WorldWideScience
 
 
1

Enhanced Mechanical Properties of Graphene/Copper Nanocomposites Using a Molecular-Level Mixing Process.  

UK PubMed Central (United Kingdom)

RGO flakes are homogeneously dispersed in a Cu matrix through a molecular-level mixing process. This novel fabrication process prevents the agglomeration of the RGO and enhances adhesion between the RGO and the Cu. The yield strength of the 2.5 vol% RGO/Cu nanocomposite is 1.8 times higher than that of pure Cu. The strengthening mechanism of the RGO is investigated by a double cantilever beam test using the graphene/Cu model structure.

Hwang J; Yoon T; Jin SH; Lee J; Kim TS; Hong SH; Jeon S

2013-08-01

2

Photodissociation processes in molecular beams  

International Nuclear Information System (INIS)

[en]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

1979-01-01

3

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”.

I. Digel; P. Kayser; G. M. Artmann

2008-01-01

4

Molecular networks and system-level properties.  

Science.gov (United States)

Molecular systems biology aims to describe the functions of complex biological processes through recursive integration of molecular analysis, modeling, simulation and theory. It focuses on networks that originate from interconnection of genes, proteins and metabolites whose dynamic interactions generate, as an emergent property of the system, the corresponding function. Although evolutionary optimized, intracellular biochemical parameters, such as the expression level of gene products or the affinity between two or more proteins, must have a permissible range that gives robustness against perturbations to the system. Using the yeast G(1)-to-S transition network as an example we show that sophisticated relations exist among network structure, emergent property and robustness. Different emergent properties are generated from the same network by changing the strength of its interactions, not only by altering expression level, but also through mono and multi-site phosphorylation/dephosphorylation. Besides, multi-site protein phosphorylation modules, widespread in cell cycle, may ensure robust and coherent timing of cell cycle transitions as it happens for the onset of DNA replication. In conclusion, the modulation of biological function/emergent property by modifying interaction strength provides an efficient, highly tunable device to regulate biological processes. Furthermore, the principles outlined herein may provide new insight to network analysis in drug discovery. PMID:19616593

Alberghina, Lilia; Hfer, Thomas; Vanoni, Marco

2009-07-17

5

Temperature- and pressure-dependent densities, self-diffusion coefficients, and phase behavior of monoacid saturated triacylglycerides: toward molecular-level insights into processing.  

UK PubMed Central (United Kingdom)

Using molecular-dynamics (MD) simulations the densities and self-diffusion coefficients of a range of liquid monoacid triacylglycerides (TAGs) have been studied as a function of temperature and, for the first time, pressure. While offset by their ambient properties, the response of the TAGs to temperature and pressure is qualitatively similar. Application of pressure was found to significantly increase densities and reduce diffusion of the TAG molecules, suggesting that it may have as much a role in processing and crystallizing TAGs as supercooling does. A solution of glycerol tripalmitate and glycerol trihexanoate was also studied, showing that application of pressure should lead to a significant decrease in the saturation point of the solution, which is an important consideration for processing TAGs. Different solid/liquid interfaces of glycerol tripalmitate have also been investigated. Although crystal growth could not be observed, dissolution of one interface was seen in the MD simulations. The results suggest that over moderate distances the melting of TAGs may be cooperative in nature, rather than involving dissolution of individual TAG molecules.

Greiner M; Reilly AM; Briesen H

2012-05-01

6

Molecular Simulation: Understanding Polymer Gels at the Molecular Level  

UK PubMed Central (United Kingdom)

It is shown how insight into fundamental atomistic processes in water-swollen poly(vinyl alcohol)can be obtained from molecular simulation. Molecular dynamics is used both to calculatequantitatively diffusion coefficients and to examine the qualitative concepts of different statesof water in such systems. While concentration-dependent diffusion coefficients are useful quantitiesin their own right, here they are also being used to validate the simulations. With confidencein the simulated dynamics established, the distribution of re-orientational correlationtimes of water molecules is calculated. It shows that, above the freezing point of water, there isonly a single, albeit broad, distribution of correlation times, whereas at 250 K the distributionbecomes bimodal. The concept of different dynamical states of water in this hydrogel, therefore,makes sense at low temperatures but not at room temperature or above. Moreover, contrary tothe purported picture of "free" and "bound" wa...

7

Occupation number dependence of molecular energy levels  

International Nuclear Information System (INIS)

The Roothaan expression for the energy of a closed-shell molecular system is generalized in order to apply to open shells. A continuous variation from 0 to 2 is supposed for each level's occupation number, extending to this range tbe correction due to the spurious repulsion appearing in the half-electron method. The characteristic equations of the X? method are applied to the energy expressions. The one level case is discussed in detail. Ionic and excited states of the 1,3 transbutadiene ? system are analyzed.

1977-01-01

8

Effect of molecular weight on polymer processability  

Energy Technology Data Exchange (ETDEWEB)

Differences in rheological behavior due to the polymer molecular weight and molecular weight distribution have been shown with the MPT. SBR polymers having high molecular weight fractions develop higher stress relaxation time values due to the higher degree of polymer entanglements. Tests conducted at increasing temperatures show the diminishing influence of the polymer entanglements upon stress relaxation time. EPDM polymers show stress relaxation time and head pressure behavior which correlates with mill processability. As anticipated, compounded stock of EPDM have broad molecular weight distribution has higher stress relaxation time values than EPDM compounds with narrow molecular weight distribution.

Karg, R.F.

1983-01-01

9

[Biochemistry of neoplastic transformation: changes at the molecular level which affect the form and regulation of cell growth. Possible relation between other processes  

UK PubMed Central (United Kingdom)

This work summarizes the molecular modifications taking place after neoplastic transformation leading to changes in morphology and growth. Cytoskeleton and microtubules are involved in cell morphology changes, and abnormalities of growth regulation are implicated in cell transformation.

Avila J

1983-01-01

10

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.

2008-01-01

11

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 radiopharmacy course to PhD program, depending on the following factors; (1) National interest and policies on bio/medical sector; (2) Size of the nuclear medicine community in the respective country; (3) Institution interest and policies; and (4) Existing infrastructure and programs. Current Radiopharmacy Education in Singapore: In Singapore, all of the major nuclear medicine centers are supervised by radiopharmacists with PhD degree. All of the nuclear medicine technologists in the major centers have got training in radiopharmacy both in theory and hands-on practice. Final-year radiology students in Polytechnic have to go through a series of lectures on radiopharmacy and also practicals in hospital radiopharmacy laboratory. But due to the Government's initiatives on biomedical industries and also due to a global trend, interest in bio/medical imaging is rising among scientists and students. There is a need to fulfil this demand by introducing new course or modules at the University level. Designing an university-level module on molecular imaging chemistry: In National University of Singapore, a graduate student (MSc and PhD) level 5 module on ''Medical Imaging'' has already been introduced and a new module on ''Molecular Imaging Chemistry'' will be introduced soon. A module of this kind should serve as a link between chemistry, molecular imaging and clinical application with emphasis on chemical probe design. And should introduce contemporary topics and emerging concepts in chemistry related to molecular imaging. A brief introduction on different modalities of molecular imaging and principles of biomedical imaging should be introduced including principles of medical imaging equipment. How this knowledge will direct the chemical synthesis should be highlighted (lead directed synthesis). There should be a coverage on pharmacology and drug discovery process as imaging probes could be considered as drugs. Here is an example of an outline for such module: - Introduction: - What is molecular imaging? - Why molecular imaging? - What is biomedical imaging? - Different modalities of molecular imaging; - Different types of molecular imaging; - In vitro, ex vivo, in vivo imaging; Drug discovery process; - Pharmacological basis. Molecular Imaging Chemistry: - general construct of imaging probe (molecular reporter system); - Bioimaging factors influencing chemical probe synthesis; Optical imaging probes; - Radioimaging probes; - MR contrast agents; - Probes for other modalities, X ray, ultrasound, etc. Examples of practical applications. (author)

2007-01-01

12

BioMOL: a computer-assisted biological modeling tool for complex chemical mixtures and biological processes at the molecular level.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A chemical engineering approach for the rigorous construction, solution, and optimization of detailed kinetic models for biological processes is described. This modeling capability addresses the required technical components of detailed kinetic modeling, namely, the modeling of reactant structure an...

Klein, Michael T; Hou, Gang; Quann, Richard J; Wei, Wei; Liao, Kai H; Yang, Raymond S H; Campain, Julie A; Mazurek, Monica A

13

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

14

1978 bibliography of atomic and molecular processes  

International Nuclear Information System (INIS)

[en]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

1980-01-01

15

1980 bibliography of atomic and molecular processes  

International Nuclear Information System (INIS)

[en]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

1982-01-01

16

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

17

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

18

1980 bibliography of atomic and molecular processes  

Energy Technology Data Exchange (ETDEWEB)

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.

1982-02-01

19

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.

1980-01-01

20

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

 
 
 
 
21

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

22

Levels of Processing in Mild Disabilities.  

Science.gov (United States)

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

Al-Hilawani, Yasser A.; And Others

23

Strong correlation between molecular configurations and charge-transfer processes probed at the single-molecule level by surface-enhanced Raman scattering.  

UK PubMed Central (United Kingdom)

Single-molecule (SM) electrochemistry studied by surface-enhanced Raman scattering (SERS) with high spectral resolution reveals a picture in which the frequency of Raman modes is correlated with the electrochemical process through the interaction with the surface. Previously unexplored phenomena can be revealed by the synergy of electrochemistry and SM-SERS, which explores in this case subtler spectroscopic aspects (like the frequency of a vibration within the inhomogeneous broadening of a many-molecules Raman peak) to gain the information. We demonstrate, among other things, that the interaction with the surface is correlated both with the molecule vibrational frequencies and with the ability of single molecules to be reduced/oxidized at different potentials along the electrochemical cycle. Qualitative models of the interaction of molecules with surfaces are also touched upon.

Corts E; Etchegoin PG; Le Ru EC; Fainstein A; Vela ME; Salvarezza RC

2013-02-01

24

Strong correlation between molecular configurations and charge-transfer processes probed at the single-molecule level by surface-enhanced Raman scattering.  

