuit to perform controlling of a digital synthesizer. This DSP, which is based on digital synthesis, generates analog si...

Vogrinec, Jernej

2013-01-01

231

The fabrication of rare earth covalent luminescent hybrid materials with potential molecular bridge by in situ sol-gel process  

International Nuclear Information System (INIS)

1,2,4-Benzenetricar boxylic acid (abbreviated as TMA) was modified to achieve a functional molecular bridge (TMA-APMES) with double reactivity by the reaction with a cross-linking molecule (3-aminopropyl-methyl-diethoxylsiliane, APMES). The modified functional ligand further behaves as a bridge both coordinates to Ln3+ through oxygen atom and occurs in situ sol-gel process with matrix precursor (tetraethoxysilane, TEOS) through co-hydrolysis and co-polycondensation reaction. Then a novel molecular hybrid material (named as hybrid Ln3+) with double chemical bond (Tb-O coordination bond and Si-O covalent bond) resulted. Ultraviolet absorption, phosphorescence, and fluorescence spectra were applied to characterize the photophysical properties of the obtained hybrid material. The strong luminescence of Tb3+ substantiates optimum energy couple and effective intramolecular energy transfer between the triplet state energy of modified ligand bridge and emissive energy level of Tb3+

232

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

Directory of Open Access Journals (Sweden)

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.

Mamidala Praveen

2012-01-01

233

Molecular engineering of secretory machinery components for high-level secretion of proteins in Bacillus species.  

Science.gov (United States)

Secretory expression of valuable enzymes by Bacillus subtilis and its related species has attracted intensive work over the past three decades. Although many proteins have been expressed and secreted, the titers of some recombinant enzymes are still low to meet the needs of practical applications. Signal peptides that located at the N-terminal of nascent peptide chains play crucial roles in the secretion process. In this mini-review, we summarize recent progress in secretory expression of recombinant proteins in Bacillus species. In particular, we highlighted and discussed the advances in molecular engineering of secretory machinery components, construction of signal sequence libraries and identification of functional signal peptides with high-throughput screening strategy. The prospects of future research are also proposed. PMID:25212246

Kang, Zhen; Yang, Sen; Du, Guocheng; Chen, Jian

2014-11-01

234

Accretion-Driven Turbulence as Universal Process: Galaxies, Molecular Clouds, and Protostellar Disks  

CERN Document Server

When cosmic structures form, they grow in mass via accretion from their surrounding environment. The energy associated with this transport of material provides a ubiquitous source of internal turbulence. We propose that accretion will drive turbulent motions in a wide range of astrophysical objects and study this process in the case of galaxies, molecular clouds and protoplanetary disks. We use a combination of numerical simulations and analytical arguments to predict the level of turbulence as a function of the accretion rate, the dissipation scale, and the density contrast, and compare with observational data. We find that in Milky Way type galaxies the turbulence in the non star-forming outer parts of the disk can be explained by accretion, provided that the galaxies accrete at a rate comparable to the rate at which they form stars. We note that the extended outer disk carries the bulk of the turbulent energy in the galaxy. Our approach fails for dwarf galaxies and we expect other sources to dominate. We c...

Klessen, Ralf S

2009-01-01

235

Treatment of High-Level Waste Arising from Pyrochemical Processes  

International Nuclear Information System (INIS)

JSC “SSC RIAR” has been performing research and development activities in support of closed fuel cycle of fast reactor since the middle of 1960s. Fuel cycle involves fabrication and reprocessing of spent nuclear fuel (SNF) using pyrochemical methods of reprocessing in molten alkali metal chlorides. At present pyrochemical methods of SNF reprocessing in molten chlorides has reached such a level in their development that makes it possible to compare their competitiveness with classic aqueous methods. Their comparative advantage lies in high safety, compactness, high protectability as to nonproliferation of nuclear materials, and reduction of high level waste volume

236

Towards understanding the molecular mechanism of the endocytosis-like process in the bacterium Gemmata obscuriglobus.  

Science.gov (United States)

An endocytosis-like process of protein uptake in the planctomycete Gemmata obscuriglobus is a recently discovered process unprecedented in the bacterial world. The molecular mechanisms underlying this process are not yet characterized. A homolog of the MC (membrane-coating) proteins of eukaryotes has been proposed to be involved in the mechanism of this process, but its relationship to eukaryote proteins is controversial. However, a number of other proteins of G. obscuriglobus with domains homologous to those involved in endocytosis in eukaryotes can also be identified. Here we critically evaluate current bioinformatic knowledge, and suggest practical experimental steps to overcome the limits of bioinformatics in elucidating the molecular mechanism of endocytosis in bacteria. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey. PMID:24144586

Fuerst, John A; Sagulenko, Evgeny

2014-08-01

237

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

Energy Technology Data Exchange (ETDEWEB)

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).

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

2014-02-21

238

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

International Nuclear Information System (INIS)

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)

239

Application of nonlinear optical techniques for the investigation of molecular properties and collisional processes  

International Nuclear Information System (INIS)

Molecular collisional processes were studied by using two different nonlinear optical techniques utilizing CO2 lasers. The first study used the techniques of saturation spectroscopy to study the momentum transfer in one direction which occurs when CO2 collides with itself, H2, Ne, NH3, and CH3F. Average CO2 velocity changes determined from these experiments were typically 1/10 the thermal velocity or less. A theoretical model was also developed to explain the experimental observations of CO2 with foreign gas perturbers. Generally good agreement between this model and the data was obtained. The second technique utilized the high-resolution capabilities of Doppler-free two-photon absorption (DFTPA) for the study of molecular properties and collisional processes in the two molecules CH3F and NH3. The first observation of DFTPA in molecular systems using two fixed-frequency CO2 optical fields in combination with molecular Stark tuning is reported. The pressure broadening coefficient and the pressure shift of the O ? ?3 transition were measured; broadening coefficients for the foreign gas perturbers of He and CF3I were determined. A self-broadening coefficient of the O ? 2?2 transition was also measured; foreign gas broadening coefficients for the collision partners H2, D2, He, Ne, and Xe were determined. Spectroscopic information was also obtained about these two molecular systems. (62 figures, 33 tables, 182 references) (U.S.)

240

Incisive probing of intermolecular interactions in molecular crystals: core level spectroscopy combined with density functional theory.  

Science.gov (United States)

The ?-form of crystalline para-aminobenzoic acid (PABA) has been examined as a model system for demonstrating how the core level spectroscopies X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine-structure (NEXAFS) can be combined with CASTEP density functional theory (DFT) to provide reliable modeling of intermolecular bonding in organic molecular crystals. Through its dependence on unoccupied valence states NEXAFS is an extremely sensitive probe of variations in intermolecular bonding. Prediction of NEXAFS spectra by CASTEP, in combination with core level shifts predicted by WIEN2K, reproduced experimentally observed data very well when all significant intermolecular interactions were correctly taken into account. CASTEP-predicted NEXAFS spectra for the crystalline state were compared with those for an isolated PABA monomer to examine the impact of intermolecular interactions and local environment in the solid state. The effects of the loss of hydrogen-bonding in carboxylic acid dimers and intermolecular hydrogen bonding between amino and carboxylic acid moieties are evident, with energy shifts and intensity variations of NEXAFS features arising from the associated differences in electronic structure and bonding. PMID:25248405

Stevens, Joanna S; Seabourne, Che R; Jaye, Cherno; Fischer, Daniel A; Scott, Andrew J; Schroeder, Sven L M

2014-10-23

 
 
 
 
241

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

Energy Technology Data Exchange (ETDEWEB)

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.

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

242

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

International Nuclear Information System (INIS)

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

243

Low-level radioactive waste processing at nuclear power plants  

International Nuclear Information System (INIS)

The 1991 Liquid Processing Source Book for PWR's provides updated information as a result of an industry-wide survey, and is a revision of the SOURCE BOOK released in February, 1990. The information supplied by radioactive waste managers, operations supervisors, and health physics personnel provides an up-to-date comparison of technical and managerial practices at plants across the United States, and will prove to be a valuable resource when making processing, vendor, and personnel changes or briefing plant managers concerning similar decisions at other utilities. The systems information, description of water management practices, organizational structure, and contact data have been supplied by cognizant plant personnel and are accurate as of the publication date. Volume 2 presents a liquid radwaste sourcebook for pressurized water reactors

244

Level 1 remedial investigation work plan, 300 Area Process Ponds  

Energy Technology Data Exchange (ETDEWEB)

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.

1987-06-01

245

University level genetics students’ competencies in selected science process skills  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Science process skills are essential for all practicing scientists. These skills include various practices that are needed to glean new knowledge as well as to represent existing knowledge. For example, an ability to use mathematics to represent relationships between variables is important in any scientific discipline. Furthermore, understanding scientific method is imperative in any research field. In addition, being literate with tabulated and graphical data is not only important for the sc...

Aldous, Colleen Michelle

2005-01-01

246

Processing highly tritiated water desorbed from molecular sieve bed using PERMCAT  

Energy Technology Data Exchange (ETDEWEB)

Highlights: Black-Right-Pointing-Pointer HTW processed with PERMCAT. Black-Right-Pointing-Pointer Processing of highly tritiated water (HTW). Black-Right-Pointing-Pointer 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 Multiplication-Sign 10{sup 14} Bq kg{sup -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.

Parracho, A.I. [EURATOM/CCFE Fusion Association, Culham Science Centre, Abingdon, Oxon OX14 3DB (United Kingdom); Demange, D., E-mail: david.demange@kit.edu [Karlsruhe Institute of Technology (KIT), Institute for Technical Physics, Tritium Laboratory Karlsruhe, Herrmann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen (Germany); Knipe, S. [EURATOM/CCFE Fusion Association, Culham Science Centre, Abingdon, Oxon OX14 3DB (United Kingdom); Le, L.T.; Simon, K.H.; Welte, S. [Karlsruhe Institute of Technology (KIT), Institute for Technical Physics, Tritium Laboratory Karlsruhe, Herrmann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen (Germany)

2012-08-15

247

Processing highly tritiated water desorbed from molecular sieve bed using PERMCAT  

International Nuclear Information System (INIS)

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.

248

High Level Waste (HLW) Processing Experience with Increased Waste Loading  

International Nuclear Information System (INIS)

The Defense Waste Processing Facility (DWPF) Engineering requested characterization of glass samples that were taken after the second melter had been operational for about 5 months. After the new melter had been installed, the waste loading had been increased to about 38 weight percentage after a new quasicrystalline liquidus model had been implemented. The DWPF had also switched from processing with refractory Frit 200 to a more fluid Frit 320. The samples were taken after DWPF observed very rapid buildup of deposits in the upper pour spout bore and on the pour spout insert while processing the high waste loading feedstock. These samples were evaluated using various analytical techniques to determine the cause of the crystallization. The pour stream sample was homogeneous, amorphous, and representative of the feed batch from which it was derived. Chemical analysis of the pour stream sample indicated that a waste loading of 38.5 weight per cent had been achieved. The data analysis indicated that surface crystallization, induced by temperature and oxygen fugacity gradients in the pour spout, caused surface crystallization to occur in the spout and on the insert at the higher waste loadings even though there was no crystallization in the pour stream

249

Vibrational origin of the fast relaxation processes in molecular glass-formers  

CERN Document Server

We study the interaction of the relaxation processes with the density fluctuations by molecular dynamics simulation of a flexible molecule model for o-terphenyl (oTP) in the liquid and supercooled phases. We find evidence, besides the structural relaxation, of a secondary vibrational relaxation whose characteristic time, few ps, is slightly temperature dependent. This i) confirms the result by Monaco et al. [Phys. Rev, E 62, 7595 (2000)] of the vibrational nature of the fast relaxation observed in Brillouin Light Scattering (BLS) experiments in oTP; and ii) poses a caveat on the interpretation of the BLS spectra of molecular systems in terms of a purely center of mass dynamics.

Mossa, S; Ruocco, G

2002-01-01

250

Molecular motors that digest their track to rectify Brownian motion: processive movement of exonuclease enzymes  

International Nuclear Information System (INIS)

A general model is presented for the processive movement of molecular motors such as ?-exonuclease, RecJ and exonuclease I that use digestion of a DNA track to rectify Brownian motion along this track. Using this model, the translocation dynamics of these molecular motors is studied. The sequence-dependent pausing of ?-exonuclease, which results from a site-specific high affinity DNA interaction, is also studied. The theoretical results are consistent with available experimental data. Moreover, the model is used to predict the lifetime distribution and force dependence of these paused states.

251

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

International Nuclear Information System (INIS)

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)

252

Corrosion and failure processes in high-level waste tanks  

International Nuclear Information System (INIS)

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

253

Investigating carbon dynamics in Siberian peat bogs using molecular-level analyses  

Science.gov (United States)

Total hydrolysable carbohydrates, and lignin and cutin acid compounds were analyzed in peat cores collected 56.8 N (SIB04), 58.4 N (SIB06), 63.8 N (G137) and 66.5 N (E113) in the Western Siberian Lowland to investigate vegetation, chemical compositions and the stage of decomposition. Sphagnum mosses dominated peatland vegetation in all four cores. High-resolution molecular analyses revealed rapid vegetation changes on timescales of 50-200 years in the southern cores Sib4 and Sib6. Syringyl and vanillyl (S/V) ratios and cutin acids indicated these vegetation changes were due to varying inputs of angiosperm and gymnosperm and root material. In the G137 and E113 cores lichens briefly replaced sphagnum mosses and vascular plants. Molecular decomposition indicators used in this study tracked the decomposition of different organic constituents of peat organic matter. The carbohydrate decomposition index was sensitive to the polysaccharide component of all peat-forming plants, whereas acid/aldehyde ratios of S and V phenols (Ac/AlS,V) followed the lignin component of vascular plants. Low carbohydrate decomposition indices in peat layers corresponded well with elevated (Ad/Al)S,V ratios. This suggested both classes of biochemicals were simultaneously decomposed, and decomposition processes were associated with extensive total mass loss in these ombrotrophic systems. Selective decomposition or transformation of lignin was observed in the permafrost-influenced northern cores G137 and E113. Both cores exhibited the highest (Ad/Al)S,V ratios, almost four-fold higher than measured in peat-forming plants. The extent of decomposition in the four peat cores did not uniformly increase with age, but showed episodic extensive decomposition events. Variable decomposition events independent of climatic conditions and vegetation shifts highlight the complexity of peatland dynamics.

Kaiser, K.; Benner, R. H.

2013-12-01

254

Predicting the residual aluminum level in water treatment process  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In water treatment processes, aluminum salts are widely used as coagulation chemical. High dose of aluminum has been proved to be at least a minor health risk and some evidence points out that aluminum could increase the risk of Alzheimer's disease. Thus it is important to minimize the amount of residual aluminum in drinking water and water used at food industry. In this study, the data of a water treatment plant (WTP) was analyzed and the residual aluminum in drinking water was predicted usi...

Tomperi, J.; Pelo, M.; Leiviska?, K.

2013-01-01

255

Predicting the residual aluminum level in water treatment process  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In water treatment processes, aluminum salts are widely used as coagulation chemical. High dose of aluminum has been proved to be at least a minor health risk and some evidence points out that aluminum could increase the risk of Alzheimer's disease thus it is important to minimize the amount of residual aluminum in drinking water and water used at food industry. In this study, the data of a water treatment plant (WTP) was analyzed and the residual aluminum in drinking water was predicted usin...

Tomperi, J.; Pelo, M.; Leiviska?, K.

2012-01-01

256

Molecular Characterization of Soybean Mosaic Virus NIa Protein and its Processing Event in Bacterial Expression  

Directory of Open Access Journals (Sweden)

Full Text Available Soybean mosaic virus (SMV-CN18 is an Rsv resistance-breaking (RB isolate to overcome soybean resistance genes Rsv1, Rsv3 and Rsv4. The aim of this study was to characterize nuclear inclusion protein a (NIa protein of RB isolate at the molecular level and demonstrate its processing into genome-linked protein (VPg and NIa-Pro domains in Esherichia coli containing a bacterial expression pET vector inserted with NIa gene. The full-length of NIa gene was synthesized by reverse transcription-polymerase chain reaction (RT-PCR and its 1298 nucleotides (nt and 432 amino acids (aa were deduced. The nt and aa sequences of NIa gene of SMV-CN18 shared high identities with the corresponding sequences of the NIa gene of the known SMV isolates, suggesting that the NIa is a highly conserved protein. The NIa-Pro domain contains a highly conserved structural motif for proteolysis, while the VPg domain contains a nuclear localization signal (NLS, a putative NTP-binding site and cellular factor-binding sites. The phylogenetic tree revealed that less divergence of NIa protein exists among twelve SMV isolates, which can be supported by a low bootstrap value between clades. In addition, the full-length of NIa gene, amplified by RT-PCR, was ligated into pET-28b E. coli expression vector with an N-terminal His6-tag. Optimal conditions for expression were at 1mM treatment of IPTG at 25°C for 5 hr. The released protein from bacterial lysates remained soluble and proved the processing form of the NIa polyprotein. E. coli expression system shows the processed product of 29 kDa VPg in SDS-PAGE confirmed by western blot analysis in both crude extracts and purified elution products, using Ni2+-NTA resin. The present study indicates that the N-terminal region of NIa which is processed and expressed in bacteria.

Bong K. Choi

2006-01-01

257

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

Energy Technology Data Exchange (ETDEWEB)

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.

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

2009-01-01

258

La modificación covalente de proteínas. Un nivel cualitativamente superior de la información molecular / Covalent Modifications of Proteins. A qualitative higher level of molecular information  

Scientific Electronic Library Online (English)

Full Text Available SciELO Cuba | Language: Spanish Abstract in spanish Introducción: La información molecular es una propiedad principal de las biomacromoléculas, especialmente proteínas y ácidos nucleicos, que permite la realización de funciones con un alto grado de especificidad. Ella deriva de la variedad en los componentes de las macromoléculas. Objetivo: Demostrar [...] que la modificación covalente de proteínas constituye un nivel nuevo y superior de información molecular. Método: Se analizaron artículos de los últimos 5 años, publicados en revistas nacionales y de circulación internacional, disponibles en las bases de datos HINARI, PubMed y Perii y localizados mediante el sitio www.infomed.sld.cu. Desarrollo: Se exponen los mecanismos y características principales del proceso y posteriormente algunos de los efectos principales de la modificación covalente sobre las funciones y propiedades de las proteínas. Conclusiones: La modificación covalente es un mecanismo que amplía el campo de acción de las proteínas permitiendo un rápido cambio en sus propiedades funcionales y, por lo tanto, constituye un nivel nuevo y cualitativamente superior de información molecular. Abstract in english Introduction: Molecular information is an essential property of biomacromolecules, especially proteins and nucleic acids. This property allows carrying out specific functions. It derives from variability of macromolecules components. Objetive: To prove that covalent modification of proteins represen [...] ts a new and higher level of molecular information. Method: Papers published during the last five years in national and international journals were analyzed. These articles are available in HINARI, PubMed, and Perii databases and were localized through www.infomed.sld.cu. Main text: First, the mechanism and features of covalent modifications of protein are presented. Next, the principal effects on protein functions and properties are analyzed. Conclusions: We conclude that covalent modification of proteins represents a new and higher level of molecular information.

Rolando A, Hernández Fernández.

259

La modificación covalente de proteínas. Un nivel cualitativamente superior de la información molecular / Covalent Modifications of Proteins. A qualitative higher level of molecular information  

Scientific Electronic Library Online (English)

Full Text Available SciELO Cuba | Language: Spanish Abstract in spanish Introducción: La información molecular es una propiedad principal de las biomacromoléculas, especialmente proteínas y ácidos nucleicos, que permite la realización de funciones con un alto grado de especificidad. Ella deriva de la variedad en los componentes de las macromoléculas. Objetivo: Demostrar [...] que la modificación covalente de proteínas constituye un nivel nuevo y superior de información molecular. Método: Se analizaron artículos de los últimos 5 años, publicados en revistas nacionales y de circulación internacional, disponibles en las bases de datos HINARI, PubMed y Perii y localizados mediante el sitio www.infomed.sld.cu. Desarrollo: Se exponen los mecanismos y características principales del proceso y posteriormente algunos de los efectos principales de la modificación covalente sobre las funciones y propiedades de las proteínas. Conclusiones: La modificación covalente es un mecanismo que amplía el campo de acción de las proteínas permitiendo un rápido cambio en sus propiedades funcionales y, por lo tanto, constituye un nivel nuevo y cualitativamente superior de información molecular. Abstract in english Introduction: Molecular information is an essential property of biomacromolecules, especially proteins and nucleic acids. This property allows carrying out specific functions. It derives from variability of macromolecules components. Objetive: To prove that covalent modification of proteins represen [...] ts a new and higher level of molecular information. Method: Papers published during the last five years in national and international journals were analyzed. These articles are available in HINARI, PubMed, and Perii databases and were localized through www.infomed.sld.cu. Main text: First, the mechanism and features of covalent modifications of protein are presented. Next, the principal effects on protein functions and properties are analyzed. Conclusions: We conclude that covalent modification of proteins represents a new and higher level of molecular information.

Rolando A, Hernández Fernández.

2014-02-01

260

Molecular dynamics study of nonequilibrium processes of evaporation and condensation at a vapor-liquid interface  

Science.gov (United States)

Nonequilibrium processes of evaporation and condensation at a vapor-liquid interface are studied by molecular dynamics simulations, which is devised to be free from any artificial constraints on molecular motions in the vicinity of the interface. To decrease statistical fluctuations on the results, the dynamics of a vapor-liquid two-phase system of almost 0.3 million Lennard-Jones molecules is simulated for more than 107 steps. The system with a steady evaporation or condensation mass flux can be realized by driving two vapor regions on the both sides of a planar liquid film, and thus the simulation is free from artificial controls of molecular motions in the liquid film and in the neighborhood of the interfaces. This enables us to evaluate the mass, momentum, and energy fluxes, which are relevant to the velocity distribution of molecules leaving the interface when the nonequilibrium evaporation or condensation occurs there.

Yano, Takeru

2012-11-01

 
 
 
 
261

High level radioactive waste vitrification process equipment component testing  

Energy Technology Data Exchange (ETDEWEB)

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.

Siemens, D.H.; Heath, W.O.; Larson, D.E.; Craig, S.N.; Berger, D.N.; Goles, R.W.

1985-04-01

262

Ecotoxicity of triphenyltin on the marine copepod Tigriopus japonicus at various biological organisations: from molecular to population-level effects.  

Science.gov (United States)

Triphenyltin compounds (TPTs), as effective biocides for different industrial and agricultural purposes, have been detected in coastal marine environments worldwide, in particular in Asian countries. However, little is known about their toxicity to marine organisms. This study comprehensively investigated the molecular, individual and population responses of the marine copepod, Tigriopus japonicus upon waterborne exposure to TPT chloride (TPTCl). Our results indicated that TPTCl was highly toxic to adult T. japonicus, with a 96-h LC50 concentration at 6.3 ?g/L. As shown in a chronic full life-cycle test, T. japonicus exposed to 1.0 ?g/L TPTCl exhibited a delay in development and a significant reduction of population growth, in terms of the intrinsic rate of increase (r m ). Based on the negative relationship between the r m and exposure concentration, a critical effect concentration was estimated at 1.6 ?g/L TPTCl; at or above which population extinction could occur. At 0.1 ?g/L TPTCl or above, the sex ratio of the second generation of the copepod was significantly altered and changed to a male-biased population. At molecular level, the inhibition of the transcriptional expression of glutathione S-transferase related genes might lead to dysfunction of detoxification, and the inhibition of retinoid X receptor mRNA expression implied an interruption of the growth and moulting process in T. japonicus. As the only gene that observed up-regulated in this study, the expression of heat shock protein 70 (hsp70) increased in a concentration-dependent manner, indicating its function in protecting the copepod from TPT-mediated oxidative stress. The study advances our understanding on the ecotoxicity of TPT, and provides some initial data on its toxic mechanisms in small crustaceans like copepods. PMID:24981692

Yi, Andy Xianliang; Han, Jeonghoon; Lee, Jae-Seong; Leung, Kenneth M Y

2014-09-01

263

Radio-adaptation: cellular and molecular features of a response to low levels of ionizing radiation  

International Nuclear Information System (INIS)

It is well established that sublethal doses of DNA damaging agents induce protective mechanisms against a subsequent high dose treatment ; for instance, the phenomenon of radio-adaptation in the case of ionizing radiations. Since the early observation described in 1984, numerous studies have confirmed the radio-adaptive response in terms of reduction of chromosomal breaks for varied biological models in vitro and in vivo. Evidence for an adaptive response against the induction of gene mutations and the lethal effect is clearly demonstrated. This paper reviews the experimental results describing various aspects of these adaptive responses expressed on these different biological end-points. The molecular mechanism underlying radio-adaptation still remains nuclear. The development of this phenomenon requires de novo synthesis of transcripts and proteins during the time interval between the two doses. Some data are consistent with the hypotheses that these gene products would be involved in the activation of DNA repair pathways and antioxidant systems. However, a major question still remains unanswered; indeed, it is not clear whether or not the radio-adaptation could affect the estimation of cancer risk related with low level exposure to ionizing radiation, a major concern in radioprotection. Until such data are available, it is yet unwise to evoke the beneficial effects of radio-adaptation. (authors)

264

Insights into the uranium(VI) speciation with Pseudomonas fluorescens on a molecular level.  

Science.gov (United States)

Microorganisms have great potential to bind and thus transport actinides in the environment. Thus microbes indigenous to designated nuclear waste disposal sites have to be investigated regarding their interaction mechanisms with soluble actinyl ions when assessing the safety of a planned repository. This paper presents results on the pH-dependent sorption of U(VI) onto Pseudomonas fluorescens isolated from the granitic rock aquifers at Äspö Hard Rock Laboratory, Sweden. To characterize the U(VI) interaction on a molecular level, potentiometric titration in combination with time-resolved laser-induced fluorescence spectroscopy (TRLFS) were applied. This paper as a result is one of the very few sources which provide stability constants of U(VI) complexed by cell surface functional groups. In addition the bacteria-mediated liberation of inorganic phosphate in dependence on [U(VI)] at different pHs was studied to judge the influence of phosphate release on U(VI) mobilization. The results demonstrate that in the acidic pH range U(VI) is bound by the cells mainly via protonated phosphoryl and carboxylic sites. The complexation by carboxylic groups can be observed over a wide pH range up to around pH 7. At neutral pH fully deprotonated phosphoryl groups are mainly responsible for U(VI) binding. U(VI) can be bound by P. fluorescens with relatively high thermodynamic stability. PMID:23007661

Lütke, Laura; Moll, Henry; Bernhard, Gert

2012-11-21

265

An azanorbornadiene anchor for molecular-level construction on silicon(100)  

Science.gov (United States)

N-trimethylsilyl-7-azanorbornadiene (TMSAN) is synthesized and chemisorbed on the silicon(100)-2 × 1 surface under ultra-high vacuum conditions and the resulting structure is determined using scanning tunnelling microscopy (STM). The binding exhibits poor short-range order, similar to that for norbornadiene. Patterning of the adsorbate is demonstrated following STM electron-stimulated depassivation of a silicon(100)-2 × 1-H surface, indicating that the placement of TMSAN on the surface can be controlled. Density-functional theory (DFT) calculations verify the close analogy between the binding of TMSAN and its much studied parent compound, norbornadiene. This analogue is novel, however, in that it can provide anchor points for construction at the molecular level above the silicon surface. How such construction could proceed is controlled by the topology of the nitrogen atom and the torsional potential for rotation about the N-Si bond. While these key features are not readily apparent from the STM results, DFT predicts that TMSAN above silicon(100) adopts a structure containing an azimuthal rotor: the nitrogen atom is in a planar configuration so that the N-Si bond is normal to the silicon surface, there being also nearly free rotation about the N-Si bond. Further, variants of TMSAN are considered in which a double-well potential for nitrogen inversion is predicted, suggesting that chemical control can be established over the architectural function of this class of compounds.

Wang, Bing; Zheng, Xiaolai; Michl, Josef; Foley, Edward T.; Hersam, Mark C.; Bilic, Ante; Crossley, Maxwell J.; Reimers, Jeffrey R.; Hush, Noel S.

2004-03-01

266

MULTI LEVEL SEMANTIC EXTRACTION FOR CRICKET VIDEO BY TEXT PROCESSING  

Directory of Open Access Journals (Sweden)

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.

Dr. SUNITHA ABBURU

2010-10-01

267

Process development for processing of (a) low level sludges and (b) intermediate level liquid waste at ANSTO  

International Nuclear Information System (INIS)

The work is divided in two main parts. The first part involved inactive tests for the drying of radioactive sludges produced in the Effluent Plant from liquid low-active waste streams. The simulated waste containing aluminium hydroxide, sodium carbonate, nitrate, sulfate and chloride was prepared, and comprehensive tests of the approach were performed to estimate its applicability in management of the Effluent Plant-produced radioactive waste. The optimal regimes of the drum dryer performance were found, and the approach will be commissioned for treatment of the actual thickened waste sludge. The tests concerning drum durability, stainless steel coupon corrosion testing and operating regime were conducted. The second part of the work dealt with intermediate level liquid waste generated during Mo- 99 radioisotope production that shall ultimately be sent for final disposal. The Synroc ANSTO technology was chosen as a preferable form for intermediate level solid waste disposal. The suggested technology comprises incorporation of the waste into ceramic matrix through liquid impregnation into a precursor; drying; and calcination followed by hot isostatic pressing. The resulting form represents the most durable one for ultimate disposal. The mock-up facility featuring all the above stages was constructed and operated to comprehensively test the impregnation, drying and calcinations in an integrated operation under non-active conditions. The results of the mock-up operation ons. The results of the mock-up operation are presented. (author)

268

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

Directory of Open Access Journals (Sweden)

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.