Science.gov (United States)

Single-molecule (SM) electrochemistry studied by surface-enhanced Raman scattering (SERS) with high spectral resolution reveals a picture in which the frequency of Raman modes is correlated with the electrochemical process through the interaction with the surface. Previously unexplored phenomena can be revealed by the synergy of electrochemistry and SM-SERS, which explores in this case subtler spectroscopic aspects (like the frequency of a vibration within the inhomogeneous broadening of a many-molecules Raman peak) to gain the information. We demonstrate, among other things, that the interaction with the surface is correlated both with the molecule vibrational frequencies and with the ability of single molecules to be reduced/oxidized at different potentials along the electrochemical cycle. Qualitative models of the interaction of molecules with surfaces are also touched upon. PMID:23384115

Corts, Emiliano; Etchegoin, Pablo G; Le Ru, Eric C; Fainstein, Alejandro; Vela, Mara E; Salvarezza, Roberto C

2013-02-11

25

Molecular sieving silica membrane fabrication process  

Energy Technology Data Exchange (ETDEWEB)

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

Raman, Narayan K. (400 Maple St. SE., Apartment 112, Albuquerque, NM 87106); Brinker, Charles Jeffrey (14 Eagle Nest Dr., NE., Albuquerque, NM 87122)

1998-01-01

26

Molecular sieving silica membrane fabrication process  

Energy Technology Data Exchange (ETDEWEB)

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

Raman, Narayan K. (Monroeville, PA); Brinker, Charles Jeffrey (Albuquerque, NM)

1999-01-01

27

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

28

Solvent resistant nanofiltration: separating on a molecular level.  

Science.gov (United States)

Over the past decade, solvent resistant nanofiltration (SRNF) has gained a lot of attention, as it is a promising energy- and waste-efficient unit process to separate mixtures down to a molecular level. This critical review focuses on all aspects related to this new burgeoning technology, occasionally also including literature obtained on aqueous applications or related membrane processes, if of relevance to understand SRNF better. An overview of the different membrane materials and the methods to turn them into suitable SRNF-membranes will be given first. The membrane transport mechanism and its modelling will receive attention in order to understand the process and the reported membrane performances better. Finally, all SRNF-applications reported so far - in food chemistry, petrochemistry, catalysis, pharmaceutical manufacturing - will be reviewed exhaustively (324 references). PMID:18197351

Vandezande, Pieter; Gevers, Lieven E M; Vankelecom, Ivo F J

2007-10-08

29

Solvent resistant nanofiltration: separating on a molecular level.  

UK PubMed Central (United Kingdom)

Over the past decade, solvent resistant nanofiltration (SRNF) has gained a lot of attention, as it is a promising energy- and waste-efficient unit process to separate mixtures down to a molecular level. This critical review focuses on all aspects related to this new burgeoning technology, occasionally also including literature obtained on aqueous applications or related membrane processes, if of relevance to understand SRNF better. An overview of the different membrane materials and the methods to turn them into suitable SRNF-membranes will be given first. The membrane transport mechanism and its modelling will receive attention in order to understand the process and the reported membrane performances better. Finally, all SRNF-applications reported so far - in food chemistry, petrochemistry, catalysis, pharmaceutical manufacturing - will be reviewed exhaustively (324 references).

Vandezande P; Gevers LE; Vankelecom IF

2008-02-01

30

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 evo...

Fetterman Christina D; Rannala Bruce; Walter Michael A

31

Computational molecular engineering as an emerging technology in process engineering  

CERN Multimedia

The present level of development of molecular force field methods is assessed from the point of view of simulation-based engineering, outlining the immediate perspective for further development and highlighting the newly emerging discipline of Computational Molecular Engineering (CME) which makes basic research in soft matter physics fruitful for industrial applications. Within the coming decade, major breakthroughs can be reached if a research focus is placed on processes at interfaces, combining aspects where an increase in the accessible length and time scales due to massively parallel high-performance computing will lead to particularly significant improvements.

Horsch, Martin; Vrabec, Jadran; Hasse, Hans

2013-01-01

32

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

33

Plasma detachment with molecular processes in divertor plasmas  

Energy Technology Data Exchange (ETDEWEB)

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

Ohno, N.; Ezumi, N.; Nishijima, D.; Takamura, S. [Dept. of Energy Engineering and Science, Graduate School of Engineering, Nagoya Univ., Nagoya, Aichi (Japan); Krasheninnikov, S.I.; Pigarov, A.Yu. [MIT Plasma Science and Fusion Center, Cambridge, MA (United States)

2000-01-01

34

Transdifferentiation: a cell and molecular reprogramming process.  

UK PubMed Central (United Kingdom)

Evidence has emerged recently indicating that differentiation is not entirely a one-way process, and that it is possible to convert one cell type to another, both in vitro and in vivo. This phenomenon is called transdifferentiation, and is generally defined as the stable switch of one cell type to another. Transdifferentiation plays critical roles during development and in regeneration pathways in nature. Although this phenomenon occurs rarely in nature, recent studies have been focused on transdifferentiation and the reprogramming ability of cells to produce specific cells with new phenotypes for use in cell therapy and regenerative medicine. Thus, understanding the principles and the mechanism of this process is important for producing desired cell types. Here some well-documented examples of transdifferentiation, and their significance in development and regeneration are reviewed. In addition, transdifferentiation pathways are considered and their potential molecular mechanisms, especially the role of master switch genes, are considered. Finally, the significance of transdifferentiation in regenerative medicine is discussed.

Sisakhtnezhad S; Matin MM

2012-06-01

35

Molecular-level understanding of the carbonisation of polysaccharides.  

UK PubMed Central (United Kingdom)

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.

Shuttleworth PS; Budarin V; White RJ; Gun'ko VM; Luque R; Clark JH

2013-07-01

36

Designing interfaces at the molecular level  

Energy Technology Data Exchange (ETDEWEB)

The creation of organized thin films (OTFs) of organic compounds has developed into an increasingly important research area at the frontier of analytical chemistry. In this Report we present an overview of the development and application of OTFs to analytical chemistry. We will discuss the origins and preparative methodologies of Langmuir-Blodgett (LB) and spontaneously adsorbed (SA) films, the two most used routes toward the creation of OTFs. We will also examine the structural attributes of OTFs that can be used to clarify the issues related to transduction mechanisms that are important to analytical chemistry and to designing interfacial architectures with advanced functions. We highlight a few of the many uses of OTFs, beginning with fundamental studies of interfacial processes, followed by emerging applications to chemical analysis. Reviews of applications of OTFs in other areas provide additional fundamental and technological information. 42 refs., 3 figs.

Zhong, C.J. [Iowa State Univ., Ames, IA (United States); Porter, M.D. [Ames Lab., IA (United States)]|[Iowa State Univ., Ames, IA (United States)

1995-12-01

37

Transdifferentiation: a cell and molecular reprogramming process.  

Science.gov (United States)

Evidence has emerged recently indicating that differentiation is not entirely a one-way process, and that it is possible to convert one cell type to another, both in vitro and in vivo. This phenomenon is called transdifferentiation, and is generally defined as the stable switch of one cell type to another. Transdifferentiation plays critical roles during development and in regeneration pathways in nature. Although this phenomenon occurs rarely in nature, recent studies have been focused on transdifferentiation and the reprogramming ability of cells to produce specific cells with new phenotypes for use in cell therapy and regenerative medicine. Thus, understanding the principles and the mechanism of this process is important for producing desired cell types. Here some well-documented examples of transdifferentiation, and their significance in development and regeneration are reviewed. In addition, transdifferentiation pathways are considered and their potential molecular mechanisms, especially the role of master switch genes, are considered. Finally, the significance of transdifferentiation in regenerative medicine is discussed. PMID:22526624

Sisakhtnezhad, Sajjad; Matin, Maryam M

2012-04-25

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).

2004-01-01

39

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

40

Statistical kinetics of processive molecular motors  

Science.gov (United States)

We describe new theoretical and experimental tools for studying biological motor proteins at the single molecule scale. These tools enable measurements of molecular fuel economies, thereby providing insight into the pathways for conversion of biochemical energy into mechanical work. Kinesin is an ATP-dependent motor that moves processively along microtubules in discrete steps of 8 nm. How many molecules of ATP are hydrolysed per step? To determine this coupling ratio, we develop a fluctuation analysis, which relates the variance in records of mechanical displacement to the number of rate-limiting biochemical transitions in the engine cycle. Using fluctuation analysis and optical trapping interferometry, we determine that near zero load, single molecules of kinesin hydrolyse one ATP nucleotide per 8-nm step. To study kinesin behavior under load, we use a molecular force clamp, capable of maintaining constant loads on single kinesin motors moving processively. Analysis of records of motion under variable ATP concentrations and loads reveals that kinesin is a `tightly- coupled' motor, maintaining the 1:1 coupling ratio up to loads of ~ 5 pN. Moreover, a Michaelis-Menten analysis of velocity shows that the kinesin cycle contains at least two load- dependent transitions. The rate of one of these transitions affects ATP affinity, while the other does not. Therefore, the kinesin stall force must depend on the ATP concentration, as is demonstrated experimentally. These findings rule out existing theoretical models of kinesin motility. We develop a simple theoretical formalism describing a tightly-coupled mechanism for movement. This `energy-landscape' formalism quantitatively accounts for motile properties of RNA polymerase (RNAP), the enzyme that transcribes DNA into RNA. The shapes of RNAP force-velocity curves indicate that biochemical steps limiting transcription rates at low loads do not generate movement. Modeling suggests that high loads may halt RNAP by promoting a structural change which moves all or part of the enzyme backwards along the DNA through a distance of 5-10 base pairs. Using the energy landscape formalism, we also propose a model for kinesin. The model incorporates both the ATP-dependent and the ATP-independent mechanical transitions in the motor cycle and explains experimental measurements of kinesin velocity.

Schnitzer, Mark Jacob

1999-10-01

 
 
 
 
41

Processing letters in words at different levels.  