Sherwood Julie S

2009-09-01

269

Biologia molecular do processo de infecção por Agrobacterium spp. / Molecular biology of the infection process by Agrobacterium spp.  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: Portuguese Abstract in portuguese Agrobacterium tumefaciens é o agente causal da galha-da-coroa, doença que afeta a maioria das plantas dicotiledôneas e caracteriza-se pelo crescimento de tumores na junção entre o caule e a raiz (coroa). A formação desses tumores é o resultado de um processo natural de transferência de genes de Agro [...] bacterium spp. para o genoma da planta infetada. Esses genes estão contidos em um plasmídio de alto peso molecular (120 a 250 kb), denominado Ti ("tumor inducing"), presente em todas as linhagens patogênicas de Agrobacterium spp. Duas regiões do plasmídio Ti estão diretamente envolvidas na indução do tumor: a região-T, que corresponde ao segmento de DNA transferido para a célula vegetal, e a região de virulência (região vir), que contém genes envolvidos na síntese de proteínas responsáveis pelo processo de transferência da região-T. Esta região, uma vez transferida e integrada no genoma da célula vegetal, passa a ser denominada de T-DNA ("transferred DNA"). Os genes presentes no T-DNA codificam enzimas envolvidas na via de biossíntese de reguladores de crescimento, auxinas e citocininas. A síntese desses reguladores pelas células transformadas causa um desbalanço hormonal, levando à formação do tumor no local da infecção. Outro grupo de genes presentes no T-DNA codifica enzimas responsáveis pela síntese de opinas, que são catabolisadas especificamente pela bactéria colonizadora, como fonte de nutrientes. O conhecimento preliminar das bases moleculares envolvidas no processo de infecção de uma planta hospedeira por Agrobacterium spp., permitiu a utilização desta bactéria como vetor natural de transformação genética de plantas. Abstract in english Agrobacterium tumefaciens is the causal agent of crown gall disease that affects most dicotyledonous plants and is characterized by growth of tumors in the region between the plant stem and root (crown). The development of tumors is the result of a natural transfer process of Agrobacterium spp. gene [...] s to the genome of the infected plant. These genes are found on a high molecular weight plasmid denominated Ti (tumor inducing), present in all pathogenic Agrobacterium spp. strains. Two Ti plasmid regions are directly involved in tumor induction. The T-region, which corresponds to the segment of transferred DNA to the plant cells, and the virulence (vir) region, which contains genes involved in the synthesis of proteins required for T-region transfer. This region, when transferred and integrated to the plant cell genome, is called T-DNA (transferred DNA). The genes present in T-DNA encode enzymes involved in the biosynthesis of plant growth regulators, auxin and cytokinin. The synthesis of these regulators by transformed cells results in a hormonal inbalance, leading to the development of tumors where the infection took place. Another group of genes present in T-DNA encodes enzymes required for opine synthesis, which are specifically catabolised by the colonizing bacterium as the source of nutrients. Preliminary knowledge of the molecular basis involved in the infection process of the host plant by Agrobacterium spp. allowed the use of this bacterium as a natural vector for plant genetic transformation.

Gisele M. de, Andrade; Laudete M., Sartoretto; Ana C. M., Brasileiro.

270

Biologia molecular do processo de infecção por Agrobacterium spp. / Molecular biology of the infection process by Agrobacterium spp.  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: Portuguese Abstract in portuguese Agrobacterium tumefaciens é o agente causal da galha-da-coroa, doença que afeta a maioria das plantas dicotiledôneas e caracteriza-se pelo crescimento de tumores na junção entre o caule e a raiz (coroa). A formação desses tumores é o resultado de um processo natural de transferência de genes de Agro [...] bacterium spp. para o genoma da planta infetada. Esses genes estão contidos em um plasmídio de alto peso molecular (120 a 250 kb), denominado Ti ("tumor inducing"), presente em todas as linhagens patogênicas de Agrobacterium spp. Duas regiões do plasmídio Ti estão diretamente envolvidas na indução do tumor: a região-T, que corresponde ao segmento de DNA transferido para a célula vegetal, e a região de virulência (região vir), que contém genes envolvidos na síntese de proteínas responsáveis pelo processo de transferência da região-T. Esta região, uma vez transferida e integrada no genoma da célula vegetal, passa a ser denominada de T-DNA ("transferred DNA"). Os genes presentes no T-DNA codificam enzimas envolvidas na via de biossíntese de reguladores de crescimento, auxinas e citocininas. A síntese desses reguladores pelas células transformadas causa um desbalanço hormonal, levando à formação do tumor no local da infecção. Outro grupo de genes presentes no T-DNA codifica enzimas responsáveis pela síntese de opinas, que são catabolisadas especificamente pela bactéria colonizadora, como fonte de nutrientes. O conhecimento preliminar das bases moleculares envolvidas no processo de infecção de uma planta hospedeira por Agrobacterium spp., permitiu a utilização desta bactéria como vetor natural de transformação genética de plantas. Abstract in english Agrobacterium tumefaciens is the causal agent of crown gall disease that affects most dicotyledonous plants and is characterized by growth of tumors in the region between the plant stem and root (crown). The development of tumors is the result of a natural transfer process of Agrobacterium spp. gene [...] s to the genome of the infected plant. These genes are found on a high molecular weight plasmid denominated Ti (tumor inducing), present in all pathogenic Agrobacterium spp. strains. Two Ti plasmid regions are directly involved in tumor induction. The T-region, which corresponds to the segment of transferred DNA to the plant cells, and the virulence (vir) region, which contains genes involved in the synthesis of proteins required for T-region transfer. This region, when transferred and integrated to the plant cell genome, is called T-DNA (transferred DNA). The genes present in T-DNA encode enzymes involved in the biosynthesis of plant growth regulators, auxin and cytokinin. The synthesis of these regulators by transformed cells results in a hormonal inbalance, leading to the development of tumors where the infection took place. Another group of genes present in T-DNA encodes enzymes required for opine synthesis, which are specifically catabolised by the colonizing bacterium as the source of nutrients. Preliminary knowledge of the molecular basis involved in the infection process of the host plant by Agrobacterium spp. allowed the use of this bacterium as a natural vector for plant genetic transformation.

Gisele M. de, Andrade; Laudete M., Sartoretto; Ana C. M., Brasileiro.

2003-10-01

271

Biologia molecular do processo de infecção por Agrobacterium spp. Molecular biology of the infection process by Agrobacterium spp.  

Directory of Open Access Journals (Sweden)

Full Text Available Agrobacterium tumefaciens é o agente causal da galha-da-coroa, doença que afeta a maioria das plantas dicotiledôneas e caracteriza-se pelo crescimento de tumores na junção entre o caule e a raiz (coroa. A formação desses tumores é o resultado de um processo natural de transferência de genes de Agrobacterium spp. para o genoma da planta infetada. Esses genes estão contidos em um plasmídio de alto peso molecular (120 a 250 kb, denominado Ti ("tumor inducing", presente em todas as linhagens patogênicas de Agrobacterium spp. Duas regiões do plasmídio Ti estão diretamente envolvidas na indução do tumor: a região-T, que corresponde ao segmento de DNA transferido para a célula vegetal, e a região de virulência (região vir, que contém genes envolvidos na síntese de proteínas responsáveis pelo processo de transferência da região-T. Esta região, uma vez transferida e integrada no genoma da célula vegetal, passa a ser denominada de T-DNA ("transferred DNA". Os genes presentes no T-DNA codificam enzimas envolvidas na via de biossíntese de reguladores de crescimento, auxinas e citocininas. A síntese desses reguladores pelas células transformadas causa um desbalanço hormonal, levando à formação do tumor no local da infecção. Outro grupo de genes presentes no T-DNA codifica enzimas responsáveis pela síntese de opinas, que são catabolisadas especificamente pela bactéria colonizadora, como fonte de nutrientes. O conhecimento preliminar das bases moleculares envolvidas no processo de infecção de uma planta hospedeira por Agrobacterium spp., permitiu a utilização desta bactéria como vetor natural de transformação genética de plantas.Agrobacterium tumefaciens is the causal agent of crown gall disease that affects most dicotyledonous plants and is characterized by growth of tumors in the region between the plant stem and root (crown. The development of tumors is the result of a natural transfer process of Agrobacterium spp. genes to the genome of the infected plant. These genes are found on a high molecular weight plasmid denominated Ti (tumor inducing, present in all pathogenic Agrobacterium spp. strains. Two Ti plasmid regions are directly involved in tumor induction. The T-region, which corresponds to the segment of transferred DNA to the plant cells, and the virulence (vir region, which contains genes involved in the synthesis of proteins required for T-region transfer. This region, when transferred and integrated to the plant cell genome, is called T-DNA (transferred DNA. The genes present in T-DNA encode enzymes involved in the biosynthesis of plant growth regulators, auxin and cytokinin. The synthesis of these regulators by transformed cells results in a hormonal inbalance, leading to the development of tumors where the infection took place. Another group of genes present in T-DNA encodes enzymes required for opine synthesis, which are specifically catabolised by the colonizing bacterium as the source of nutrients. Preliminary knowledge of the molecular basis involved in the infection process of the host plant by Agrobacterium spp. allowed the use of this bacterium as a natural vector for plant genetic transformation.

Gisele M. de Andrade

2003-10-01

272

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

International Nuclear Information System (INIS)

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.

273

Molecular Basis of a Million-Fold Affinity Maturation Process in a Protein-Protein Interaction  

Energy Technology Data Exchange (ETDEWEB)

Protein engineering is becoming increasingly important for pharmaceutical applications where controlling the specificity and affinity of engineered proteins is required to create targeted protein therapeutics. Affinity increases of several thousand-fold are now routine for a variety of protein engineering approaches, and the structural and energetic bases of affinity maturation have been investigated in a number of such cases. Previously, a 3-million-fold affinity maturation process was achieved in a protein-protein interaction composed of a variant T-cell receptor fragment and a bacterial superantigen. Here, we present the molecular basis of this affinity increase. Using X-ray crystallography, shotgun reversion/replacement scanning mutagenesis, and computational analysis, we describe, in molecular detail, a process by which extrainterfacial regions of a protein complex can be rationally manipulated to significantly improve protein engineering outcomes.

D Bonsor; S Postel; B Pierce; N Wang; P Zhu; R Buonpane; Z Weng; D Kranz; E Sundberg

2011-12-31

274

An Improved Process for Fabricating High-Mobility Organic Molecular Crystal Field-Effect Transistors  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In this paper we present an improved process for producing elastomer transistor stamps and high-mobility organic field-effect transistors (FETs) based on semiconducting acene molecular crystals. In particular, we have removed the need to use a silanized Si wafer for curing the stamps and to handle a fragile micron-thickness polydimethylsiloxane (PDMS) insulating film and laminate it, bubble free, against the PDMS transistor stamp. We find that despite the altered design, rou...

Micolich, A. P.; Bell, L. L.; Hamilton, A. R.

2007-01-01

275

Level of Detail and Level of Development: Commissioning processes and Information Modelling  

Directory of Open Access Journals (Sweden)

Full Text Available The essence of Information Modelling in the Construction Industry lies in the methods of evolution of the information content through the lifecycle of the commission and the work. Such progress in the levels of development of the model is profoundly different from normal progress as it is strongly affected by the goals of whoever is managing the Information Model itself. The subjects that appear to benefit most from this seem to be governments, delegated project contractors, authorities or promoters and finally and in particular, lenders.

Angelo Ciribini

2013-10-01

276

Magnetic field-dependent molecular and chemical processes in biochemistry, genetics and medicine  

Science.gov (United States)

The molecular concept (paradigm) in magnetobiology seems to be most substantiated and significant for explaining the biomedical effects of electromagnetic fields, for the new medical technology of transcranial magnetic stimulation of cognitive activity, for the nuclear magnetic control of biochemical processes and for the search of new magnetic effects in biology and medicine. The key structural element of the concept is a radical ion pair as the receiver of magnetic fields and the source of magnetic effects. The existence of such pairs was recently detected in the two life-supporting processes of paramount importance — in enzymatic ATP and DNA syntheses. The bibliography includes 80 references.

Buchachenko, A. L.

2014-01-01

277

Homology modeling, molecular dynamics and atomic level interaction study of snake venom 5' nucleotidase.  

Science.gov (United States)

5' Nucleotidase (5' NUC) is a ubiquitously distributed enzyme known to be present in snake venoms (SV) that is responsible primarily for causing dysregulation of physiological homeostasis in humans by inducing anticoagulant effects and by inhibiting platelet aggregation. It is also known to act synergistically with other toxins to exert a more pronounced anti-coagulant effect during envenomation. Its structural and functional role is not yet ascertained clearly. The 3D structure of snake venom 5' nucleotidase (SV-5' NUC) is not yet known and was predicted by us for the first time using a comparative homology modeling approach using Demansia vestigiata protein sequence. The accuracy and stability of the predicted SV-5' NUC structure were validated using several computational approaches. Key interactions of SV-5' NUC were studied using experimental studies/molecular docking analysis of the inhibitors vanillin, vanillic acid and maltol. All these inhibitors were found to dock favorably following pharmacologically relevant absorption, distribution, metabolism and excretion (ADME) profiles. Further, atomic level docking interaction studies using inhibitors of the SV-5' NUC active site revealed amino acid residues Y65 and T72 as important for inhibitor-(SV-5' NUC) interactions. Our in silico analysis is in good agreement with experimental inhibition results of SV-5' NUC with vanillin, vanillic acid and maltol. The present study should therefore play a guiding role in the experimental design of new SV-5' NUC inhibitors for snake bite management. We also identified a few pharmacophoric features essential for SV-5' NUC inhibitory activity that can be utilized further for the discovery of putative anti-venom agents of therapeutic value for snake bite management. PMID:24567162

Arafat, A Syed Yasir; Arun, A; Ilamathi, M; Asha, J; Sivashankari, P R; D'Souza, Cletus J M; Sivaramakrishnan, V; Dhananjaya, B L

2014-03-01

278

Stepping and Crowding of Molecular Motors: Statistical Kinetics from an Exclusion Process Perspective  

Science.gov (United States)

Motor enzymes are remarkable molecular machines that use the energy derived from the hydrolysis of a nucleoside triphosphate to generate mechanical movement, achieved through different steps that constitute their kinetic cycle. These macromolecules, nowadays investigated with advanced experimental techniques to unveil their molecular mechanisms and the properties of their kinetic cycles, are implicated in many biological processes, ranging from biopolymerisation (e.g. RNA polymerases and ribosomes) to intracellular transport (motor proteins such as kinesins or dyneins). Although the kinetics of individual motors is well studied on both theoretical and experimental grounds, the repercussions of their stepping cycle on the collective dynamics still remains unclear. Advances in this direction will improve our comprehension of transport process in the natural intracellular medium, where processive motor enzymes might operate in crowded conditions. In this work, we therefore extend the current statistical kinetic analysis to study collective transport phenomena of motors in terms of lattice gas models belonging to the exclusion process class. Via numerical simulations, we show how to interpret and use the randomness calculated from single particle trajectories in crowded conditions. Importantly, we also show that time fluctuations and non-Poissonian behavior are intrinsically related to spatial correlations and the emergence of large, but finite, clusters of co-moving motors. The properties unveiled by our analysis have important biological implications on the collective transport characteristics of processive motor enzymes in crowded conditions.

Ciandrini, Luca; Romano, M. Carmen; Parmeggiani, Andrea

2014-09-01

279

Initial elementary processes in tetrafluoroethylene plasma: An ab initio molecular orbital study  

Science.gov (United States)

Initial elementary processes in tetrafluoroethylene plasma are studied by using an ab initio molecular orbital method. The energy-surfaces at excited states are obtained by the Hartree-Fock method with a double zeta basis set, plus Rydberg orbitals. A ?-?* transition is low-lying both at singlet and triplet excited states. Vinyl-polymerization-type reactions are expected in the presence of some radical species via these transitions. The C=C bond cleaves via a triplet ?-?* transition to form CF2. The predicted elementary processes via these states are compatible with experimental results that C2F4* and CF2 are primary precursors. No excited states that bring about a C—F bond cleavage are obtained within 10 eV of the ground state. As a path for a C—F bond cleavage, a dissociative electron attachment process is found in a low energy region. This process is considered to be important for producing fluorine anions.

Sato, Kota; Komatsu, Toru; Iwabuchi, Susumu

1993-12-01

280

Amino Acid Composition, Molecular Weight Distribution and Antioxidant Stability of Shrimp Processing Byproduct Hydrolysate  

Directory of Open Access Journals (Sweden)

Full Text Available Protein hydrolysate have many practical applications in a various of industries due to the bioactive peptides related to their amino acid composition, sequence and molecular weight. The amino acid composition, molecular weight distribution and antioxidant stability of alcalase hydrolysate were investigated in this study. The hydrolysate was separated into five fractions by ultra filtration system with different molecular weight cutoff with 10, 5, 3 and 1 kDa, respectively. The protein content, 1,1-diphenyl-2-picrylhydrazyl radical scavenging activity and molecular weight of each fraction were determined. In addition, the antioxidant stability of the hydrolysate under several operating conditions was studied. The results showed that the hydrolysate was composed with high amounts of hydrophobic amino acids (40.4% which might contribute to the high antioxidant activity. The fraction with molecular weight lower than 1 kDa exhibited the highest antioxidative activity among the five fractions. The antioxidant stability experiments showed that the hydrolysate was stable when it was heated up to 100C and the relative antioxidative activity could be maintained nearly 70% at very low pH of 2.0. Glucose and sucrose had negative effects on the antioxidative activity, in which the relative activity of about 80% was retained. Sodium chloride and sodium benzoate had little or no effects on the antioxidative activity of the hydrolysate. The effects of Zn2+ and Cu2+ on the antioxidative activity were significant and dependent on metal concentration. The shrimp processing byproduct hydrolysate may be a potential natural food antioxidant in the future.

J.X. Jiang

2011-01-01

 
 
 
 
281

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

International Nuclear Information System (INIS)

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)

282

Molecular dynamics simulation of cluster-beam-surface impact processes for metallic phases  

International Nuclear Information System (INIS)

An optimised version of the DLPOLY molecular dynamics simulation code has been used to study the cluster-beam-surface impact processes for the metallic phase. The interaction of an energetic cluster of atoms with a solid surface was investigated using the Finnis-Sinclair many-body potential. The characteristics of the collision range from soft landing ( 3 eV/atom) are studied. Modification of the surface, exposed to highly energetic cluster-beams, was studied by monitoring the molecular dynamics configurations of the system in real time and defining the critical impact energies, necessary to produce implantation. The density and temperature distributions in the system of cluster-substrate under highly energetic irradiations was investigated in detail

283

Isolation and Identification of Listeria monocytogenes in Processed Meat by a Combined Cultural-molecular Method  

Directory of Open Access Journals (Sweden)

Full Text Available The isolation and identification of Listeria monocytogenes in processed meat samples by a combined cultural-molecular method is described. It allows the identification of Listeria strains by means of a hybridization technique with a specific DNA probe directed to the listerial internalin gene. The specificity of this method was found to be 100% and sensitivity was as low as 1 CFU/2.5 g of food sample. A total of 278 meat samples were tested in comparison with PCR and conventional cultural assays. A total of 42 (15.4% L. monocytogenes were detected. PCR analysis gave 3 false negative results and culture failed to detect the Listeria in 5 cases. With this cultural-molecular method the identification and quantitative detection of L. monocytogenes were achieved within 36 hours and no false positive or negative tests were obtained, thus fitting most food industry requirements.

Angela Ingianni

2007-01-01

284

Directions in low-level radioactive waste management. The siting process: establishing a low-level waste-disposal facility  

International Nuclear Information System (INIS)

The siting of a low-level radioactive waste disposal facility encompasses many interrelated activities and, therefore, is inherently complex. The purpose of this publication is to assist state policymakers in understanding the nature of the siting process. Initial discussion focuses on the primary activities that require coordination during a siting effort. Available options for determining site development, licensing, regulating, and operating responsibilities are then considered. Additionally, the document calls attention to technical services available from federal agencies to assist states in the siting process; responsibilities of such agencies are also explained. The appendices include a conceptual plan for scheduling siting activities and an explanation of the process for acquiring agreement state status. An agreement state takes responsibility for licensing and regulating a low-level waste facility within its borders

285

A Better Insight Into IT Contribution by Process Level Structure : A Case Study in Royal Greenland  

DEFF Research Database (Denmark)

Creation of IT business value through its impact on value chain processes made the objective of this research to compare and differentiate IT role at both process and firm levels. A discussion about IT’s impact at both levels are made through previous theoretical and empirical studies. The discussion is supported by an introduction to the case of study in Royal Greenland. The contribution of this paper is the results of the discussions and the case study reaching to the point that IT supporting influences are better understood and observed at process levels rather than firm output level.

Shahim, Nazli; MØller, Charles

2013-01-01

286

Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats, making access to this very difficult. The publication and wide implementation of the Human Proteome Organisation Proteomics Standards Initiative Molecular Interactions (HUPO PSI-MI format in 2004 was a major step towards the establishment of a single, unified format by which molecular interactions should be presented, but focused purely on protein-protein interactions. Results The HUPO-PSI has further developed the PSI-MI XML schema to enable the description of interactions between a wider range of molecular types, for example nucleic acids, chemical entities, and molecular complexes. Extensive details about each supported molecular interaction can now be captured, including the biological role of each molecule within that interaction, detailed description of interacting domains, and the kinetic parameters of the interaction. The format is supported by data management and analysis tools and has been adopted by major interaction data providers. Additionally, a simpler, tab-delimited format MITAB2.5 has been developed for the benefit of users who require only minimal information in an easy to access configuration. Conclusion The PSI-MI XML2.5 and MITAB2.5 formats have been jointly developed by interaction data producers and providers from both the academic and commercial sector, and are already widely implemented and well supported by an active development community. PSI-MI XML2.5 enables the description of highly detailed molecular interaction data and facilitates data exchange between databases and users without loss of information. MITAB2.5 is a simpler format appropriate for fast Perl parsing or loading into Microsoft Excel.

Cusick Michael E

2007-10-01

287

The level of knowledge about the planning of training process of female engaged in recreational fitness  

Directory of Open Access Journals (Sweden)

Full Text Available The aim of the study was to determine the level of knowledge about the planning of training process of female engaged in recreational fitness. The main method of investigation was questioning. The study involved 100 female aged 16-47 years engaged in fitness in three fitness centers in Gdansk and Sopot. The general level of knowledge of the planning of training process and its relationship with age, training experience and level of education was revealed.

Jagiello Wladyslaw

2011-07-01

288

Long-term management of high-level defense wastes at the Idaho Chemical Processing Plant  

International Nuclear Information System (INIS)

Plans and technology for the long-term management of existing and future high-level defense wastes generated at the Idaho Chemical Processing Plant are discussed. Current high-level waste management is also reviewed to show the continuity between present and future high-level waste management. 1 ref

289

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

CERN Document Server

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 {\\mu}s 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 signif...

Pedersen, Andreas; Karssemeijer, Leendertjan; Cuppen, Herma; Jónsson, Hannes

2014-01-01

290

Energy conversion processes based on molecular excited states: Progress report, August 1, 1987-July 31, 1988  

International Nuclear Information System (INIS)

The first of the two interwoven threads of our DOE-supported research efforts include studies on the preparation and photochemical properties of transition metal complexes which have metal to ligand charge transfer excited states. In sight is being gained into the electronic structure and photochemical and photophysical properties of these excited states. The second emphasis in our work has been on the preparation and characterization of thin polymeric films which contain these complexes. The goal is to learn how to vary the underlying microstructure as a basis for energy conversion applications at the molecular level. 10 refs

291

Molecular level assessment of thermal transport and thermoelectricity in materials: From bulk alloys to nanostructures  

Science.gov (United States)

The ability to manipulate material response to dynamical processes depends on the extent of understanding of transport properties and their variation with chemical and structural features in materials. In this perspective, current work focuses on the thermal and electronic transport behavior of technologically important bulk and nanomaterials. Strontium titanate is a potential thermoelectric material due to its large Seebeck coefficient. Here, first principles electronic band structure and Boltzmann transport calculations are employed in studying the thermoelectric properties of this material in doped and deformed states. The calculations verified that excessive carrier concentrations are needed for this material to be used in thermoelectric applications. Carbon- and boron nitride-based nanomaterials also offer new opportunities in many applications from thermoelectrics to fast heat removers. For these materials, molecular dynamics calculations are used to evaluate lattice thermal transport. To do this, first, an energy moment term is reformulated for periodic boundary conditions and tested to calculate thermal conductivity from Einstein relation in various systems. The influences of the structural details (size, dimensionality) and defects (vacancies, Stone-Wales defects, edge roughness, isotopic disorder) on the thermal conductivity of C and BN nanostructures are explored. It is observed that single vacancies scatter phonons stronger than other type of defects due to unsatisfied bonds in their structure. In pristine states, BN nanostructures have 4-6 times lower thermal conductivity compared to C counterparts. The reason of this observation is investigated on the basis of phonon group velocities, life times and heat capacities. The calculations show that both phonon group velocities and life times are smaller in BN systems. Quantum corrections are also discussed for these classical simulations. The chemical and structural diversity that could be attained by mixing hexagonal boron nitride and graphene provide further avenues for tuning thermal and electronic properties. In this work, the thermal conductivity of hybrid graphene/hexagonal-BN structures: stripe superlattices and BN (graphene) dots embedded in graphene (BN) are studied. The largest reduction in thermal conductivity is observed at 50% chemical mixture in dot superlattices. The dot radius appears to have little effect on the magnitude of reduction around large concentrations while smaller dots are more influential at dilute systems.

Kinaci, Alper

292

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

Directory of Open Access Journals (Sweden)

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.

Ade Febransyah

2005-01-01

293

Processing of low- and medium-level radioactive waste. Chapter 3  

International Nuclear Information System (INIS)

In a Dutch government policy formulated in 1984, it has been stated that in the Netherlands one location has to be adapted for, among other things, processing of low- and medium-level radioactive waste. This chapter deals with the radioactive waste to be processed and the processing facility to be realized. (author). 3 figs

294

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

Energy Technology Data Exchange (ETDEWEB)

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.

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

295

Mathematical models of non-linear phenomena, processes and systems: from molecular scale to planetary atmosphere  

CERN Document Server

This book consists of twenty seven chapters, which can be divided into three large categories: articles with the focus on the mathematical treatment of non-linear problems, including the methodologies, algorithms and properties of analytical and numerical solutions to particular non-linear problems; theoretical and computational studies dedicated to the physics and chemistry of non-linear micro-and nano-scale systems, including molecular clusters, nano-particles and nano-composites; and, papers focused on non-linear processes in medico-biological systems, including mathematical models of ferments, amino acids, blood fluids and polynucleic chains.

2013-01-01

296

From Molecular Structure to Global Processes : NMR Spectroscopy in Analytical/Environmental Chemistry  

Science.gov (United States)

NMR Spectroscopy is arguably the most powerful tool to elucidate structure and probe molecular interactions. A range of NMR approaches will be introduced with emphasis on addressing and understanding structure and reactivity of soil organic matter at the molecular level. The presentation will be split into three main sections. The first section will look at evidence from advanced NMR based approaches that when considered synergistically describes the major structural components in soil organic matter. Multidimensional NMR spectroscopy (1-3D NMR), automated pattern matching, spectral simulations, diffusion NMR and hybrid-diffusion NMR will be introduced in context of molecular structure. Finally the structural components in soil will be contrasted to those found in aquatic dissolved organic matter. Secondly molecular interactions of natural organic matter will be considered. Advanced structural studies have provided detailed spectral assignments which in turn permit the reactivity of various soil components to be elucidated. Aggregation and self-association of soil and dissolved organic matter will be discussed along with the structural components likely responsible for aggregation/colloid formation. Interactions of soil organic matter with anthropogenic chemicals will also be considered and NMR techniques based on "Saturation Transfer Difference" introduced. These techniques are extremely powerful and can be used to both; describe mechanistically how anthropogenic chemicals sorb to whole soils and identify the structural components (lignin, protein, cellulose, etc..) that are responsible for the binding/sorption in soil. In the last section, the "big questions" and challenges facing the field will be considered along with some novel experimental NMR based approaches that should, in future, assist in providing answers to these questions.

Simpson, A.

2009-04-01

297

Electrospray ionization mass spectrometry: chemical processes involved in the ion formation from low molecular weight organic compounds  

International Nuclear Information System (INIS)

An overview of the current literature on the chemical processes involved in the ion formation from low molecular weight organic compounds by electrospray ionization mass spectrometry is given. (author)

298

Proposal of flexible atomic and molecular process management for Monte Carlo impurity transport code based on object oriented method  

International Nuclear Information System (INIS)

mic and molecular processes and then each 'object' is defined by analyzing this information. According to the relation among plasma particle species, objects are connected with each other and change their state by themselves. Dynamic allocation of these objects to program memory is employed to adapt for arbitrary number of species and atomic/molecular reactions. Thus we can treat arbitrary species and process starting from, for instance, methane and acetylene. Such a software procedure would be useful also for industrial application plasmas, which enfolds more complicated atomic and molecular process such as SiH4. In this paper, a detailed description and idea to take care of arbitrary particle species and atomic/molecular process are presented based on object-oriented method. We will also demonstrate that this simulation is successful in a concrete example. (orig.)

299

Neuronal Ceroid Lipofuscinoses Are Connected at Molecular Level: Interaction of CLN5 Protein with CLN2 and CLN3  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Neuronal ceroid lipofuscinoses (NCLs) are neurodegenerative storage diseases characterized by mental retardation, visual failure, and brain atrophy as well as accumulation of storage material in multiple cell types. The diseases are caused by mutations in the ubiquitously expressed genes, of which six are known. Herein, we report that three NCL disease forms with similar tissue pathology are connected at the molecular level: CLN5 polypeptides directly interact with the CLN2 and CLN3 proteins ...

Vesa, Jouni; Chin, Mark H.; Oelgeschla?ger, Kathrin; Isosomppi, Juha; Dellangelica, Esteban C.; Jalanko, Anu; Peltonen, Leena

2002-01-01

300

News Note: Scientists identify molecular link between BRCA1 protein levels and obesity  

Science.gov (United States)

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 monitoring and responding to how the cells use and store energy (metabolic state).

 
 
 
 
301

The molecular genetics of the incision step in the DNA excision repair process  

International Nuclear Information System (INIS)

In this historical review one particular aspect of excision repair, DNA incision, and how it is controlled at the genetic level in bacteriophage, bacteria, S. cerevisae, D. melanogaster, rodent cells and humans is examined. In phage T4, DNA is incised by a DNA glycosylase-AP endonuclease coded for by the denV gene. In E. coli, products of three genes, uvrA, uvrB and uvrC, are required to form UVRABC excinuclease that cleaves DNA and releases a fragment 12-13 nucleotides long containing the damage site. In S. cerevisiae, genes complementing five mutants of the RAD3 epistasis group, rad1, rad2, rad3, rad4 and rad10 have been cloned and analyzed. Rodent cells sensitive to a variety of mutagenic agents and deficient in excision repair are being used in molecular studies to identify and clone human repair genes (e.g. ERCC1) capable of complementing mammalian repair defects. Most studies of the human system, have been done with cells isolated from patients xeroderma pigmentosum, and these are now beginning to be characterized at the molecular level. (author)

302

Method and device for solidifying high level liquid wastes from a re-processing plant  

International Nuclear Information System (INIS)

Purpose: To decrease the production of chlorides and reduce the amount of secondary liquid wastes by using low concentration nitric acid at a low radioactive level obtained from a condensator as scrubber feeding liquid. Constitution: In a solidification device for high level liquid wastes from a re-processing plant in which off-gases resulted from solidification of high level liquid wastes from a re-processing plant are cleaned with gas cleaning liquids and returned while being concentrated to a high level liquid waste solidification stage, the off gases produced in the concentration stage are condensed and the condensed liquids are fed as the gas cleaning liquids. (Aizawa, K.)