UK PubMed Central (United Kingdom)

Subjects indicated whether two letters, two words, or a letter and the first letter of a word were the same. Letter targets were matched more quickly than word targets when the stimuli were presented simultaneously. When the target and comparison stimuli were separated by a 3-sec interval, word targets were matched more quickly than a letter and a letter in a word. It was also shown that the physical similarity of the targets and comparison stimuli had a greater effect in the simultaneous matching conditions. These findings are consistent with a model of word processing in which letters are individually compared prior to word identification at a physical level of processing. At a higher level of processing, words may be encoded as a unit, and the identification of the letters within the word may require a decoding of the word unit.

Marmurek HH

1977-01-01

42

Processing letters in words at different levels.  

Science.gov (United States)

Subjects indicated whether two letters, two words, or a letter and the first letter of a word were the same. Letter targets were matched more quickly than word targets when the stimuli were presented simultaneously. When the target and comparison stimuli were separated by a 3-sec interval, word targets were matched more quickly than a letter and a letter in a word. It was also shown that the physical similarity of the targets and comparison stimuli had a greater effect in the simultaneous matching conditions. These findings are consistent with a model of word processing in which letters are individually compared prior to word identification at a physical level of processing. At a higher level of processing, words may be encoded as a unit, and the identification of the letters within the word may require a decoding of the word unit. PMID:21331869

Marmurek, H H

1977-01-01

43

How effective are simulated molecular-level experiments for teaching diffusion and osmosis?  

UK PubMed Central (United Kingdom)

Diffusion and osmosis are central concepts in biology, both at the cellular and organ levels. They are presented several times throughout most introductory biology textbooks (e.g., Freeman, 2002), yet both processes are often difficult for students to understand (Odom, 1995; Zuckerman, 1994; Sanger et al., 2001; and results herein). Students have deep-rooted misconceptions about how diffusion and osmosis work, especially at the molecular level. We hypothesized that this might be in part due to the inability to see and explore these processes at the molecular level. In order to investigate this, we developed new software, OsmoBeaker, which allows students to perform inquiry-based experiments at the molecular level. Here we show that these simulated laboratories do indeed teach diffusion and osmosis and help overcome some, but not all, student misconceptions.

Meir E; Perry J; Stal D; Maruca S; Klopfer E

2005-01-01

44

Wafer level 3-D ICs process technology  

CERN Multimedia

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

Tan, Chuan Seng; Reif, L Rafael

2009-01-01

45

A Property Based Approach for Simultaneous Process and Molecular Design  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In this work, property clustering techniques and group contribution methods are combined to enable simultaneous consideration of process performance requirements and molecular property constraints. Using this methodology, the process design problem is solved to identify the property targets correspo...

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

46

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...

47

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

DEFF Research Database (Denmark)

We address several general questions about quantum transport through molecular systems by an ab initio analysis of a scandium-nitrogen doped C-80 metallofullerene device. Charge transfer from the Sc3N is found to drastically change the current-voltage characteristics: the current through the Sc3N @ C-80 device is double that through a bare C-80 device. We provide strong evidence that transport in such molecular devices is mediated by molecular electronic states which have been renormalized by the device environment, such as the electrodes and external bias V-b. The renormalized molecular levels and main transmission features shift in energy corresponding to half the applied bias voltage. This is also consistent with our finding that the voltage drops by V-b/2 at each molecule/electrode contact.

Larade, Brian; Taylor, Jeremy Philip

2001-01-01

48

Low level processing of diode spectrometry results  

International Nuclear Information System (INIS)

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

1975-10-06

49

Contributions to molecular diffusion as a separation process  

International Nuclear Information System (INIS)

[en]A simple glass apparatus has been developed and used for studying separation processes based on molecular diffusion in the system methane/ethane with or without adsorbents. 13C enrichment was followed by isotopic analysis. The results obtained show that molecular and isotopic separations can be exactly described by the Rayleigh equation. (author)

1989-01-01

50

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 century

2005-08-07

51

Enhancement of Signaling Processes on Membrane through Molecular Crowding  

CERN Multimedia

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

52

Architecture for Higher Level Digital Image Processing.  

Science.gov (United States)

The report begins with a review of desired system design goals. This is followed by a description of available microprocessor hardware, a review of LISP approach to the manipulation of list structures, and a preliminary discussion of the processing requir...

T. J. Willett

1978-01-01

53

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

54

1979 bibliography of atomic and molecular processes. [Bibliography  

Energy Technology Data Exchange (ETDEWEB)

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.

1980-08-01

55

Cellular and molecular processes leading to embryo formation in sponges: evidences for high conservation of processes throughout animal evolution.  

UK PubMed Central (United Kingdom)

The emergence of multicellularity is regarded as one of the major evolutionary events of life. This transition unicellularity/pluricellularity was acquired independently several times (King 2004). The acquisition of multicellularity implies the emergence of cellular cohesion and means of communication, as well as molecular mechanisms enabling the control of morphogenesis and body plan patterning. Some of these molecular tools seem to have predated the acquisition of multicellularity while others are regarded as the acquisition of specific lineages. Morphogenesis consists in the spatial migration of cells or cell layers during embryonic development, metamorphosis, asexual reproduction, growth, and regeneration, resulting in the formation and patterning of a body. In this paper, our aim is to review what is currently known concerning basal metazoans--sponges' morphogenesis from the tissular, cellular, and molecular points of view--and what remains to elucidate. Our review attempts to show that morphogenetic processes found in sponges are as diverse and complex as those found in other animals. In true epithelial sponges (Homoscleromorpha), as well as in others, we find similar cell/layer movements, cellular shape changes involved in major morphogenetic processes such as embryogenesis or larval metamorphosis. Thus, sponges can provide information enabling us to better understand early animal evolution at the molecular level but also at the cell/cell layer level. Indeed, comparison of molecular tools will only be of value if accompanied by functional data and expression studies during morphogenetic processes.

Ereskovsky AV; Renard E; Borchiellini C

2013-03-01

56

Molecular-beam studies of primary photochemical processes  

Energy Technology Data Exchange (ETDEWEB)

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

Lee, Y.T.

1982-12-01

57

Studying genomic processes at the single-molecule level: introducing the tools and applications.  

UK PubMed Central (United Kingdom)

To understand genomic processes such as transcription, translation or splicing, we need to be able to study their spatial and temporal organization at the molecular level. Single-molecule approaches provide this opportunity, allowing researchers to monitor molecular conformations, interactions or diffusion quantitatively and in real time in purified systems and in the context of the living cell. This Review introduces the types of application of single-molecule approaches that can enhance our understanding of genome function.

Dulin D; Lipfert J; Moolman MC; Dekker NH

2013-01-01

58

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

UK PubMed Central (United Kingdom)

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

Chowdhury D

2013-06-01

59

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

Science.gov (United States)

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

Chowdhury, Debashish

2013-06-01

60

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)

2006-01-01

 
 
 
 
61

The 2-nd Conference on Isotopic and Molecular Processes. Abstracts  

International Nuclear Information System (INIS)

The proceedings of the 2-nd Conference on Isotopic and Molecular Processes held on September 27 - 29, 2001 in Cluj - Napoca, Romania, contains contributions presented as: 11 plenary lectures, 24 oral presentations and 103 posters in two sections, namely, isotopic processes and molecular processes. The main topics treated in this conference were isotope production, separation and enrichment as well as stable isotope applications. Also, studies on isotope effects in different fields are reported. Besides reports on isotope effects, exchange and separation, new methods of preparation and labelling compounds used particularly in nuclear medicine are presented. Environmental studies by means of stable isotope and radon monitoring are described. Applications of radiation effects and different nuclear methods in medicine are also addressed

2001-01-01

62

Quantitative analysis of molecular-level DNA crystal growth on a 2D surface  

Science.gov (United States)

Crystallization is an essential process for understanding a molecule's aggregation behavior. It provides basic information on crystals, including their nucleation and growth processes. Deoxyribonucleic acid (DNA) has become an interesting building material because of its remarkable properties for constructing various shapes of submicron-scale DNA crystals by self-assembly. The recently developed substrate-assisted growth (SAG) method produces fully covered DNA crystals on various substrates using electrostatic interactions and provides an opportunity to observe the overall crystallization process. In this study, we investigated quantitative analysis of molecular-level DNA crystallization using the SAG method. Coverage and crystal size distribution were studied by controlling the external parameters such as monomer concentration, annealing temperature, and annealing time. Rearrangement during crystallization was also discussed. We expect that our study will provide overall picture of the fabrication process of DNA crystals on the charged substrate and promote practical applications of DNA crystals in science and technology.

Lee, Junwye; Hamada, Shogo; Hwang, Si Un; Amin, Rashid; Son, Junyoung; Dugasani, Sreekantha Reddy; Murata, Satoshi; Park, Sung Ha

2013-01-01

63

Quantitative analysis of molecular-level DNA crystal growth on a 2D surface.  

UK PubMed Central (United Kingdom)

Crystallization is an essential process for understanding a molecule's aggregation behavior. It provides basic information on crystals, including their nucleation and growth processes. Deoxyribonucleic acid (DNA) has become an interesting building material because of its remarkable properties for constructing various shapes of submicron-scale DNA crystals by self-assembly. The recently developed substrate-assisted growth (SAG) method produces fully covered DNA crystals on various substrates using electrostatic interactions and provides an opportunity to observe the overall crystallization process. In this study, we investigated quantitative analysis of molecular-level DNA crystallization using the SAG method. Coverage and crystal size distribution were studied by controlling the external parameters such as monomer concentration, annealing temperature, and annealing time. Rearrangement during crystallization was also discussed. We expect that our study will provide overall picture of the fabrication process of DNA crystals on the charged substrate and promote practical applications of DNA crystals in science and technology.

Lee J; Hamada S; Hwang SU; Amin R; Son J; Dugasani SR; Murata S; Park SH

2013-01-01

64

The requisite level of theory for the computational design of molecularly imprinted silica xerogels.  