303

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

Energy Technology Data Exchange (ETDEWEB)

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.

Annapureddy, Harsha V.; Dang, Liem X.

2012-12-07

304

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

Science.gov (United States)

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.

Yu, Peiqiang

2011-11-01

305

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

International Nuclear Information System (INIS)

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)

306

Board-invited review: Sensitivity and responses of functional groups to feed processing methods on a molecular basis  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract In complex feed structures, there exist main chemical functional groups which are associated with nutrient utilization and availability and functionality. Each functional group has unique molecular structure therefore produce unique molecular vibration spectral profile. Feed processing has been used to improve nutrient utilization for many years. However, to date, there was little study on processing-induced changes of feed intrinsic structure and functional groups on a molecular basis within intact tissue. This is because limited research technique is available to study inherent structure on a molecular basis. Recently bioanalytical techniques: such as Synchrotron Infrared Microspectroscopy as well as Diffuse Reflectance Infrared Fourier Transform molecular spectroscopy have been developed. These techniques enable to detect molecular structure change within intact tissues. These techniques can prevent destruction or alteration of the intrinsic protein structures during processing for analysis. However, these techniques have not been used in animal feed and nutrition research. The objective of this review was show that with the advanced technique, sensitivity and responses of functional groups to feed processing on a molecular basis could be detected in my research team. These functional groups are highly associated with nutrient utilization in animals.

Yu Peiqiang

2012-12-01

307

Molecular processes underlying the floral transition in the soybean shoot apical meristem  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The transition to flowering is characterized by a shift of the shoot apical meristem (SAM) from leaf production to the initiation of a floral meristem. The flowering process is of vital importance for agriculture, but the associated events or regulatory pathways in the SAM are not well understood, especially at a system level. To address this issue, we have used a GeneChip® containing 37 744 probe sets to generate a temporal profile of gene expression during the floral initiation process in ...

Wong, Chui E.; Singh, Mohan B.; Bhalla, Prem L.

2009-01-01

308

Molecular dynamics simulation of the melting process in Ag27Cu13 core–shell nanoalloy  

International Nuclear Information System (INIS)

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 solid–solid isomerization at T = 480 K. Calculating ?shell and ?core proved that the corresponding solid–solid 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

309

Maldi-tof mass spectrometry imaging reveals molecular level changes in ultrahigh molecular weight polyethylene joint implants in correlation with lipid adsorption.  

Science.gov (United States)

Ultrahigh molecular weight polyethylene (PE-UHMW), a material with high biocompatibility and excellent mechanical properties, is among the most commonly used materials for acetabular cup replacement in artificial joint systems. It is assumed that the interaction with synovial fluid in the biocompartment leads to significant changes relevant to material failure. In addition to hyaluronic acid, lipids are particularly relevant for lubrication in an articulating process. This study investigates synovial lipid adsorption on two different PE-UHMW materials (GUR-1050 and vitamin E-doped) in an in vitro model system by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry imaging (MSI). Lipids were identified by high performance thin layer chromatography (HP-TLC) and tandem mass spectrometry (MS/MS) analysis, with an analytical focus on phospholipids and cholesterol, both being species of high importance for lubrication. Scanning electron microscopy (SEM) analysis was applied in the study to correlate molecular information with PE-UHMW material qualities. It is demonstrated that lipid adsorption preferentially occurs in rough or oxidized polymer regions. Polymer modifications were colocalized with adsorbed lipids and found with high density in regions identified by SEM. Explanted, the in vivo polymer material showed comparable and even more obvious polymer damage and lipid adsorption when compared with the static in vitro model. A three-dimensional reconstruction of MSI data from consecutive PE-UHMW slices reveals detailed information about the diffusion process of lipids in the acetabular cup and provides, for the first time, a promising starting point for future studies correlating molecular information with commonly used techniques for material analysis (e.g., Fourier-transform infrared spectroscopy, nanoindentation). PMID:25215499

Fröhlich, Sophie M; Archodoulaki, Vasiliki-Maria; Allmaier, Günter; Marchetti-Deschmann, Martina

2014-10-01

310

The effect of appraisal level on processing of emotional prosody in meaningless speech.  

Science.gov (United States)

In visual perception of emotional stimuli, low- and high-level appraisal processes have been found to engage different neural structures. Beyond emotional facial expression, emotional prosody is an important auditory cue for social interaction. Neuroimaging studies have proposed a network for emotional prosody processing that involves a right temporal input region and explicit evaluation in bilateral prefrontal areas. However, the comparison of different appraisal levels has so far relied upon using linguistic instructions during low-level processing, which might confound effects of processing level and linguistic task. In order to circumvent this problem, we examined processing of emotional prosody in meaningless speech during gender labelling (implicit, low-level appraisal) and emotion labelling (explicit, high-level appraisal). While bilateral amygdala, left superior temporal sulcus and right parietal areas showed stronger blood oxygen level-dependent (BOLD) responses during implicit processing, areas with stronger BOLD responses during explicit processing included the left inferior frontal gyrus, bilateral parietal, anterior cingulate and supplemental motor cortex. Emotional versus neutral prosody evoked BOLD responses in right superior temporal gyrus, bilateral anterior cingulate, left inferior frontal gyrus, insula and bilateral putamen. Basal ganglia and right anterior cingulate responses to emotional versus neutral prosody were particularly pronounced during explicit processing. These results are in line with an amygdala-prefrontal-cingulate network controlling different appraisal levels, and suggest a specific role of the left inferior frontal gyrus in explicit evaluation of emotional prosody. In addition to brain areas commonly related to prosody processing, our results suggest specific functions of anterior cingulate and basal ganglia in detecting emotional prosody, particularly when explicit identification is necessary. PMID:18586524

Bach, Dominik R; Grandjean, Didier; Sander, David; Herdener, Marcus; Strik, Werner K; Seifritz, Erich

2008-08-15

311

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

Science.gov (United States)

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

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

2014-01-01

312

Molecular Characterization of Arylsulfatase G: EXPRESSION, PROCESSING, GLYCOSYLATION, TRANSPORT, AND ACTIVITY.  

Science.gov (United States)

Arylsulfatase G (ARSG) is a recently identified lysosomal sulfatase that was shown to be responsible for the degradation of 3-O-sulfated N-sulfoglucosamine residues of heparan sulfate glycosaminoglycans. Deficiency of ARSG leads to a new type of mucopolysaccharidosis, as described in a mouse model. Here, we provide a detailed molecular characterization of the endogenous murine enzyme. ARSG is expressed and proteolytically processed in a tissue-specific manner. The 63-kDa single-chain precursor protein localizes to pre-lysosomal compartments and tightly associates with organelle membranes, most likely the endoplasmic reticulum. In contrast, proteolytically processed ARSG fragments of 34-, 18-, and 10-kDa were found in lysosomal fractions and lost their membrane association. The processing sites and a disulfide bridge between the 18- and 10-kDa chains could be roughly mapped. Proteases participating in the processing were identified as cathepsins B and L. Proteolytic processing is dispensable for hydrolytic sulfatase activity in vitro. Lysosomal transport of ARSG in the liver is independent of mannose 6-phosphate, sortilin, and Limp2. However, mutation of glycosylation site N-497 abrogates transport of ARSG to lysosomes in human fibrosarcoma cells, due to impaired mannose 6-phosphate modification. PMID:25135642

Kowalewski, Björn; Lübke, Torben; Kollmann, Katrin; Braulke, Thomas; Reinheckel, Thomas; Dierks, Thomas; Damme, Markus

2014-10-01

313

Assessing the Impact of Synchrotron X-ray Irradiation on Proteinaceous Specimens at Macro and Molecular Levels.  

Science.gov (United States)

Synchrotron radiation (SR) has become a preferred technique for the analysis of a wide range of archeological samples, artwork, and museum specimens. While SR is called a nondestructive technique, its effect on proteinaceous specimens has not been fully investigated at the molecular level. To investigate the molecular level effects of synchrotron X-ray on proteinaceous specimens, we propose a methodology where four variables are considered: (1) type of specimen: samples ranging from amino acids to proteinaceous objects such as silk, wool, parchment, and rabbit skin glue were irradiated; (2) synchrotron X-ray energy; (3) beam intensity; (4) irradiation time. Irradiated specimens were examined for both macroscopic and molecular effects. At macroscopic levels, color change, brittleness, and solubility enhancement were observed for several samples within 100 s of irradiation. At molecular levels, the method allowed one to quantify significant amino acid modifications. Aspartic acid (Asp), wool, parchment, and rabbit skin glue showed a significant increase in Asp racemization upon increasing irradiation time with rabbit skin glue showing the greatest increase in d-Asp formation. In contrast, Asp in silk, pure cystine (dimer of cysteine), and asparagine (Asn) did not show signs of racemization at the irradiation times studied; however, the latter two compounds showed significant signs of decomposition. Parchment and rabbit skin glue exhibited racemization of Asp, as well as racemization of isoleucine (Ile) and phenylalanine (Phe) after 100 s of irradiation with a focused beam. Under the experimental conditions and sample type and dimensions used here, more change was observed for focused and low energy (8 keV) beams than unfocused or higher energy (22 keV) beams. These results allow quantification of the change induced at the molecular level on proteinaceous specimens by synchrotron X-ray radiation and help to define accurate thresholds to minimize the probability of damage occurring to cultural heritage specimens. For most samples, damage was usually observed in the 1-10 s time scale, which is about an order of magnitude longer than SR studies of cultural heritage under X-ray fluorescence (XRF) mode; however, it is consistent with the duration of X-ray absorption spectroscopy (XAS) and microcomputed tomography (?CT) measurements. PMID:25186608

Moini, Mehdi; Rollman, Christopher M; Bertrand, Loïc

2014-10-01

314

Molecular-level mixed matrix membranes comprising Pebax {sup registered} and POSS for hydrogen purification via preferential CO{sub 2} removal  

Energy Technology Data Exchange (ETDEWEB)

The molecular-level mixed matrix membranes (MMMs) comprising Pebax {sup registered} and POSS have been developed by tuning the membrane preparation process in this work. They exhibit a simultaneous enhancement in CO{sub 2} permeability and CO{sub 2}/H{sub 2} selectivity by optimizing the POSS content at extremely low loadings. This is mainly attributed to the large cavity of POSS itself and its effect on the segmental-level polymeric chain packing. More interestingly, the Pebax {sup registered} /POSS MMMs reveal a much higher separation performance in the mixed gas test than that in the pure gas test. The highest CO{sub 2}/H{sub 2} selectivity reaches 52.3 accompanied by CO{sub 2} permeability of 136 Barrer at 8 atm and 35 C. This is due to the CO{sub 2}-induced plasticization that improves the free volume and polymer chain mobility, hence benefiting the interaction between the polymer matrix and penetrant CO{sub 2}. These features may ensure the superiority of Pebax {sup registered} /POSS molecular-level MMMs as CO{sub 2}-selective membranes in the industrial application of hydrogen purification. (author)

Li, Yi; Chung, Tai-Shung [Department of Chemical and Biomolecular Engineering, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260 (Singapore)

2010-10-15

315

Inelastic Neutron Scattering and Separation Coefficient of Absorbed Hydrogen : Molecular Alignment and Energy Levels  

DEFF Research Database (Denmark)

Inelastic neutron scattering and measurement of the ortho-para separation coefficient have been used to study the low lying rotational states of molecular hydrogen adsorbed on activated alumina. The observations are consistent with a picture in which the orientational motion of the molecules is severely hindered. Results are analyzed in terms of two models: a two-dimensional rotor and an axially constrained rotor. The latter which is more consistent with the data serves to explain preferential adsorption of orthohydrogen.

Nielsen, Mourits

1976-01-01

316

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

Energy Technology Data Exchange (ETDEWEB)

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.

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

317

Evolution of the C4 photosynthetic pathway: events at the cellular and molecular levels.  

Science.gov (United States)

The biochemistry and leaf anatomy of plants using C4 photosynthesis promote the concentration of atmospheric CO2 in leaf tissue that leads to improvements in growth and yield of C4 plants over C3 species in hot, dry, high light, and/or saline environments. C4 plants like maize and sugarcane are significant food, fodder, and bioenergy crops. The C4 photosynthetic pathway is an excellent example of convergent evolution, having evolved in multiple independent lineages of land plants from ancestors employing C3 photosynthesis. In addition to C3 and C4 species, some plant lineages contain closely related C3-C4 intermediate species that demonstrate leaf anatomical, biochemical, and physiological characteristics between those of C3 plants and species using C4 photosynthesis. These groups of plants have been extremely useful in dissecting the modifications to leaf anatomy and molecular biology, which led to the evolution of C4 photosynthesis. It is now clear that great variation exists in C4 leaf anatomy, and diverse molecular mechanisms underlie C4 biochemistry and physiology. However, all these different paths have led to the same destination-the expression of a C4 CO2 concentrating mechanism. Further identification of C4 leaf anatomical traits and molecular biological components, and understanding how they are controlled and assembled will not only allow for additional insights into evolutionary convergence, but also contribute to sustainable food and bioenergy production strategies. PMID:23708978

Ludwig, Martha

2013-11-01

318

Benchmarking energy use in the paper industry: a benchmarking study on process unit level  

Energy Technology Data Exchange (ETDEWEB)

There are large differences between paper mills in, e.g. feedstock use and grades produced, but typical processes are similar in all mills. The aim of this study is to benchmark the specific energy consumption (SEC) of similar processes within different paper mills in order to identify energy improvement potentials at process level. We have defined improvement potentials as measures that can be taken at mill/process level under assumed fixed inputs and outputs. We were able to use industrial data on detailed process level, and we conducted energy benchmarking comparisons in 23 Dutch paper mills. We calculated average SECs per process step for different paper grades, and we were able to identify ranges in SECs between mills producing the same grade. We found significant opportunities for energy efficiency improvement in the wire and press section as well as in the drying section. The total energy improvement potential based on identified best practices in these sections was estimated at 5.4 PJ (or 15 % of the total primary energy use in the selected mills). Energy use in the other processes was found to be too dependent on quality and product specifications to be able to quantify improvement potentials. Our results emphasise that even a benchmark on detailed process level does not lead to clear estimations of energy improvement potentials without accounting for structural effects and without having a decent understanding of the process.

Laurijssen, J. [Centre of Competence Paper and Board, IJsselburcht 3, 6825 BS Arnhem (Netherlands); Faaij, A.; Worrell, E. [Copernicus Institute, Utrecht University, Van Unnikgebouw, Heidelberglaan 2, 3584 CS Utrecht (Netherlands)

2013-02-15

319

The level of knowledge about the planning of training process of males engaged in recreational fitness.  

Directory of Open Access Journals (Sweden)

Full Text Available The aim of the study was to determine the level of knowledge about the planning of training process of males engaged in recreational fitness. The main method of investigation was questioning. The study involved 100 males aged 16-47 years engaged in fitness in three fitness centers in Gdansk and Sopot. The general level of knowledge of the planning of training process and its relationship with age and training experience was revealed.

Jagiello, Wladyslaw

2011-08-01

320

Higher levels of depression are associated with reduced global bias in visual processing.  

Science.gov (United States)

Negative moods have been associated with a tendency to prioritise local details in visual processing. The current study investigated the relation between depression and visual processing using the Navon task, a standard task of local and global processing. In the Navon task, global stimuli are presented that are made up of many local parts, and the participants are instructed to report the identity of either a global or a local target shape. Participants with a low self-reported level of depression showed evidence of the expected global processing bias, and were significantly faster at responding to the global, compared with the local level. By contrast, no such difference was observed in participants with high levels of depression. The reduction of the global bias associated with high levels of depression was only observed in the overall speed of responses to global (versus local) targets, and not in the level of interference produced by the global (versus local) distractors. These results are in line with recent findings of a dissociation between local/global processing bias and interference from local/global distractors, and support the claim that depression is associated with a reduction in the tendency to prioritise global-level processing. PMID:24067089

de Fockert, Jan W; Cooper, Andrew

2014-04-01

 
 
 
 
321

Immunohistochemistry of tissue prepared by a molecular-friendly fixation and processing system.  

Science.gov (United States)

A recently introduced histologic fixative (Universal Molecular Fixative [UMFIX]) has been shown to preserve macromolecules in tissue at ambient temperature. When UMFIX-exposed tissues are processed by a formalin-free, microwave-assisted rapid processing system, the resulting paraffin blocks retain good histomorphology and intact nucleic acids suitable for expression microarray analysis. Because UMFIX may be used as an alternative to formalin, the authors set out to study the effect of this new fixation and processing system on immunohistochemistry (IHC) by analyzing a range of human neoplastic and non-neoplastic specimens. Parallel slices from surgically removed specimens were fixed in formalin and UMFIX and processed in a rapid microwave-assisted tissue processor. IHC was performed following routine procedures. The staining for those antibodies that normally required antigen retrieval was carried out with and without that step. The intensity and pattern of reactions were compared in 144 tissue samples fixed by the two methods using 70 monoclonal and polyclonal antibodies. The intensity of IHC reactions for most cytoplasmic antigens was generally equal or stronger in UMFIX tissues. This was particularly true with intermediate filaments and HercepTest, where the antigen retrieval step became unnecessary. Conversely, there was a decrease in the intensity of reactions for HepPar1, bcl-2, and three nuclear antigens (Ki-67, TTF-1, and estrogen receptor). Increasing their exposure times optimized the sensitivity of the latter four antibodies. The study shows that IHC staining results of tissues fixed in UMFIX and processed by the microwave-assisted system are comparable to those obtained on formalin-fixed, similarly processed specimens. There is an enhancement of the sensitivity of few antibodies in UMFIX-exposed tissue, rendering antigen retrieval unnecessary. This increased sensitivity may be due to the effect of eliminating formalin from fixation and processing or the microwave energy. PMID:16082256

Nadji, M; Nassiri, M; Vincek, V; Kanhoush, R; Morales, A R

2005-09-01

322

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

International Nuclear Information System (INIS)

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.)

323

Impact assessment of cadmium contamination on rice (Oryza sativa L.) seedlings at molecular and population levels using multiple biomarkers  

International Nuclear Information System (INIS)

Full text: Assessment of environmental contamination on ecology (plant) at molecular and population levels is important in risk quantification and remediation study. Random amplified polymorphic DNA (RAPD) assay and related other fingerprinting techniques have been employed to detect the genotoxin-induced DNA damage and mutations. This research compared the effects occurring at molecular and population levels in rice seedlings exposed to cadmium (Cd) concentrations of 15 - 60 mg L-1 for eight days with quartz sand culture. Inhibition of root growth and increase of total soluble protein content in root tips of rice seedlings were observed with the increase of Cd concentration. For the RAPD analyzes, 12 RAPD primers of 50 - 70 % GC content were found to produce unique polymorphic band patterns and subsequently were used to produce a total of 180 bands of 179 ? 3056 bp in molecular size in the control root tips of rice seedlings. Results produced by these RAPD primers indicate that changes in RAPD profiles of root tips after Cd treatment include modifications in band intensity and gain or loss of bands by comparison with control. The effect of changes was dose-dependent. Genomic template stability compares favourably with the traditional indices such as root growth and soluble protein content. The DNA polymorphisms detected by RAPD analysis can be applied as a suitable biomarker assay for the detection of genotoxic effects of Cd contamination on plants. (autects of Cd contamination on plants. (author)

324

RECENT PROCESS AND EQUIPMENT IMPROVEMENTS TO INCREASE HIGH LEVEL WASTE THROUGHPUT AT THE DEFENSE WASTE PROCESSING FACILITY (DWPF)  

International Nuclear Information System (INIS)

The Savannah River Site's (SRS) Defense Waste Processing Facility (DWPF), the world's largest operating high level waste (HLW) vitrification plant, began stabilizing about 35 million gallons of SRS liquid radioactive waste by-product in 1996. The DWPF has since filled over 2000 canisters with about 4000 pounds of radioactive glass in each canister. In the past few years there have been several process and equipment improvements at the DWPF to increase the rate at which the waste can be stabilized. These improvements have either directly increased waste processing rates or have desensitized the process and therefore minimized process upsets and thus downtime. These improvements, which include glass former optimization, increased waste loading of the glass, the melter glass pump, the melter heated bellows liner, and glass surge protection software, will be discussed in this paper

325

CEA ATALANTE facility: Initial experiments in high-level process (CBP) and analysis (CBA) shielded lines  

International Nuclear Information System (INIS)

The two newest facilities in the Atalante complex, a high-level shielded process line (CBP) and high-level shielded analysis line (CBA), are described and their work programs detailed, notably the dissolution in CBP of 16 kg of spent fuel to demonstrate the technological feasibility of partitioning the minor actinides. The analytical support role of CBA is also discussed. (author)

326

Reading Leveled Books in Assessment-Saturated Classrooms: A Close Examination of Unmarked Processes of Assessment  

Science.gov (United States)

This article examines the reading of leveled books and the assessment of students' reading levels in a public school classroom. The purpose of the research study was to examine how these processes of assessment, which often go unnoticed, shaped the ways reading and readers were defined. The research was located in a third grade, public school…

Kontovourki, Stavroula

2012-01-01

327

Primary Process Thinking in the Same Children at Two Developmental Levels  

Science.gov (United States)

Analysis of primary process thinking of the same children at kindergarten level and at grade four revealed that amount of primary process thinking was relatively constant with development, contrary to predictions based on psychoanalytic theory. However, drive related ideation increased and formal deviations of thought decreased in quality and type…

Rivard, Eliane; Dudek, Stephanie Z.

1977-01-01

328

Assessment of Level of Implementation of the Essential Elements of the IST Process.  

Science.gov (United States)

This instrument is designed to help school administrators assess the level of implementation of the essential elements of the Instructional Support Teams (IST) process in Pennsylvania. The instrument is a rating sheet, or checklist, on which the presence and absence of components of the IST process are noted. The number of features in place is…

Kovaleski, Joseph F.

329

The Influence of Levels of Processing on Recall from Working Memory and Delayed Recall Tasks  

Science.gov (United States)

Recent research in working memory has highlighted the similarities involved in retrieval from complex span tasks and episodic memory tasks, suggesting that these tasks are influenced by similar memory processes. In the present article, the authors manipulated the level of processing engaged when studying to-be-remembered words during a reading…

Loaiza, Vanessa M.; McCabe, David P.; Youngblood, Jessie L.; Rose, Nathan S.; Myerson, Joel

2011-01-01

330

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

Energy Technology Data Exchange (ETDEWEB)

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.

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

1981-10-01

331

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

Energy Technology Data Exchange (ETDEWEB)

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

Nguyen, Trung D [ORNL; Fuentes-Cabrera, Miguel A [ORNL; Fowlkes, Jason Davidson [ORNL; Rack, Philip D [ORNL

2014-01-01

332

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

Science.gov (United States)

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 ?-helix in the second structure. The changes generated by propanol were much larger than those by methanol and ethanol.

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

2011-09-01

333

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

Energy Technology Data Exchange (ETDEWEB)

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.

Grantham, L.F.; McKisson, R.L.; Guon, J.; Flintoff, J.F.; McKenzie, D.E.

1983-02-25

334

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

International Nuclear Information System (INIS)

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

335

Nonlinear microrheology reveals entanglement-driven molecular-level viscoelasticity of concentrated DNA.  

Science.gov (United States)

We optically drive a trapped microscale probe through entangled DNA at rates up to 100× the disentanglement rate (Wi?100), then remove the trap and track subsequent probe recoil motion. We identify a unique crossover to the nonlinear regime at Wi?20. Recoil dynamics display rate-dependent dilation and complex power-law healing of the reptation tube. The force response during strain exhibits key nonlinear features such as shear thinning and yielding with power-law rate dependence. Our results, distinctly nonclassical and in accord with recent theoretical predictions, reveal molecular dynamics governed by individual stress-dependent entanglements rather than chain stretching. PMID:25216012

Chapman, Cole D; Robertson-Anderson, Rae M

2014-08-29

336

Nonlinear Microrheology Reveals Entanglement-Driven Molecular-Level Viscoelasticity of Concentrated DNA  

Science.gov (United States)

We optically drive a trapped microscale probe through entangled DNA at rates up to 100× the disentanglement rate (Wi ?100), then remove the trap and track subsequent probe recoil motion. We identify a unique crossover to the nonlinear regime at Wi ?20. Recoil dynamics display rate-dependent dilation and complex power-law healing of the reptation tube. The force response during strain exhibits key nonlinear features such as shear thinning and yielding with power-law rate dependence. Our results, distinctly nonclassical and in accord with recent theoretical predictions, reveal molecular dynamics governed by individual stress-dependent entanglements rather than chain stretching.

Chapman, Cole D.; Robertson-Anderson, Rae M.

2014-08-01

337

Molecular-level mechanisms of nanoparticle detachment in laser-induced plasma shock waves  

International Nuclear Information System (INIS)

Detachment and detachment mechanisms of nanoparticles from flat surfaces subjected to shock waves are investigated by employing molecular gas dynamic simulations using the direct simulation Monte Carlo method and experimental transient pressure data. Two mechanisms for nanoparticle detachment based on rolling moment resistance of the adhesion bond and the elastic restitution effect are introduced. As a result of present simulations, it is computationally demonstrated that the pulsed laser-induced shock waves can generate sufficient rolling moments to detach sub-100-nm particles and initiate removal. The transient moment exerted on a 60 nm polystyrene latex particle on a silicon substrate is presented and discussed

338

Field-dependent magnetic parameters in {Ni4Mo12}: Magnetostriction at the molecular level?  

CERN Document Server

We investigate the bulk magnetic, electron paramagnetic resonance, and magneto-optical properties of {Ni4Mo12}, a magnetic molecule with antiferromagnetically coupled tetrahedral {Ni4Mo12} in a diamagnetic molybdenum matrix. The low-temperature magnetization exhibits steps at irregular field intervals, a result that cannot be explained using a Heisenberg model even if it is augmented by magnetic anisotropy and biquadratic terms. Allowing the exchange and anisotropy parameters to depend on the magnetic field provides the best fit to our data, suggesting that the molecular structure (and thus the interactions between spins) may be changing with applied magnetic field.

Schnack, J; Luban, M; Koegerler, P; Morosan, E; Fuchs, R; Modler, R; Nojiri, H; Rai, R C; Cao, J; Musfeldt, J L; Xing Wei; Nojiri, Hiroyuki; Rai, Ram C.; Cao, Jinbo

2006-01-01

339

ARTICLE Molecular Dynamic Simulation on the Absorbing Process of Isolating and Coating of ?-olefin Drag Reducing Polymer  

Science.gov (United States)

The absorbing process in isolating and coating process of ?-olefin drag reducing polymer was studied by molecular dynamic simulation method, on basis of coating theory of ?-olefin drag reducing polymer particles with polyurethane as coating material. The distributions of sodium laurate, sodium dodecyl sulfate, and sodium dodecyl benzene sulfonate on the surface of ?-olefin drag reducing polymer particles were almost the same, but the bending degrees of them were obviously different. The bending degree of SLA molecules was greater than those of the other two surfactant molecules. Simulation results of absorbing and accumulating structure showed that, though hydrophobic properties of surfactant molecules were almost the same, water density around long chain sulfonate sodium was bigger than that around alkyl sulfate sodium. This property goes against useful absorbing and accumulating on the surface of ?-olefin drag reducing polymer particles; simulation results of interactions of different surfactant and multiple hydroxyl compounds on surface of particles showed that, interactions of different surfactant and one kind of multiple hydroxyl compound were similar to those of one kind of surfactant and different multiple hydroxyl compounds. These two contrast types of interactions also exhibited the differences of absorbing distribution and closing degrees to surface of particles. The sequence of closing degrees was derived from simulation; control step of addition polymerization interaction in coating process was absorbing mass transfer process, so the more closed to surface of particle the multiple hydroxyl compounds were, the easier interactions with isocyanate were. Simulation results represented the compatibility relationship between surfactant and multiple hydroxyl compounds. The isolating and coating processes of ?-olefin drag reducing polymer were further understood on molecule and atom level through above simulation research, and based on the simulation, a referenced theoretical basis was provided for practical optimal selection and experimental preparation of ?-olefin drag reducing polymer particles suspension isolation agent.

Li, Bing; Sheng, Xiang; Xing, Wen-guo; Dong, Gui-lin; Liu, Yong-jun; Zhang, Chang-qiao; Chen, Xiang-jun; Zhou, Ning-ning; Qin, Zhan-bo

2010-12-01

340

Influence of molecular processes on the hydrogen atomic system in an expanding argon--hydrogen plasma  

International Nuclear Information System (INIS)

An expanding thermal arc plasma in argon--hydrogen is investigated by means of emission spectroscopy. The hydrogen can be added to the argon flow before it enters the thermal arc plasma source, or it can be flushed directly into the vacuum expansion vessel (1--20 vol % H2). The atomic state distribution function for hydrogen, measured at a downstream distance of 20 mm, turns out to be very different in the two cases. For injection in the arc, three-particle recombination is a primary source of hydrogen excitation, whereas measurements with hydrogen injected into the vessel clearly point to a molecular channel (dissociative recombination of formed ArH+) populating atomic hydrogen levels. copyright 1995 American Institute of Physics

 
 
 
 
341

Molecular dynamic simulation of dicarboxylic acid coated aqueous aerosol: structure and processing of water vapor.  

Science.gov (United States)

Organic monolayers at the surfaces of aqueous aerosols play an important role in determining the mass, heat transfer rate and surface reactivity of atmospheric aerosols. They can potentially contribute to the formation of cloud condensation nuclei (CCN) and are involved in a series of chemical reactions occurring in atmosphere. Recent studies even suggest that organic-coated interfaces could have played some role in prebiotic biochemistry and the origin of life. However, creating reproducible, well-characterized aqueous aerosol particles coated with organic films is an experimental challenge. This opens the opportunity for computer simulations and modeling of these complex structures. In this work, molecular dynamics simulation was used to probe the structure and the interfacial properties of the dicarboxylic acid coated aqueous aerosol. Low molecular weight dicarboxylic acids of various chain lengths and water solubility were chosen to coat a water droplet consisting of 2440 water molecules. For malonic acid coated aerosol, the surface acid molecules dissolved into the water core and formed an ordered structure due to the hydrophobic interactions. The acid and the water are separated inside the aerosol. For other nanoaerosols coated with low solubility acids, phase separation between water and acid molecules was observed on the surface of the particle. To study the water processing of the coated aerosols, the water vapor accommodation factors were calculated. PMID:21479309

Ma, Xiaofei; Chakraborty, Purnendu; Henz, Brian J; Zachariah, Michael R

2011-05-28

342

A sulfuric-lactic acid process for efficient purification of fungal chitosan with intact molecular weight.  