Science.gov (United States)

The present manuscript reports the first application of molecular modelling to the design of molecularly imprinted polymers (MIPs) prepared by alkoxysilane sol-gel polymerization. The major goal was to determine the requisite level of theory for the selection of suitable alkoxysilane functional monomers. A comparative study, applied to the design of a MIP for beta-damascenone, involving different levels of theory, basis set superposition error (BSSE) correction and basis set augmentation and also semi-empirical methods, was performed. The computations results suggest that the use of the 3-21G basis set concomitantly with a method for BSSE correction represents a good compromise between theory level and computation time for the successful screening of functional monomers. Additionally, a few selected MIPs and their corresponding non-imprinted congeners (NIPs) were prepared and tested in the role of solid-phase extraction (SPE) sorbents. The confrontation of the computational results with the observed performance and morphological characteristics of the prepared MIPs suggest that besides the strength and type of interactions existing between template and functional monomers other concomitant features, related with the sol-gel process, must also be accounted for so that effective molecular imprinting is achieved in an alkoxysilane xerogel. Nevertheless, since an optimal template-functional monomer interaction is a necessary condition for successful imprinting, the choice of the best monomers is still of the greatest importance and the proposed computational method may constitute an expeditious and reliable screening tool. PMID:18396031

Azenha, Manuel; Kathirvel, Porkodi; Nogueira, Pedro; Fernando-Silva, Antnio

2008-03-02

65

Polycyclic imide derivatives: synthesis and effective tuning of lowest unoccupied molecular orbital levels through molecular engineering.  

Science.gov (United States)

A series of fluoranthene-fused imide derivatives were facilely developed through a Diels-Alder reaction followed by decarbonylation. The investigation of their photophysical and electrochemical properties demonstrated that their LUMO levels were effectively tuned from -3.2 to -3.8 eV through the introduction of a fused imide unit, which provides a platform to design new air-stable and solution-processable n-type materials. PMID:21070013

Ding, Lin; Ying, Han-Ze; Zhou, Yan; Lei, Ting; Pei, Jian

2010-11-11

66

Polycyclic imide derivatives: synthesis and effective tuning of lowest unoccupied molecular orbital levels through molecular engineering.  

UK PubMed Central (United Kingdom)

A series of fluoranthene-fused imide derivatives were facilely developed through a Diels-Alder reaction followed by decarbonylation. The investigation of their photophysical and electrochemical properties demonstrated that their LUMO levels were effectively tuned from -3.2 to -3.8 eV through the introduction of a fused imide unit, which provides a platform to design new air-stable and solution-processable n-type materials.

Ding L; Ying HZ; Zhou Y; Lei T; Pei J

2010-12-01

67

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

68

Molecular-Level Design of Heterogeneous Chiral Catalysis  

International Nuclear Information System (INIS)

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.

2012-01-01

69

Chemodiversity and molecular plasticity: recognition processes as explored by property spaces.  

UK PubMed Central (United Kingdom)

In the last few years, a need to account for molecular flexibility in drug-design methodologies has emerged, even if the dynamic behavior of molecular properties is seldom made explicit. For a flexible molecule, it is indeed possible to compute different values for a given conformation-dependent property and the ensemble of such values defines a property space that can be used to describe its molecular variability; a most representative case is the lipophilicity space. In this review, a number of applications of lipophilicity space and other property spaces are presented, showing that this concept can be fruitfully exploited: to investigate the constraints exerted by media of different levels of structural organization, to examine processes of molecular recognition and binding at an atomic level, to derive informative descriptors to be included in quantitative structure--activity relationships and to analyze protein simulations extracting the relevant information. Much molecular information is neglected in the descriptors used by medicinal chemists, while the concept of property space can fill this gap by accounting for the often-disregarded dynamic behavior of both small ligands and biomacromolecules. Property space also introduces some innovative concepts such as molecular sensitivity and plasticity, which appear best suited to explore the ability of a molecule to adapt itself to the environment variously modulating its property and conformational profiles. Globally, such concepts can enhance our understanding of biological phenomena providing fruitful descriptors in drug-design and pharmaceutical sciences.

Vistoli G; Pedretti A; Testa B

2011-06-01

70

Exploring the impact of and perceptions about interactive, self-explaining environments in molecular-level animations  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This mixed-method study investigates the effects of interactivity in animations of a molecular-level process and explores perceptions about the animated learning tool used. Treatments were based on principles of cognitive psychology designed to study the main effects of treatment and spatial ability...

Falvo, David A.; Urban, Michael J.; Suits, Jerry P.

71

The molecular reaction vessels for a transesterification process created by molecular imprinting technique.  

UK PubMed Central (United Kingdom)

A polymeric catalyst was synthesized by co-polymerizing 4(5)-vinylimidazole and itaconic acid with trimethylpropanol trimethacrylate micro spheres. The catalyst obtained catalysed the transesterification process between p-nitrophenyl acetate and hexanol with maximal initial velocity(nu(max)) of 4.73 +/- 0.47 microM min(-1) mg(-1), and turnover rate (k(cat)) of 8.67 min(-1). Using p-nitrophenyl acetate as template, molecular imprinting process enhanced the nu(max) of the polymeric catalyst 3-fold. Each imprinted site can be considered as a single molecular reaction vessel, and achieved a k(cat) of 169 min(-1) towards the conversion of p-nitrophenyl acetate in hexanol.

Meng Z; Sode K

2005-05-01

72

Molecular Level Design of Heterogeneous Chiral Catalysis. (Final Report, September 15, 2003-November 15, 2006).  

Science.gov (United States)

The production of enantiomerically pure chiral compounds is of great importance in the pharmaceutical industry. Although processes involving chiral catalysis and separations involving solid surfaces are known, the molecular-scale details of these processe...

A. J. Gellman D. S. Sholl

2006-01-01

73

Levels of processing: the evolution of a framework  

Scientific Electronic Library Online (English)

Full Text Available 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 from the shallowest level (perceptual processing-the subject initially perceives the physical and sensory characteristics of the stimulus) to the deepest level (semantic processin (more) g-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.

Ekuni, Roberta; Vaz, Leonardo Jos; Bueno, Orlando Francisco Amodeo

2011-12-01

74

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

75

Entendendo o Processo Molecular da Tumorignese Understanding the Molecular Process of Tumorigenesis  

Directory of Open Access Journals (Sweden)

Full Text Available Nos ltimos 25 anos, o reconhecimento dos mecanismos gentico-moleculares implicados na gnese e na progresso do cncer tem permitido obter novos mtodos de diagnstico e de acompanhamento, redirecionando de forma drstica a teraputica do paciente com neoplasia. Alguns marcadores moleculares j esto sendo utilizados na rotina e devero prover testes sensveis e especficos para o diagnstico precoce, estadiamento e acompanhamento do paciente com cncer. As caractersticas moleculares de cada tumor devero permitir predio do seu comportamento, ajudando a delinear estratgias teraputicas mais efetivas. Apresentamos de forma didtica os principais mecanismos controladores do ciclo celular e do crescimento, definindo a importncia de oncogenes erroneamente ativados e de genes supressores tumorais perdidos ou no-funcionantes, dos genes envolvidos na programao e manuteno da vida celular e de outros genes que atuam no processo de tumorignese. Os mecanismos de progresso tumoral, invaso e metastatizao distncia so revistos enfatizando-se a aplicao prtica do conhecimento a respeito de tais mecanismos. Lembramos o papel da instabilidade gentica e dos fenmenos epigenticos na definio fenotpica do cncer, sugerindo as aplicaes da gentica molecular na terapia gnica do cncer.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 being 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

2002-01-01

76

Boolean and fuzzy logic implemented at the molecular level  

Science.gov (United States)

In this work, it is shown how to implement both hard and soft computing by means of two structurally related heterocyclic compounds: flindersine (FL) and 6(5H)-phenanthridinone (PH). Since FL and PH have a carbonyl group in their molecular skeletons, they exhibit Proximity Effects in their photophysics. In other words, they have an emission power that can be modulated through external inputs such as temperature (T) and hydrogen-bonding donation (HBD) ability of solvents. This phenomenology can be exploited to implement both crisp and fuzzy logic. Fuzzy Logic Systems (FLSs) wherein the antecedents of the rules are connected through the AND operator, are built by both the Mamdanis and Sugenos models. Finally, they are adopted as approximators of the proximity effect phenomenon and tested for their prediction capabilities. Moreover, FL as photochromic compound is also a multiply configurable crisp logic molecular element.

Gentili, Pier Luigi

2007-07-01

77

Inhibition Of Molecular And Biological Processes Using Modified Oligonucleotides  

Energy Technology Data Exchange (ETDEWEB)

A method of inhibiting at least one molecular process in a sample, comprising administering to the sample an oligonucleotide or polynucleotide containing at least one monomeric unit having formula (I): wherein A is an organic moiety, n is at least 1, and each X is independently selected from the group consisting of --NRCOCONu, --NHCOCR.sub.2 CR.sub.2 CONu, --NHCOCR.dbd.CRCONu, and --NHCOSSCONu, wherein each R independently represents H or a substituted or unsubstituted alkyl group, and Nu represents a nucleophile, or a salt of the compound.

Kozyavkin, Sergei A. (Germantown, MD); Malykh, Andrei G. (Germantown, MD); Polouchine, Nikolai N. (Montgomery Village, MD); Slesarev, Alexei I. (Germantown, MD)

2003-04-15

78

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

DEFF Research Database (Denmark)

We present a new view and an analytical formalism of electron flow through a donor-acceptor molecule inserted between a pair of metal electrodes. The donor and acceptor levels are strongly coupled to an environmental nuclear continuum. The formalism applies to molecular donor-acceptor systems both in vacuum or air, and in aqueous solution under electrochemical potential control. Multifarious patterns of rectified electron flow from the negatively to the positively biased electrode arise. The electronic interaction between the donor and acceptor fragments, mutually and with the electrodes, can be weak, corresponding to the fully diabatic limit. The rectification process then reduces to a sequence of vibrationally relaxed single-electron transfer steps. In the limits where the interactions are strong, denoted as the partially and fully adiabatic limits, the character of the rectification process is different, and electron flow proceeds coherently, without vibrational relaxation. In still another class of mechanisms the electronic level broadening of either donor or acceptor from the adjacent electrode is so strong that it is comparable to the vibrational broadening. The process then reduces to a three-level transition similar to STM of large redox molecules. Recent data for rectification in hexadecyl-quinolinium tricyanodimethanide monolayers by Metzger and co-workers [J. Am. Chem. Soc. 119, 10455 (1997); Acc. Chem. Res. 32, 950 (1999)], are discussed in terms of the reported views and formalism.