Science.gov (United States)

The most recent method of fungal chitosan purification, i.e., two steps of dilute sulfuric acid treatment, pretreatment of cell wall at room temperature for phosphate removal and extraction of chitosan from the phosphate free cell wall at high temperature, significantly reduces the chitosan molecular weight. This study was aimed at improvement of this method. In the pretreatment step, to choose the best conditions, cell wall of Rhizopus oryzae, containing 9% phosphate, 10% glucosamine, and 21% N-acetyl glucosamine, was treated with sulfuric, lactic, acetic, nitric, or hydrochloric acid, at room temperature. Sulfuric acid showed the best performance in phosphate removal (90%) and cell wall recovery (89%). To avoid depolymerisation of chitosan, hot sulfuric acid extraction was replaced with lactic acid treatment at room temperature, and a pure fungal chitosan was obtained (0.12 g/g cell wall). Similar pretreatment and extraction processes were conducted on pure shrimp chitosan and resulted in a chitosan recovery of higher than 87% while the reduction of chitosan viscosity was less than 15%. Therefore, the sulfuric-lactic acid method purified the fungal chitosan without significant molecular weight manipulation. PMID:24211428

Naghdi, Mitra; Zamani, Akram; Karimi, Keikhosro

2014-02-01

343

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

Energy Technology Data Exchange (ETDEWEB)

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.

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

1996-08-01

344

Characterization of deep acceptor level in as-grown ZnO thin film by molecular beam epitaxy  

Science.gov (United States)

We report deep level transient spectroscopy results from ZnO layers grown on silicon by molecular beam epitaxy (MBE). The hot probe measurements reveal mixed conductivity in the as-grown ZnO layers, and the current—voltage (I—V) measurements demonstrate a good quality p-type Schottky device. A new deep acceptor level is observed in the ZnO layer having activation energy of 0.49 ±0.03 eV and capture cross-section of 8.57 × 10-18 cm2. Based on the results from Raman spectroscopy, photoluminescence, and secondary ion mass spectroscopy (SIMS) of the ZnO layer, the observed acceptor trap level is tentatively attributed to a nitrogen-zinc vacancy complex in ZnO.

Asghar, M.; K., Mahmood; A. Hasan, M.; T. Ferguson, I.; Tsu, R.; Willander, M.

2014-09-01

345

Cilnidipine regulates glucose metabolism and levels of high-molecular adiponectin in diet-induced obese mice.  

Science.gov (United States)

The aim of the present study is to examine the effects of the antihypertensive drug cilnidipine on glucose metabolism and adipocytokines, including adiponectin, in diet-induced obese (DIO) mice. The effects of cilnidipine on insulin sensitivity and the levels of adiponectin in DIO mice were examined after the mice had been treated with cilnidipine dissolved in water at a dose of 0.2?g?l(-1) for 14 days. As expected, treatment with cilnidipine decreased the systolic and diastolic blood pressures in DIO mice, compared with control mice (PCilnidipine treatment improved glucose and insulin sensitivity in DIO mice. In addition, cilnidipine treatment dramatically increased the level of adiponectin in white adipose tissue (Pcilnidipine treatment. Finally, the secretion of adiponectin from adipocytes was increased after cilnidipine treatment. Taken together, these results indicate that cilnidipine improves insulin tolerance and adiponectin levels, especially high-molecular type adiponectin, in DIO mice. PMID:23051658

Ueno, Daisuke; Masaki, Takayuki; Gotoh, Koto; Chiba, Seiichi; Kakuma, Tetsuya; Yoshimatsu, Hironobu

2013-03-01

346

Outdoor thoron progeny levels in the environment of a thorium processing facility  

International Nuclear Information System (INIS)

Measurements of outdoor concentrations of thoron progeny in environment of a thorium compounds processing facility is presented. The geometric mean concentration of thoron progeny in the immediate vicinity of the plant is 32 mWL and at 100 metres away (western side) from the plant the concentration reduces to 8 mWL. The gaseous discharge through stacks is not significantly altering the environmental concentration of thoron progeny whereas the concentration is mostly due to storage of thorium hydroxide and other solid waste sources at the site including open trenches. The outdoor thoron progeny levels observed at 500 m northwestern side of the plant (residential area) are comparable to the natural background levels in the area and no significant enhancement attributable to thorium compounds processing facility is observed in the environment. The environmental levels of thoron progeny observed during monazite processing operations and thorium concentrate processing are comparable. (author)

347

Application of the activation process model to the molecules, positive molecular ions, clusters, and proteins surrounded of IR laser radiation  

Science.gov (United States)

In 1990 the activation process model was proposed [1]. Development of the activation process model [2,3] led to description of either adiabatic or non-adiabatic processes for a molecular structure transformation [4]. The model is based on two simple assumptions: 1. During the transformation process, the potential energy of a molecular particle changes discretely or in quanta: the transformation process appears to be a series of quantum subsystems occurring in sequence (these subsystems may also be defined as identical quantum oscillators); 2. In the field of IR-laser radiation, an energy exchange between IR radiation and atoms of the molecular particle results in discrete translation of these atoms which absorb oscillation energy by identical quanta up to molecular structure complete transformation. The numerical simulation carried out according to the model offered has allowed to describe such processes as: dissociation of SF6 molecule [4] and styrene ion C 8H 8 + [5]; selfdiffusion processes in Si, Ge and GaAs clusters [6]; folding and insertion for the ?-barrel outer membrane protein A (OmpA) of Escherichia coli into dioleoylphosphatidylcholine (DOPC) bilayers [7]. So, we can see this model has a significant field of application to the activation processes stimulated by IR laser radiation.

Stepanov, Anatoly V.

2007-06-01

348

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

Science.gov (United States)

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.

Dhas, M. Kumara; Jawahar, A.; Benial, A. Milton Franklin

2014-04-01

349

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

International Nuclear Information System (INIS)

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

350

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

Energy Technology Data Exchange (ETDEWEB)

The Electron spin resonance studies on the reduction process of nitroxyl spin probes were carried out for 1mM {sup 14}N 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 {sup 14}N 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.

Dhas, M. Kumara; Benial, A. Milton Franklin, E-mail: miltonfranklin@yahoo.com [Department of Physics, NMSSVN College, Nagamalai, Madurai-625019, Tamilnadu (India); Jawahar, A. [Department of Chemistry, NMSSVN College, Nagamalai, Madurai-625019, Tamilnadu (India)

2014-04-24

351

Molecular dynamics simulations of atomic assembly in the process of GaN film growth  

International Nuclear Information System (INIS)

Molecular dynamics simulations using a Coulomb-Buckingham potential have been used to investigate the process of wurtzite GaN films growth, including the appearance of films in early stage, regulation of growth, structure of the surface and the dynamic features. The simulations show that the N atoms and Ga atoms are absorbed on the lattice of substrate and take on a distinct sandwich structure. Time evolution of the mean square displacements and diffusion coefficient of the deposited atoms are observed, the results show that the clusters will become stable with the increase of time steps and the atoms reach the initial stable state after 25 ps; N atoms reach the equilibrium positions more quickly than Ga atoms. It is proved by radial distribution function and the ratio of vacancy of every deposited layer that the crystalline characters of the films will become better as the time steps increase and weaker from bottom to top.

352

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

Science.gov (United States)

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.

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

2008-07-01

353

Mapping Variable Ring Polymer Molecular Dynamics: A Path-Integral Based Method for Nonadiabatic Processes  

CERN Document Server

We introduce mapping-variable ring polymer molecular dynamics (MV-RPMD), a model dynamics for the direct simulation of multi-electron processes. An extension of the RPMD idea, this method is based on an exact, imaginary time path-integral representation of the quantum Boltzmann operator using continuous Cartesian variables for both electronic states and nuclear degrees of freedom. We demonstrate the accuracy of the MV-RPMD approach in calculations of real-time, thermal correlation functions for a range of two-state single-mode model systems with different coupling strengths and asymmetries. Further, we show that the ensemble of classical trajectories employed in these simulations preserves the Boltzmann distribution and provides a direct probe into real-time coupling between electronic state transitions and nuclear dynamics.

Ananth, Nandini

2013-01-01

354

Level scheme of /sup 148/Pm and the s-process neutron density  

International Nuclear Information System (INIS)

A level scheme of /sup 148/Pm up to 800 keV is deduced from gamma-ray coincidence data and published particle transfer data. Approximately 106 gamma-ray transitions have been placed between 36 levels. We have identified three levels below 500 keV in excitation which decay to both the ground state and to the isomeric level at 137 keV. The presence of these levels guarantees that /sup 148/Pm/sup g//sup ,//sup m/ are in thermal equilibrium during the s process. The s-process neutron density inferred from the branch point at /sup 148/Pm is deduced to be 3 x 108/cm3

355

Molecular Dynamics Simulations of the Roller Nanoimprint Process: Adhesion and Other Mechanical Characteristics  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Molecular dynamics simulations using tight-binding many body potential are carried out to study the roller imprint process of a gold single crystal. The effect of the roller tooth’s taper angle, imprint depth, imprint temperature, and imprint direction on the imprint force, adhesion, stress distribution, and strain are investigated. A two-stage roller imprint process was obtained from an imprint force curve. The two-stage imprint process included the imprint forming with a rapid increase of imprint force and the unloading stage combined with the adhesion stage. The results show that the imprint force and adhesion rapidly increase with decreasing taper angle and increasing imprint depth. The magnitude of the maximum imprint force and the time at which this maximum occurs are proportional to the imprint depth, but independent of the taper angle. In a comparison of the imprint mechanisms with a vertical imprint case, while high stress and strain regions are concentrated below the mold for vertical imprint, they also occur around the mold in the case of roller imprint. The regions were only concentrated on the substrate atoms underneath the mold in vertical imprint. Plastic flow increased with increasing imprint temperature.

Fang Te-Hua

2009-01-01

356

Planarization process of single crystalline silicon asperity under abrasive rolling effect studied by molecular dynamics simulation  

Energy Technology Data Exchange (ETDEWEB)

In the chemical mechanical polishing (CMP) process, the complex behaviors of abrasive particles play important roles in the planarization of wafer surface. Particles embedded in the pad remove materials by ploughing, while particles immersed in the slurry by rolling across the wafer surface. In this paper, processes of the particle rolling across a silicon surface with an asperity under various down forces and external driving forces were studied using molecular dynamics (MD) simulation method. The simulations clarified the asperity shape evolution during the rolling process and analyzed the energy changes of the simulation system and the interaction forces acted on the silica particle. It was shown that both the down force and the driving force had important influences on the amount of the material removed. With relatively small down forces and driving forces applied on the particle, the material removal occurred mainly in the front end of the asperity; when the down forces and driving forces were large enough, e.g., 100 nN, the material removal could take place at the whole top part of the asperity. The analysis of energy changes and interaction forces provided favorable explanations to the simulation results. (orig.)

Si, Lina [Tsinghua University, State Key Laboratory of Tribology, Beijing (China); Beijing Institute of Technology, School of Mechanical Engineering, Beijing (China); Guo, Dan; Luo, Jianbin; Xie, Guoxin [Tsinghua University, State Key Laboratory of Tribology, Beijing (China)

2012-10-15

357

Study of crater formation and sputtering process with large gas cluster impact by molecular dynamics simulations  

International Nuclear Information System (INIS)

Molecular dynamics (MD) simulations of large argon clusters impacting on silicon solid targets were performed in order to study the transient process of crater formation and sputtering. The MD simulations demonstrate that the initial momentum of incident cluster is transferred to target surface atoms through multiple collision mechanism, where the initial momentum, which is along to the surface normal before impact, is deflected to lateral direction. This momentum transfer process was analyzed by the calculation of the velocity at the crater edge (the interface between cluster and target). In the case of Ar1000 cluster impact on Si(1 0 0) target at low energy per atom less than 40 eV/atom, the maximum value of lateral velocity of the crater edge increases in proportional to the velocity of incident cluster atoms. On the other hand, the crater edge velocity saturates over 40 eV/atom of incident energy per atom. In this case, the whole of constituent cluster atoms are implanted into the target and expand in both lateral and reflective directions at the subsurface region of the target. These MD simulations demonstrated that this collisional process result in the high yield sputtering of the target atoms.

358

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

International Nuclear Information System (INIS)

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. ? ? ? 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 simulationstained 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 ?=0.1 and 1, over several orders of magnitude. The only difference seen at ? = 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.

359

Interfacial electrostatics of self-assembled monolayers of alkane thiolates on Au(111): work function modification and molecular level alignments.  

Science.gov (United States)

We have isolated at T dimethyl disulfide (DMDS) layer on Au(111) and studied how the vibrational states, S core hole level shifts, valence band photoemission, and work function measurements evolve upon transforming this system into chemisorbed methylthiolate (MT) self-assembled monolayers (SAM) by heating above 200 K. By combining these observations with detailed theoretical electronic structure simulations, at the density functional level, we have been able to obtain a detailed picture of the electronic interactions at the interface between Au and adsorbed thiolates and disulfides. All of our measurements may be interpreted with a simple model where MT is bound to the Au surface with negligible charge transfer. Interfacial dipoles arising from Pauli repulsion between molecule and metal surface electrons are present for the weakly adsorbed DMDS layer but not for the chemisorbed species. Instead, for the chemisorbed species, interfacial dipoles are exclusively controlled by the molecular dipole, its interaction with the dipoles on neighboring molecules, and its orientation to the surface. The ramifications of these results for alignment of molecular levels and interfacial properties of this class of materials are discussed. PMID:16771338

Rousseau, R; De Renzi, V; Mazzarello, R; Marchetto, D; Biagi, R; Scandolo, S; del Pennino, U

2006-06-01

360

The quest for probiotic effector molecules--unraveling strain specificity at the molecular level.  

Science.gov (United States)

Pharmaceutical agents are widely applied for the treatment of gastrointestinal (and systemic) disorders and their role as modulators of host cell responses is relatively well characterized. By contrast, we are only beginning to understand the molecular mechanisms by which health-promoting, probiotic bacteria act as host cell modulators. The last decade has seen a rapid development of the genomics field for the widely applied probiotic genus Lactobacillus, and nowadays dozens of full genome sequences are available, as well as sophisticated post genomic and genetic engineering tools. This development has enabled comparative (functional) genomics approaches to identify the bacterial effector molecules involved in molecular communication with the host system that may underlie the probiotic effects observed. These efforts can also be complemented with dedicated mutagenesis approaches to eliminate or alter these effector molecules, followed by assessment of the host interaction consequences thereof, allowing the elucidation of the molecular mechanisms involved in probiotic health effects. Many of these approaches have pinpointed that the Lactobacillus cell envelope contains several effector molecules that are pivotal in the direct signaling capacity of these bacteria that underlies their immunomodulatory effects, including lipoteichoic acid, peptidoglycan, and (glyco)proteins. Moreover, the cell envelope contains several compounds such as wall teichoic acid and capsular polysaccharides that may not be involved in direct signaling to the host cell, but still affect signaling through shielding of other bacterial effector molecules. Initial structural studies revealed subtle strain- and species-specific biochemical differences in the canonical cell envelope compounds that are involved in these host interactions. These biochemical variations include the degree and positioning of d-alanyl and glycosyl substitution in lipoteichoic acids, and acetylation of peptidoglycan. Furthermore, specific peptides derived from peptidoglycan and envelope associated (glyco)proteins were recently identified as potent immunomodulators. The latter findings are exciting in the light of the possibility of more pharmacological application of these bioactive probiotic molecules, and especially cost-effective production and targeted delivery of bioactive peptides seems to emerge as a feasible strategy to harness this knowledge. PMID:23059538

Lee, I-Chiao; Tomita, Satoru; Kleerebezem, Michiel; Bron, Peter A

2013-03-01

 
 
 
 
361

A flexible approach for early production of high-level waste glass: A process canister  

International Nuclear Information System (INIS)

A process canister, which has several advantages, is being considered for use at the West Valley Demonstration Project. The plan is to cast an acceptable high-level waste glass in process canisters. These canisters are low-cost molds which are suitable for casting the high-level waste glass in the production plant and for storing on-site. Before shipping to a federal repository, the processing canisters could be packaged in approved repository disposal canisters. This approach would allow the Project to fix the design of the process equipment and facility at an early stage while providing the flexibility of meeting disposal canister acceptance criteria that are not yet final. Due to the unique nature of the West Valley Demonstration Project, the process canisters appear to provide a simple, yet efficient, way for providing a waste package with uncontaminated exterior surfaces for interim storage before shipping to the repository

362

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

Energy Technology Data Exchange (ETDEWEB)

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.

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

2008-01-15

363

Stern layer formation induced by hydrophobic interactions: a molecular level study.  

Science.gov (United States)

The molecular ionic surface structure and charge of the electric double layer around a nanodroplet and its structural change induced by hydrophobic effects are measured using vibrational coherent surface scattering spectroscopy, second harmonic scattering, and electrokinetic mobility measurements. Tetraalkylammonium chloride salts were added to negatively charged nanoscopic oil droplets in water. When we vary the alkyl chain length of the cation from CH3 to C4H10, both the size of the cation and its hydrophobic interaction are increased. We find that tetramethylammonium ions change the electrokinetic potential and the water structure but do not detectably adsorb to the interface. Tetrapropylammonium and tetrabutylammonium ions clearly adsorb to the interface. The corresponding (Stern) layer appears to be a mixed monolayer of anions and cations. An estimate of the amount of cations in the Stern layer is also made. PMID:24320786

Scheu, Rüdiger; Chen, Yixing; Subinya, Mireia; Roke, Sylvie

2013-12-26

364

Tannin signatures of barks, needles, leaves, cones, and wood at the molecular level  

Science.gov (United States)

We analyzed 117 tissues from 77 different plant species for molecular tannin. Tannin was measured in 89 tissues (as high as 10.5 wt.% total tannin), including procyanidin (PC) tannin in 88 tissues, prodelphinidin (PD) tannin in 50, and propelargonidin (PP) tannin in 24. In addition to tannin, several flavones, flavanones, and triterpenoids were measured, the latter which yielded as much as 4.5 wt.%. Compositions varied considerably between species, including several that yielded comparatively rare tannin or triterpenoids. Conifer needles were distinguished by high yields of PD tannin overall and relative to PC tannin. Dicotyledon leaves were characterized by the presence of flavones and triterpenoids. Barks were marked by flavanones and tetracosanoic acid. Based on these trends, relationships that could be useful as geochemical parameters were developed for distinguishing needles, leaves, and barks as possible components of litter, soil, or sedimentary mixtures.

Hernes, Peter J.; Hedges, John I.

2004-03-01

365

Effects of diacerein at the molecular level in the osteoarthritis disease process.  

Science.gov (United States)

In osteoarthritis (OA), the alterations in joint tissues are numerous and involve morphological, biochemical and metabolic changes and an upregulation of the inflammatory pathways. The focus of this article is a brief narrative review of the effects of diacerein, an antirheumatic drug from the anthraquinone chemical class, and its active metabolite, rhein, on the factors that participate in the complex interaction between OA tissues and cells leading to the progression of joint structural changes. PMID:22870441

Martel-Pelletier, Johanne; Pelletier, Jean-Pierre

2010-04-01

366

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

International Nuclear Information System (INIS)

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

367

Mercury reduction and removal during high-level radioactive waste processing and vitrification  

International Nuclear Information System (INIS)

A reference process for immobilizing the high-level radioactive waste in borosilicate glass has been developed at the Savannah River Plant. This waste contains a substantial amount of mercury from separations processing. Because mercury will not remain in borosilicate glass at the processing temperature, mercury must be removed before vitrification or must be handled in the off-gas system. A process has been developed to remove mercury by reduction with formic acid prior to vitrification. Additional benefits of formic acid treatment include improved sludge handling and glass melter redox control

368

Number representation is influenced by numerical processing level: an ERP study.  

Science.gov (United States)

The same numerical magnitude can be manifested in different physical notations. However, how the numbers with distinct notations are mentally represented is still unclear. Here, we hypothesized that how the number is mentally represented is influenced by the numerical processing level of the tasks. If the task only needed a low-level processing, the representation would be dependent on the surface forms of the numbers, exhibiting a numerical notation-dependent effect. By contrast, if the task required a deeper magnitude processing, the processing would utilize an abstract numerical format whose effects are notation independent. To test this hypothesis, we manipulated the notation type and the numerical processing level of the tasks. An ERP component N270 was taken to index the mismatch between the internal representation and the probed number. The results showed that N270 was enhanced when the magnitude was mismatched between two numbers. More importantly, under the task requiring a low-level processing (e.g., magnitude comparison), compared with the same notations, the latency of N270 difference wave was delayed by different notations, exhibiting a notation-dependent effect. However, in the task involving a deeper processing (e.g., magnitude addition), the N270 latencies were earlier for probes having distinct notations (Mandarin or Arabic number) than for probes having the same notations as in the addition operation (Mahjong). Moreover, no difference was found on N270 latencies between the two distinct notations but with similar degree of familiarity. Taken together, these results support our hypothesis that the numerical processing level affects the number representation. PMID:22252738

Liang, Junying; Yin, Jun; Chen, Tong; Chen, Hui; Ding, Xiaowei; Shen, Mowei

2012-04-01

369

Error Reduction in Molecular Tagging Velocimetry (MTV) Processing Using Image Filtering  

Science.gov (United States)

Prior work has shown that the error level in MTV measurements is closely tied to the image SN level. In practice the SN ratio will depend on experimental conditions such as attenuation, Field of View, laser power, camera, etc.; however, there is a minimum SN level that can be achieved for any given experiment. Experience has shown that MTV images typically have a SN=2-8. It is therefore desirable to be able to lower image noise after the images are acquired to reduce measurement error. In this work post processing MTV images using image filtering schemes such as Gaussian Blur, FFT (band pass), median filtering etc. was investigated using synthetic MTV images with added random noise. The synthetic images were filtered and then processed using a direct correlation technique. The results showed that for very noisy images (i.e. SN<4) the all filtering techniques improved the displacement error by 10-40%. As the SN increased filtering because less effective in decreasing error and in some cases increased the measurement error. The FFT band pass filter was most effective and improved measurement error for all SN levels.

Caso, Michael; Bohl, Douglas

2011-11-01

370

Molecular diversity and evolutionary processes of Alternaria solani in Brazil inferred using genealogical and coalescent approaches.  

Science.gov (United States)

Alternaria spp. form a heterogeneous group of saprophytic and plant-pathogenic fungi widespread in temperate and tropical regions. However, the relationship between evolutionary processes and genetic diversity with epidemics is unknown for several plant-pathogenic Alternaria spp. The interaction of Alternaria solani populations with potato and tomato plants is an interesting case study for addressing questions related to molecular evolution of an asexual fungus. Gene genealogies based on the coalescent process were used to infer evolutionary processes that shape the A. solani population. Sequences of the rDNA internal transcribed spacer (ITS) region and the genes which encode the allergenic protein alt a 1 (Alt a 1) and glyceraldehyde-3-phosphate dehydrogenase (Gpd) were used to estimate haplotype and nucleotide diversity as well as for the coalescent analyses. The highest number of parsimony informative sites (n = 14), nucleotide diversity (0.007), and the average number of nucleotide differences (3.20) were obtained for Alt a 1. Although the highest number of haplotypes (n = 7) was generated for ITS, haplotype diversity was the lowest (0.148) for this region. Recombination was not detected. Subdivision was inferred from populations associated with hosts but there was no evidence of geographic subdivision, and gene flow is occurring among subpopulations. In the analysis of the Alt a 1, balancing selection and population expansion or purifying selection could have occurred in A. solani subpopulations associated with potato and tomato plants, respectively. There is strong evidence that the subpopulation of A. solani that causes early blight in potato is genetically distinct from the subpopulation that causes early blight in tomato. The population of A. solani is clonal, and gene flow and mutation are the main evolutionary processes shaping its genetic structure. PMID:19453237

Lourenço, Valdir; Moya, Andrés; González-Candelas, Fernando; Carbone, Ignazio; Maffia, Luiz A; Mizubuti, Eduardo S G

2009-06-01

371

Algorithms of Two-Level Parallelization for DSMC of Unsteady Flows in Molecular Gasdynamics  

CERN Document Server

The general scheme of two-level parallelization (TLP) for direct simulation Monte Carlo of unsteady gas flows on shared memory multiprocessor computers has been described. The high efficient algorithm of parallel independent runs is used on the first level. The data parallelization is employed for the second one. Two versions of TLP algorithm are elaborated with static and dynamic load balancing. The method of dynamic processor reallocation is used for dynamic load balancing. Two gasdynamic unsteady problems were used to study speedup and efficiency of the algorithms. The conditions of efficient application field for the algorithms have been determined. %%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%

Bogdanov, A V; Grishin, I A; Khanlarov, G O; Lukianov, G A; Zakharov, V V; Bogdanov, Alexander V.; Bykov, Nick Yu.; Grishin, Igor A.; Khanlarov, Gregory O.; Lukianov, German A.; Zakharov, Vladimir V.

1999-01-01

372

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

International Nuclear Information System (INIS)

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

373

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

Energy Technology Data Exchange (ETDEWEB)

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.

Marra, J.E.; Bennett, W.M.; Elder, H.H.; Lee, E.D.; Marra, S.L.; Rutland, P.L.

1997-09-01

374

Donut-shaped chambers for analysis of biochemical processes at the cellular and subcellular levels.  

Science.gov (United States)

In order to study cell-cell variation with respect to enzymatic activity, individual live cell analysis should be complemented by measurement of single cell content in a biomimetic environment on a cellular scale arrangement. This is a challenging endeavor due to the small volume of a single cell, the low number of target molecules and cell motility. Micro-arrayed donut-shaped chambers (DSCs) of femtoliter (fL), picoliter (pL), and nanoliter (nL) volumes have been developed and produced for the analysis of biochemical reaction at the molecular, cellular and multicellular levels, respectively. DSCs are micro-arrayed, miniature vessels, in which each chamber acts as an individual isolated reaction compartment. Individual live cells can settle in the pL and nL DSCs, share the same space and be monitored under the microscope in a noninvasive, time-resolved manner. Following cell lysis and chamber sealing, invasive kinetic measurement based on cell content is achieved for the same individual cells. The fL chambers are used for the analysis of the same enzyme reaction at the molecular level. The various DSCs were used in this proof-of-principle work to analyze the reaction of intracellular esterase in both primary and cell line immune cell populations. These unique DSC arrays are easy to manufacture and offer an inexpensive and simple operating system for biochemical reaction measurement of numerous single cells used in various practical applications. PMID:24829933

Zurgil, N; Ravid-Hermesh, O; Shafran, Y; Howitz, S; Afrimzon, E; Sobolev, M; He, J; Shinar, E; Goldman-Levi, R; Deutsch, M

2014-07-01

375

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

Science.gov (United States)

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.

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

2013-03-01

376

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

International Nuclear Information System (INIS)

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.)

377

Endopolygalacturonases reveal molecular features for processivity pattern and tolerance towards acetylated pectin.  

Science.gov (United States)

Endopolygalacturonases (EndoPGs) hydrolyse the 1-4 linkages between two alpha-d-galacturonic acids (GalA) of the smooth homogalacturonan regions of pectin. GalA may be methyl-esterified on the carboxylic group and acetyl-esterified on the hydroxylic groups. EndoPG activity most often decreases with such increasing degree of substitution. In this paper, we used bioinformatics and molecular modelling technics to explain the tolerance profile at the molecular scale and processivity scheme of three endoPGs with respect to acetylated pectin substrate; the first two enzymes originate from Aspergillus niger (AnPGI and AnPGII) and the third from Fusarium moniliforme (FmPG). Partly acetylated and methylated homogalacturonan fragments in complex with the three PGs were successively modelled in silico. The amino acid residues involved in substrate binding were identified for each enzyme. Similarly, the docking pattern of the differently decorated oligomers in the catalytic groove was individually characterized for each enzyme. This work shows full agreement with our previous extensive mass spectrometry analysis of the hydrolytic products that established distinct tolerance profiles for the three endoPGs and earlier work that ascertained processivity, specifically for AnPGI. In our previous work, AnPGI was shown to be the most powerful enzyme among the three enzymes with an enhanced tolerance towards O2- and O3-acetylated substrates. We report here amino acids of AnPGI that are unique in binding the pectin backbone and that are identified as possibly crucial for its specificity, namely S191(An)(PGI)/D240(An)(PGI). Similarly, topologically equivalent residues in AnPGII and FmPG were identified that could impede such binding; S234(An)(PGII)/S91(An)(PGII) and S245(Fm)(PG)/V89(Fm)(PG). In addition, we report here, from normal mode analysis computed on AnPG1, a shear bending motion of 15 A of amplitude that fully accredits the processive action pattern for this enzyme, with D240(An)(PGI) and R96(An)(PGI) working as crampons to favour the sliding of the substrate. Conversely, the same method clearly evidences a hinge binding motion for AnPGII and FmPG that should only authorize one hydrolytic event per enzyme/substrate encounter. PMID:18852070

André-Leroux, G; Tessier, D; Bonnin, E

2009-01-01

378

The impact of environmental stress on male reproductive development in plants: biological processes and molecular mechanisms.  

Science.gov (United States)

In plants, male reproductive development is extremely sensitive to adverse climatic environments and (a)biotic stress. Upon exposure to stress, male gametophytic organs often show morphological, structural and metabolic alterations that typically lead to meiotic defects or premature spore abortion and male reproductive sterility. Depending on the type of stress involved (e.g. heat, cold, drought) and the duration of stress exposure, the underlying cellular defect is highly variable and either involves cytoskeletal alterations, tapetal irregularities, altered sugar utilization, aberrations in auxin metabolism, accumulation of reactive oxygen species (ROS; oxidative stress) or the ectopic induction of programmed cell death (PCD). In this review, we present the critically stress-sensitive stages of male sporogenesis (meiosis) and male gametogenesis (microspore development), and discuss the corresponding biological processes involved and the resulting alterations in male reproduction. In addition, this review also provides insights into the molecular and/or hormonal regulation of the environmental stress sensitivity of male reproduction and outlines putative interaction(s) between the different processes involved. PMID:23731015

De Storme, Nico; Geelen, Danny

2014-01-01

379

Proteomic characterization of cellular and molecular processes that enable the Nanoarchaeum equitans-Ignicoccus hospitalis relationship  

Energy Technology Data Exchange (ETDEWEB)

Nanoarchaeum equitans, the only cultured representative of the Nanoarchaeota, is dependent on direct physical contact with its host, the hyperthermophile Ignicoccus hospitalis. The molecular mechanisms that enable this relationship are unknown. Using whole-cell proteomics, differences in the relative abundance of >75% of predicted protein-coding genes from both Archaea were measured to identify the specific response of I. hospitalis to the presence of N. equitans on its surface. A purified N. equitans sample was also analyzed for evidence of interspecies protein transfer. The depth of cellular proteome coverage achieved here is amongst the highest reported for any organism. Based on changes in the proteome under the specific conditions of this study, I. hospitalis reacts to N. equitans by curtailing genetic information processing (replication, transcription) in lieu of intensifying its energetic, protein processing and cellular membrane functions. We found no evidence of significant Ignicoccus biosynthetic enzymes being transported to N. eq