Kuznetsov, A.M.; Ulstrup, Jens

2002-01-01

79

78 FR 18481 - Project-Level Predecisional Administrative Review Process  

Science.gov (United States)

...Service 36 CFR Part 218 RIN 0596-AD07 Project-Level Predecisional Administrative Review...predecisional administrative review for proposed projects and activities implementing land management...postdecisional administrative appeal process for project decisions. This rule revises Forest...

2013-03-27

80

THE THEORETICAL ASPECTS OF INTEGRATION PROCESSES ON THE REGIONAL LEVEL  

Directory of Open Access Journals (Sweden)

Full Text Available In this article theoretical aspects of interregional integration processes are covered. Different approaches areresulted in understanding the essence of integration between separate regions, hierarchical levels of integration,legitimacy use of theories of the international integration is found out at the analysis of regional interrelations. It isoffered the authors approach for the allocation of types of integration processes at a level of region

Ihor YASKAL; Alexandru NEDELEA

2010-01-01

 
 
 
 
81

High-Level Waste System Process Interface Description  

International Nuclear Information System (INIS)

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

1999-01-01

82

Simulation of deacidification process by molecular distillation of deodorizer distillate  

Scientific Electronic Library Online (English)

Full Text Available 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 condensation. Physical and transport properties have been evaluated using correlations, which are functions of temperature and composition. The obtained partial differential equation (more) 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 C, 130 C, and 140 C) were carried out in a KDL4 (UIC) molecular distillation apparatus to verify the model.

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

2008-12-01

83

Simulation of deacidification process by molecular distillation of deodorizer distillate  

Directory of Open Access Journals (Sweden)

Full Text Available 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 condensation. 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 C, 130 C, and 140 C) were carried out in a KDL4 (UIC) molecular distillation apparatus to verify the model.

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

2008-01-01

84

A compound poisson process for relaxing the molecular clock.  

UK PubMed Central (United Kingdom)

The molecular clock hypothesis remains an important conceptual and analytical tool in evolutionary biology despite the repeated observation that the clock hypothesis does not perfectly explain observed DNA sequence variation. We introduce a parametric model that relaxes the molecular clock by allowing rates to vary across lineages according to a compound Poisson process. Events of substitution rate change are placed onto a phylogenetic tree according to a Poisson process. When an event of substitution rate change occurs, the current rate of substitution is modified by a gamma-distributed random variable. Parameters of the model can be estimated using Bayesian inference. We use Markov chain Monte Carlo integration to evaluate the posterior probability distribution because the posterior probability involves high dimensional integrals and summations. Specifically, we use the Metropolis-Hastings-Green algorithm with 11 different move types to evaluate the posterior distribution. We demonstrate the method by analyzing a complete mtDNA sequence data set from 23 mammals. The model presented here has several potential advantages over other models that have been proposed to relax the clock because it is parametric and does not assume that rates change only at speciation events. This model should prove useful for estimating divergence times when substitution rates vary across lineages.

Huelsenbeck JP; Larget B; Swofford D

2000-04-01

85

A compound poisson process for relaxing the molecular clock.  

Science.gov (United States)

The molecular clock hypothesis remains an important conceptual and analytical tool in evolutionary biology despite the repeated observation that the clock hypothesis does not perfectly explain observed DNA sequence variation. We introduce a parametric model that relaxes the molecular clock by allowing rates to vary across lineages according to a compound Poisson process. Events of substitution rate change are placed onto a phylogenetic tree according to a Poisson process. When an event of substitution rate change occurs, the current rate of substitution is modified by a gamma-distributed random variable. Parameters of the model can be estimated using Bayesian inference. We use Markov chain Monte Carlo integration to evaluate the posterior probability distribution because the posterior probability involves high dimensional integrals and summations. Specifically, we use the Metropolis-Hastings-Green algorithm with 11 different move types to evaluate the posterior distribution. We demonstrate the method by analyzing a complete mtDNA sequence data set from 23 mammals. The model presented here has several potential advantages over other models that have been proposed to relax the clock because it is parametric and does not assume that rates change only at speciation events. This model should prove useful for estimating divergence times when substitution rates vary across lineages. PMID:10747076

Huelsenbeck, J P; Larget, B; Swofford, D

2000-04-01

86

Multiscale mechanobiology: mechanics at the molecular, cellular, and tissue levels  

Science.gov (United States)

Mechanical force is present in all aspects of living systems. It affects the conformation of molecules, the shape of cells, and the morphology of tissues. All of these are crucial in architecture-dependent biological functions. Nanoscience of advanced materials has provided knowledge and techniques that can be used to understand how mechanical force is involved in biological systems, as well as to open new avenues to tailor-made bio-mimetic materials with desirable properties. In this article, we describe models and show examples of how force is involved in molecular functioning, cell shape patterning, and tissue morphology.

2013-01-01

87

Effects of group argumentation processes on level of grounds  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This study investigates the affects of interactive processes of argumentation in collaborative learning on the level of grounds. More specifically, it focuses on how discourse moves and participant structures are related to the level of grounds. 136 notes from on-line collaborative learning discours...

Lu, J; Chiu, M; Law, N

88

Cascading Activation across Levels of Representation in Children's Lexical Processing  

Science.gov (United States)

Recent work in adult psycholinguistics has demonstrated that activation of semantic representations begins long before phonological processing is complete. This incremental propagation of information across multiple levels of analysis is a hallmark of adult language processing but how does this ability develop? In two experiments, we elicit

Huang, Yi Ting; Snedeker, Jesse

2011-01-01

89

Cascading Activation Across Levels of Representation in Children's Lexical Processing  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Recent work in adult psycholinguistics has demonstrated that activation of semantic representations begins long before phonological processing is complete. This incremental propagation of information across multiple levels of analysis is a hallmark of adult language processing but how does this abil...

Snedeker, Jesse; Huang, Yi Ting

90

The Composing Processes of Unskilled Writers at the College Level.  

Science.gov (United States)

This paper uses five case studies of unskilled writers at the college level to provide insights into the composing process. Each student's writing process was tape-recorded and observed by the instructor in four sessions. The tapes and written observations were charted and analyzed for exhibited behavior patterns in comparison to the written

Perl, Sondra

91

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

92

Group Psychotherapy Levels of Interventions: A Clinical Process Commentary.  

UK PubMed Central (United Kingdom)

Trainees may experience greater effectiveness as therapists by conceptualizing group therapy interactions as occurring at different levels of functioning. We teach group therapy trainees to be aware of and flexibly direct their interventions to three levels of the group: (a) the intraindividual level, (b) the interpersonal level, and (3) the group-as-a-whole level. Within this conceptualization, we also encourage trainees to reinforce the group structure especially related to safety and secure base and to help group members to self-reflect about their interactions within the group. In this clinical process commentary, we describe a process of pregroup assessment and preparation that includes evaluating individual core relational patterns (CRPs) and how these patterns might express themselves in the three levels of group functioning. A running case presentation provides examples of a CRP formulation, levels of group functioning, and therapist interventions that are specific to each level. Making use of each group level within every session may allow the novice group therapist to sort the complex information they receive in a meaningful way. A therapist who can flexibly attend to and work within each group level will optimize the effectiveness of their interventions. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

Tasca GA; Francis K; Balfour L

2013-09-01

93

0-level Vacuum Packaging RT Process for MEMS Resonators  

CERN Multimedia

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

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

2008-01-01

94

Low-energy electron-collision processes in molecular chlorine  

International Nuclear Information System (INIS)

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

1994-01-01

95

Biological implication of atomic collisions at the molecular level  

International Nuclear Information System (INIS)

[en]First biological models of radiation action were based on the average enerey deposited in the cell nucleus. Later theories have stressed the importance of the energy deposition at the nanometer level. Clusters of ionizations generated by K-electron removal seem to be a highly efficient mechanism for the induction of cell inactivation by heavy ions. Calculations and experimental results reported here support this hypothesis. (orig.)

1997-01-01

96

Biological implication of atomic collisions at the molecular level  

Energy Technology Data Exchange (ETDEWEB)

First biological models of radiation action were based on the average enerey deposited in the cell nucleus. Later theories have stressed the importance of the energy deposition at the nanometer level. Clusters of ionizations generated by K-electron removal seem to be a highly efficient mechanism for the induction of cell inactivation by heavy ions. Calculations and experimental results reported here support this hypothesis. (orig.). 13 refs.

Touati, A.; Herve du Penhoat, M.A.; Gobert, F.; Champion, C.; Fayard, B.; Abel, F.; L`Hoir, A.; Moulin, J.; Chetioui, A. [Paris-7 Univ., 75 (France). Groupe de Physique des Solides; Bailly-Despiney, I. [CEA/DSV/DRR/, Lab. de Radiotoxicologie, BP. 12, 19680 Bruyeres le Chatel (France); Sabatier, L. [CEA/DSV/DRR/, Lab. de Radiobiologie et Oncologie, BP. 6, Fontenay aux Roses Cedex (France)

1997-10-01

97

Molecular sieve sensors for selective detection at the nanogram level  

Energy Technology Data Exchange (ETDEWEB)

The invention relates to a selective chemical sensor for selective detection of chemical entities even at the nanogram level. The invention further relates to methods of using the sensor. The sensor comprises: (a) a piezoelectric substrate capable of detecting mass changes resulting from adsorption of material thereon; and (b) a coating applied to the substrate, which selectively sorbs chemical entities of a size smaller than a preselected magnitude.

Bein, Thomas (Albuquerque, NM); Brown, Kelly D. (Albuquerque, NM); Frye, Gregory C. (Albuquerque, NM); Brinker, Charles J. (Albuquerque, NM)

1992-01-01

98

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; Michael J. Urban; Jerry P. Suits

2011-01-01

99

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

Energy Technology Data Exchange (ETDEWEB)

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

Gilchrest, B.A.; Yaar, M. (Tufts Univ., Boston, MA (United States). School of Medicine Boston Univ., MA (United States). School of Medicine)

1992-09-01

100

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

International Nuclear Information System (INIS)

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

1992-01-01

 
 
 
 
101

Method of processing low-level radioactive liquid wastes  

International Nuclear Information System (INIS)

Purpose: To effectively reduce the radioactivity density of low-level radioactive liquid wastes discharged from enriched uranium conversion processing steps or the likes. Method: Hydrazin is added to low-level radioactive liquid wastes, which are in contact with iron hydroxide-cation exchange resins prepared by processing strongly acidic-cation exchange resins with ferric chloride and aqueous ammonia to form hydrorizates of ferric ions in the resin. Hydrazine added herein may be any of hydrazine hydrate, hydrazine hydrochloride and hydranine sulfate. The preferred addition amount is more than 100 mg per one liter of the liquid wastes. If it is less than 100 mg, the reduction rate for the radioactivety density (procession liquid density/original liquid density) is decreased. This method enables to effectively reduce the radioactivity density of the low-level radioactive liquid wastes containing a trace amount of radioactive nucleides. (Yoshihara, H.).

1983-06-15

102

Quantification of chromatin condensation level by image processing.  

UK PubMed Central (United Kingdom)

The level of chromatin condensation is related to the silencing/activation of chromosomal territories and therefore impacts on gene expression. Chromatin condensation changes during cell cycle, progression and differentiation, and is influenced by various physicochemical and epigenetic factors. This study describes a validated experimental technique to quantify chromatin condensation. A novel image processing procedure is developed using Sobel edge detection to quantify the level of chromatin condensation from nuclei images taken by confocal microscopy. The algorithm was developed in MATLAB and used to quantify different levels of chromatin condensation in chondrocyte nuclei achieved through alteration in osmotic pressure. The resulting chromatin condensation parameter (CCP) is in good agreement with independent multi-observer qualitative visual assessment. This image processing technique thereby provides a validated unbiased parameter for rapid and highly reproducible quantification of the level of chromatin condensation.

Irianto J; Lee DA; Knight MM

2013-10-01

103

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

Energy Technology Data Exchange (ETDEWEB)

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

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

1996-02-01

104

Reducing process noise in superconducting helium liquid level probes  

Energy Technology Data Exchange (ETDEWEB)

This memo presents methods to reduce the process noise accompanying the use of superconducting helium liquid level probes in a splashing environment. The development of these methods followed unsatisfactory operation of unmodified, commercially available, level probes used in each of the 24 valve box dewars of Tevatron refrigerators. The dewars function both as reservoirs of refrigeration and as phase separators at the inlet of the cold compressors used in subatmospheric magnet cooling operation.

Brubaker, J.

1995-03-01

105

Effects of delayed laboratory processing on platelet serotonin levels.  

UK PubMed Central (United Kingdom)

BACKGROUND: Despite the availability of established guidelines for measuring platelet serotonin, these guidelines may be difficult to follow in a hospital setting where time to processing may vary from sample to sample. PURPOSE: The purpose of this study was to evaluate the effect of the time to processing of human blood samples on the stability of the enzyme-linked immunosorbent assay (ELISA) for the determination of platelet serotonin levels in human plasma. METHOD: Human blood samples collected from a convenience sample of eight healthy volunteers were analyzed to determine platelet serotonin levels from plasma collected in ethylene diamine tetra acetic acid (EDTA) tubes and stored at 4C for 3 hr, 5 hr, 8 hr, and 12 hr. RESULTS: Refrigeration storage at 4C for 3 hr, 5 hr, 8 hr, and 12 hr altered the platelet serotonin measurement when compared to immediate processing. The bias for the samples stored at 4C for 3 hr was 102.3 (217.39 ng/10(9) platelets), for 5 hr was 200.1 (132.76 ng/10(9) platelets), for 8 hr was 146.9 (221.41 ng/10(9) platelets), and for 12 hr was -67.6 (349.60 ng/10(9) platelets). DISCUSSION: Results from this study show that accurate measurement of platelet serotonin levels is dependent on time to processing. Researchers should therefore follow a standardized laboratory guideline for obtaining immediate platelet serotonin levels after blood sample collection.

Sanner JE; Frazier L; Udtha M

2013-01-01

106

Molecular signature of cancer at gene level or pathway level? Case studies of colorectal cancer and prostate cancer microarray data.  

UK PubMed Central (United Kingdom)

With recent advances in microarray technology, there has been a flourish in genome-scale identification of molecular signatures for cancer. However, the differentially expressed genes obtained by different laboratories are highly divergent. The present discrepancy at gene level indicates a need for a novel strategy to obtain more robust signatures for cancer. In this paper we hypothesize that (1) the expression signatures of different cancer microarray datasets are more similar at pathway level than at gene level; (2) the comparability of the cancer molecular mechanisms of different individuals is related to their genetic similarities. In support of the hypotheses, we summarized theoretical and experimental evidences, and conducted case studies on colorectal and prostate cancer microarray datasets. Based on the above assumption, we propose that reliable cancer signatures should be investigated in the context of biological pathways, within a cohort of genetically homogeneous population. It is hoped that the hypotheses can guide future research in cancer mechanism and signature discovery.

Chen J; Wang Y; Shen B; Zhang D

2013-01-01

107

Regulation of leaf hydraulics: from molecular to whole plant levels  

Science.gov (United States)

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

Prado, Karine; Maurel, Christophe

2013-01-01

108

Vector-Valued Image Processing by Parallel Level Sets.  

UK PubMed Central (United Kingdom)

Vector-valued images such as RGB colour images or multi-modal medical images show a strong inter-channel correlation which is not exploited by most image processing tools. We propose a new notion of treating vector-valued images which is based on the angle between the spatial gradients of their channels. By minimizing a cost functional which penalizes large angles, images with parallel level sets can be obtained. After formally introducing this idea and the corresponding cost functionals we discuss their ?ateaux derivatives which lead to a diffusion like gradient descent scheme. We illustrate the properties of this cost functional by several examples in denoising and demosaicking of RGB colour images. They show that parallel level sets are a suitable concept for colour image enhancement. Demosaicking with parallel level sets gives visually perfect results for low noise levels. Furthermore, the proposed functional yields sharper images than the other approaches in comparison.

Ehrhardt M; Arridge S

2013-08-01

109

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; Mller, T; von Issendorff, B

2011-01-28

110

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

UK PubMed Central (United Kingdom)

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.

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

2011-01-01

111

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

UK PubMed Central (United Kingdom)

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.

Salmenkova EA

2013-01-01

112

CELLmicrocosmos - Integrativecellmodelingatthe molecular,mesoscopicandfunctionallevel  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The modeling of cells is an important application area of Systems Biology. In the context of this work, three cytological levels are defined: the mesoscopic, the molecular and the functional level. A number of related approaches which are quite diverse will be introduced during this work which can b...

Sommer, Bjrn

113

Energy exchange processes in molecular cloud W40  

Energy Technology Data Exchange (ETDEWEB)

We have studied the principal energy-exchange in molecular cloud (dark nebula) Westerhout 40 (G28.8+3.5). From the molecular spectral lines of /sup 12/CO and /sup 13/CO and the infrared observational data, the basic physical parameters of molecular cloud W40 may be estimated, and the cooling and heating rates for the gas and dust may then be calculated. From our calculations, we have also discussed the energy relations of the gas, dust, and embedded infrared source in molecular cloud W40.

Xu, L.; Xing, J.; Wu, Y.; Xie, S.; Zhao, J.

1982-07-01

114

Molecular dynamics study on Ar ion bombardment effects in amorphous SiO2 deposition processes  

International Nuclear Information System (INIS)

[en]Argon ion bombardment effects on growing amorphous SiO2 films during reactive sputtering deposition processes were examined based on molecular dynamics (MD) and Monte Carlo (MC) simulation techniques. The system we have considered here is a film that is subject to energetic Ar bombardment while it is formed by surface reactions of Si and O atoms separately supplied at low kinetic energies. It has been found that (1) Ar injections preferentially sputter O atoms from the surface over Si and (2) also have a compressing effect on the growing film during the deposition process. In other words, our MD/MC simulations have demonstrated at the atomic level that, with higher energy Ar injections, an amorphous SiO2 film grown in a reactive sputtering deposition process is denser and more Si rich

2006-12-15

115

Photoinduced Charge and Energy Transfer Processes in Molecular Aggregates  

Energy Technology Data Exchange (ETDEWEB)

This project involved the experimental probing of the electronic excited states generated by photoinduced (center-to-center) electron and energy transfer processes in several classes of transition metal donor/acceptor (D/A) complexes. Some of the general properties inferred from these studies should be useful in the design of new systems for energy conversion applications. Pursuit of the project goals has involved the determination of electron transfer efficiencies and the detailed study of variations in the electronic spectra of D/A complexes. This has resulted in the study of some very fundamental issues of photoinduced charge transfer and the identification of some of the constraints on its efficiency. The experimental studies of the competition between the degradative non-radiative unimolecular relaxation of transition metal excited states and their transfer of charge from these excited states to external acceptors have involved a range of techniques such as transient decay kinetics, photoacoustic calorimetry and transient or stationary state spectroscopy. The substrates synthesized for these studies were selected to provide model systems, or series of model systems to probe the validity of models of electronic excited states and their reactivity. The work during the last few years has focused largely, but not exclusively, on the use of emission spectral band shapes to probe the properties of charge transfer (CT) excited states. Bandshape variations are one of the very few approaches for systematically probing electronic excited states and good band shape resolution is necessary in order to gain information about the structural variations that correlate with excited state reactivity. Differences in molecular structure correlate with differences in chemical reactivity, and the variations in emission bandshapes are well known to relate to variations in the molecular structural differences between the excited and ground electronic states. However, it is has been rarely noticed that configurational mixing of the lowest energy excited state with other electronic states leads to unique distortions of the lowest energy excited state which result in modifications in the vibronic structure and bandshape of the emission. We have used the emission sideband shapes to evaluate patterns of ground state-excited state and excited state-excited state configurational mixing in some simple series of complexes.

John F. Endicott

2009-10-20

116

Mixing Processes in High-Level Waste Tanks - Final Report  

International Nuclear Information System (INIS)

[en]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

1999-01-01

117

Mixing Processes in High-Level Waste Tanks - Final Report  

Energy Technology Data Exchange (ETDEWEB)

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.

Peterson, P.F.

1999-05-24

118

Cognitive load privileges memory-based over data-driven processing, not group-level over person-level processing.  

Science.gov (United States)

In the current paper, we argue that categorization and individuation, as traditionally discussed and as experimentally operationalized, are defined in terms of two confounded underlying dimensions: a person/group dimension and a memory-based/data-driven dimension. In a series of three experiments, we unconfound these dimensions and impose a cognitive load. Across the three experiments, two with laboratory-created targets and one with participants' friends as the target, we demonstrate that cognitive load privileges memory-based over data-driven processing, not group- over person-level processing. We discuss the results in terms of their implications for conceptualizations of the categorization/individuation distinction, for the equivalence of person and group processes, for the ultimate 'purpose' and meaningfulness of group-based perception and, fundamentally, for the process of categorization, broadly defined. PMID:22449026

Skorich, Daniel P; Mavor, Kenneth I

2012-03-27

119

Cognitive load privileges memory-based over data-driven processing, not group-level over person-level processing.  

UK PubMed Central (United Kingdom)

In the current paper, we argue that categorization and individuation, as traditionally discussed and as experimentally operationalized, are defined in terms of two confounded underlying dimensions: a person/group dimension and a memory-based/data-driven dimension. In a series of three experiments, we unconfound these dimensions and impose a cognitive load. Across the three experiments, two with laboratory-created targets and one with participants' friends as the target, we demonstrate that cognitive load privileges memory-based over data-driven processing, not group- over person-level processing. We discuss the results in terms of their implications for conceptualizations of the categorization/individuation distinction, for the equivalence of person and group processes, for the ultimate 'purpose' and meaningfulness of group-based perception and, fundamentally, for the process of categorization, broadly defined.

Skorich DP; Mavor KI

2013-09-01

120

Levels of processing and language modality specificity in working memory.  

UK PubMed Central (United Kingdom)

Neural networks underpinning working memory demonstrate sign language specific components possibly related to differences in temporary storage mechanisms. A processing approach to memory systems suggests that the organisation of memory storage is related to type of memory processing as well. In the present study, we investigated for the first time semantic, phonological and orthographic processing in working memory for sign- and speech-based language. During fMRI we administered a picture-based 2-back working memory task with Semantic, Phonological, Orthographic and Baseline conditions to 11 deaf signers and 20 hearing non-signers. Behavioural data showed poorer and slower performance for both groups in Phonological and Orthographic conditions than in the Semantic condition, in line with depth-of-processing theory. An exclusive masking procedure revealed distinct sign-specific neural networks supporting working memory components at all three levels of processing. The overall pattern of sign-specific activations may reflect a relative intermodality difference in the relationship between phonology and semantics influencing working memory storage and processing.

Rudner M; Karlsson T; Gunnarsson J; Rnnberg J

2013-03-01

 
 
 
 
121

Cascading activation across levels of representation in children's lexical processing.  

UK PubMed Central (United Kingdom)

ABSTRACTRecent work in adult psycholinguistics has demonstrated that activation of semantic representations begins long before phonological processing is complete. This incremental propagation of information across multiple levels of analysis is a hallmark of adult language processing but how does this ability develop? In two experiments, we elicit measures of incremental activation of semantic representations during word recognition in children. Five-year-olds were instructed to select a target (logs) while their eye-movements were measured to a competitor (key) that was semantically related to an absent phonological associate (lock). We found that, like adults, children made increased looks to competitors relative to unrelated control items. However, unlike adults, children continued to look at the competitor even after the target word was uniquely identified and were more likely to incorrectly select this item. Altogether, these results suggest that early lexical processing involves cascading activation but less efficient resolution of competing entries.

Huang YT; Snedeker J

2010-08-01

122

Levels of processing and acute effects of marijuana on memory.  

UK PubMed Central (United Kingdom)

Subjects' memory for lists of words was tested following the smoking of a single marijuana cigarette containing 1.4% delta 9-THC or a placebo cigarette. During list presentation, each word was preceded by an orienting question which required one of four types of linguistic information (orthographic, phonetic, semantic, or syntactic). Free recall tests were administered immediately after each list (IFR) and following IFR for all five lists (FFR). Results indicated that subjects recalled fewer words while intoxicated with marijuana. There was no interaction between drug condition and level of processing in IFR, but a complex relationship mediated by time was seen in FFR. Drug subjects were more likely to forget meaningfully processed words on recently presented lists. The data provided little support for the hypothesis that marijuana differentially affects the processing and retention of different types of linguistic information.

Belmore SM; Miller LL

1980-08-01

123

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.

2000-01-01

124

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

125

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

126

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

International Nuclear Information System (INIS)

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

1981-01-01

127

Melt-processing method for low level radioactive wastes  

International Nuclear Information System (INIS)

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

1996-09-24

128

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

Energy Technology Data Exchange (ETDEWEB)

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

Soetaert, Anneleen [Department of Biology, Laboratory for Ecophysiology, Biochemistry and Toxicology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium)]. E-mail: anneleen.soetaert@ua.ac.be; Vandenbrouck, Tine [Department of Biology, Laboratory for Ecophysiology, Biochemistry and Toxicology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Ven, Karlijn van der [Department of Biology, Laboratory for Ecophysiology, Biochemistry and Toxicology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Maras, Marleen [Department of Biology, Laboratory for Ecophysiology, Biochemistry and Toxicology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Remortel, Piet van [Department of Mathematics and Informatics, Intelligent Systems Laboratory, University of Antwerp, Middelheimlaan 1, B-2020 Antwerp (Belgium); Blust, Ronny [Department of Biology, Laboratory for Ecophysiology, Biochemistry and Toxicology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Coen, Wim M. de [Department of Biology, Laboratory for Ecophysiology, Biochemistry and Toxicology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium)

2007-07-20

129

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

International Nuclear Information System (INIS)

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

2007-07-20

130

Decontamination of low-level process effluents by reverse osmosis  

International Nuclear Information System (INIS)

A new facility is under construction at the Savannah River Plant to decontaminate process effluents containing low levels of radionuclides and hazardous chemicals prior to discharge to a surface stream. The facility is called the F/H Effluent Treatment Facility (F/H ETF). The effluentes are composed primarily of evaporator condensates which are currently discharged to seepage basins. The new facility will allow closure of the basins in order to meet the provisions of the Resource Conservation and Recovery Act. The 50 million dollar facility will contain advanced water treatment systems representative of the best currently available technology. The paper paper describes the facility and summarizes bench and pilot scale process development work that has been used to establish the design bases for the facility.

1987-01-01

131

Exploring the energy landscape of the charge transport levels in organic semiconductors at the molecular scale.  

UK PubMed Central (United Kingdom)

The extraordinary semiconducting properties of conjugated organic materials continue to attract attention across disciplines including materials science, engineering, chemistry, and physics, particularly with application to organic electronics. Such materials are used as active components in light-emitting diodes, field-effect transistors, or photovoltaic cells, as a substitute for (mostly Si-based) inorganic semiconducting materials. Many strategies developed for inorganic semiconductor device building (doping, p-n junctions, etc.) have been attempted, often successfully, with organics, even though the key electronic and photophysical properties of organic thin films are fundamentally different from those of their bulk inorganic counterparts. In particular, organic materials consist of individual units (molecules or conjugated segments) that are coupled by weak intermolecular forces. The flexibility of organic synthesis has allowed the development of more efficient opto-electronic devices including impressive improvements in quantum yields for charge generation in organic solar cells and in light emission in electroluminescent displays. Nonetheless, a number of fundamental questions regarding the working principles of these devices remain that preclude their full optimization. For example, the role of intermolecular interactions in driving the geometric and electronic structures of solid-state conjugated materials, though ubiquitous in organic electronic devices, has long been overlooked, especially when it comes to these interfaces with other (in)organic materials or metals. Because they are soft and in most cases disordered, conjugated organic materials support localized electrons or holes associated with local geometric distortions, also known as polarons, as primary charge carriers. The spatial localization of excess charges in organics together with low dielectric constant (?) entails very large electrostatic effects. It is therefore not obvious how these strongly interacting electron-hole pairs can potentially escape from their Coulomb well, a process that is at the heart of photoconversion or molecular doping. Yet they do, with near-quantitative yield in some cases. Limited screening by the low dielectric medium in organic materials leads to subtle static and dynamic electronic polarization effects that strongly impact the energy landscape for charges, which offers a rationale for this apparent inconsistency. In this Account, we use different theoretical approaches to predict the energy landscape of charge carriers at the molecular level and review a few case studies highlighting the role of electrostatic interactions in conjugated organic molecules. We describe the pros and cons of different theoretical approaches that provide access to the energy landscape defining the motion of charge carriers. We illustrate the applications of these approaches through selected examples involving OFETs, OLEDs, and solar cells. The three selected examples collectively show that energetic disorder governs device performances and highlights the relevance of theoretical tools to probe energy landscapes in molecular assemblies.

Cornil J; Verlaak S; Martinelli N; Mityashin A; Olivier Y; Van Regemorter T; D'Avino G; Muccioli L; Zannoni C; Castet F; Beljonne D; Heremans P

2013-02-01

132

Exploring the energy landscape of the charge transport levels in organic semiconductors at the molecular scale.  

Science.gov (United States)

The extraordinary semiconducting properties of conjugated organic materials continue to attract attention across disciplines including materials science, engineering, chemistry, and physics, particularly with application to organic electronics. Such materials are used as active components in light-emitting diodes, field-effect transistors, or photovoltaic cells, as a substitute for (mostly Si-based) inorganic semiconducting materials. Many strategies developed for inorganic semiconductor device building (doping, p-n junctions, etc.) have been attempted, often successfully, with organics, even though the key electronic and photophysical properties of organic thin films are fundamentally different from those of their bulk inorganic counterparts. In particular, organic materials consist of individual units (molecules or conjugated segments) that are coupled by weak intermolecular forces. The flexibility of organic synthesis has allowed the development of more efficient opto-electronic devices including impressive improvements in quantum yields for charge generation in organic solar cells and in light emission in electroluminescent displays. Nonetheless, a number of fundamental questions regarding the working principles of these devices remain that preclude their full optimization. For example, the role of intermolecular interactions in driving the geometric and electronic structures of solid-state conjugated materials, though ubiquitous in organic electronic devices, has long been overlooked, especially when it comes to these interfaces with other (in)organic materials or metals. Because they are soft and in most cases disordered, conjugated organic materials support localized electrons or holes associated with local geometric distortions, also known as polarons, as primary charge carriers. The spatial localization of excess charges in organics together with low dielectric constant (?) entails very large electrostatic effects. It is therefore not obvious how these strongly interacting electron-hole pairs can potentially escape from their Coulomb well, a process that is at the heart of photoconversion or molecular doping. Yet they do, with near-quantitative yield in some cases. Limited screening by the low dielectric medium in organic materials leads to subtle static and dynamic electronic polarization effects that strongly impact the energy landscape for charges, which offers a rationale for this apparent inconsistency. In this Account, we use different theoretical approaches to predict the energy landscape of charge carriers at the molecular level and review a few case studies highlighting the role of electrostatic interactions in conjugated organic molecules. We describe the pros and cons of different theoretical approaches that provide access to the energy landscape defining the motion of charge carriers. We illustrate the applications of these approaches through selected examples involving OFETs, OLEDs, and solar cells. The three selected examples collectively show that energetic disorder governs device performances and highlights the relevance of theoretical tools to probe energy landscapes in molecular assemblies. PMID:23140088

Cornil, J; Verlaak, S; Martinelli, N; Mityashin, A; Olivier, Y; Van Regemorter, T; D'Avino, G; Muccioli, L; Zannoni, C; Castet, F; Beljonne, D; Heremans, P

2012-11-09

133

Empirical Multiresolution Models Applicable to Gray-Level Image Processing  

UK PubMed Central (United Kingdom)

This paper deals with empirical multiresolution linear models intended for image processing. Such models containinformation about gray-level compos!tion of regions in the image. First, a general method for building these models fromsamples of selected images is described. Then, a measure of their quality, based on the Jensen-Shannon divergence, isintroduced. This divergence is also ued as a distance measure for classifying images. Applications in non-linear imagefiltering are provided, giving better result than classical median filtering. 1997 Published by Elsevier Science B.V.

Maria Josh Gqarcia-salinas A; Juan Francisco Gmez-lopera A; Pedro Luis Luque-escamilla B; Jos Martinez-aroza C; Ramn Rom/tn-rold/tn B; J. Carlos Segura-luna D

134

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2000-08-01

135

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

136

A case study: application of statistical process control tool for determining process capability and sigma level.  

UK PubMed Central (United Kingdom)

UNLABELLED: Statistical process control is the application of statistical methods to the measurement and analysis of variation process. Various regulatory authorities such as Validation Guidance for Industry (2011), International Conference on Harmonisation ICH Q10 (2009), the Health Canada guidelines (2009), Health Science Authority, Singapore: Guidance for Product Quality Review (2008), and International Organization for Standardization ISO-9000:2005 provide regulatory support for the application of statistical process control for better process control and understanding. In this study risk assessments, normal probability distributions, control charts, and capability charts are employed for selection of critical quality attributes, determination of normal probability distribution, statistical stability, and capability of production processes, respectively. The objective of this study is to determine tablet production process quality in the form of sigma process capability. By interpreting data and graph trends, forecasting of critical quality attributes, sigma process capability, and stability of process were studied. The overall study contributes to an assessment of process at the sigma level with respect to out-of-specification attributes produced. Finally, the study will point to an area where the application of quality improvement and quality risk assessment principles for achievement of six sigma-capable processes is possible. LAY ABSTRACT: Statistical process control is the most advantageous tool for determination of the quality of any production process. This tool is new for the pharmaceutical tablet production process. In the case of pharmaceutical tablet production processes, the quality control parameters act as quality assessment parameters. Application of risk assessment provides selection of critical quality attributes among quality control parameters. Sequential application of normality distributions, control charts, and capability analyses provides a valid statistical process control study on process. Interpretation of such a study provides information about stability, process variability, changing of trends, and quantification of process ability against defective production. Comparative evaluation of critical quality attributes by Pareto charts provides the least capable and most variable process that is liable for improvement. Statistical process control thus proves to be an important tool for six sigma-capable process development and continuous quality improvement.

Chopra V; Bairagi M; Trivedi P; Nagar M

2012-03-01

137

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

Scientific Electronic Library Online (English)

Full Text Available 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 problem identifies the property targets corresponding to the desired process performance. The second reverse problem is the reverse of a property prediction problem, which identifi (more) es 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.

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

2010-09-01

138

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; N. G. Chemmangattuvalappil; C. C. Solvason; M. R. Eden

2010-01-01

139

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

Scientific Electronic Library Online (English)

Full Text Available Abstract in spanish En este artculo se discute el fenmeno del empoderamiento y se analiza la distincin terica 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 diferenciacin es poco viable en trminos objetivos y absolutos o de esencia, pero s til, en trminos analticos, desde la percepcin de la propia comunidad involucrada, (more) que debe ser comprendida por el colaborador externo. Tambin se propone establecer una diferencia entre contexto y nivel de empoderamiento, y analizar el contexto del fenmeno en los niveles individual, organizacional y comunitario del agregado social, lo que aporta claridad a su definicin. De esta manera adquiere centralidad la concepcin del empoderamiento como proceso en sucesivos contextos que benefician no slo 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 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 (more) ) 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

Silva, Carmen; Martnez, Mara Loreto

2004-11-01

140

Process technology for vitrification of high level waste  

International Nuclear Information System (INIS)

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

2009-10-01

 
 
 
 
141

Role of the Maillard reaction in aging and age-related diseases. Studies at the cellular-molecular level.  

UK PubMed Central (United Kingdom)

Abstract Increase in life expectancy concerns most populations but more importantly developed countries. This increase is accompanied by the shift of chronic diseases to the senior population, especially cardiovascular diseases and diabetes type II. Aging mechanisms, mostly post-genetic, comprise among others the Maillard reaction which strongly contributes by several harmful processes to the age-dependent decline of tissue structure and function. Several of these mechanisms were studied in our laboratory at the cellular-molecular level and will be described in this review with respect to their role in aging and age-related pathologies, especially cardiovascular diseases.

Robert L; Labat-Robert J

2013-03-01

142

COPRED: prediction of fold, GO molecular function and functional residues at the domain level.  

UK PubMed Central (United Kingdom)

SUMMARY: Only recently the first resources devoted to the functional annotation of proteins at the domain level started to appear. The next step is to develop specific methodologies for predicting function at the domain level based on these resources, and to implement them in web servers to be used by the community. In this work, we present COPRED, a web server for the concomitant prediction of fold, molecular function and functional sites at the domain level, based on a methodology for domain molecular function prediction and a resource of domain functional annotations previously developed and benchmarked. Availability and implementation: COPRED can be freely accessed at http://csbg.cnb.csic.es/copred. The interface works in all standard web browsers. WebGL (natively supported by most browsers) is required for the in-line preview and manipulation of protein 3D structures. The website includes a detailed help section and usage examples. CONTACT: pazos@cnb.csic.es.

Lpez D; Pazos F

2013-07-01

143

Tree-indexed processes: a high level crossing analysis  

Directory of Open Access Journals (Sweden)

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

Mark Kelbert; Yuri Suhov

2003-01-01

144

The determinants of the molecular substitution process in turtles.  

UK PubMed Central (United Kingdom)

Neutral rates of molecular evolution vary across species, and this variation has been shown to be related to biological traits. One of the first patterns to be observed in vertebrates has been an inverse relationship between body mass (BM) and substitution rates. The effects of three major life-history traits (LHT) that covary with BM - metabolic rate, generation time and longevity (LON) - have been invoked to explain this relationship. However, most of the theoretical and empirical evidence supporting this relationship comes from endothermic vertebrates, that is, mammals and birds, in which the environmental conditions, especially temperature, do not have a direct impact on cellular and molecular biology. We analysed the variations in mitochondrial and nuclear rates of synonymous substitution across 224 turtle species and examined their correlation with two LHT (LON and BM) and two environmental variables [latitude (LAT) and habitat]. Our analyses indicate that in turtles, neutral rates of molecular evolution are hardly correlated with LON or BM. Rather, both the mitochondrial and nuclear substitution rates are significantly correlated with LAT - faster evolution in the tropics - and especially so for aquatic species. These results question the generality of the relationships reported in mammals and birds and suggest that environmental factors might be the strongest determinants of the mutation rate in ectotherms.

Loureno JM; Glmin S; Chiari Y; Galtier N

2013-01-01

145

The determinants of the molecular substitution process in turtles.  

Science.gov (United States)

Neutral rates of molecular evolution vary across species, and this variation has been shown to be related to biological traits. One of the first patterns to be observed in vertebrates has been an inverse relationship between body mass (BM) and substitution rates. The effects of three major life-history traits (LHT) that covary with BM - metabolic rate, generation time and longevity (LON) - have been invoked to explain this relationship. However, most of the theoretical and empirical evidence supporting this relationship comes from endothermic vertebrates, that is, mammals and birds, in which the environmental conditions, especially temperature, do not have a direct impact on cellular and molecular biology. We analysed the variations in mitochondrial and nuclear rates of synonymous substitution across 224 turtle species and examined their correlation with two LHT (LON and BM) and two environmental variables [latitude (LAT) and habitat]. Our analyses indicate that in turtles, neutral rates of molecular evolution are hardly correlated with LON or BM. Rather, both the mitochondrial and nuclear substitution rates are significantly correlated with LAT - faster evolution in the tropics - and especially so for aquatic species. These results question the generality of the relationships reported in mammals and birds and suggest that environmental factors might be the strongest determinants of the mutation rate in ectotherms. PMID:23176666

Loureno, J M; Glmin, S; Chiari, Y; Galtier, N

2012-11-23

146

Impact of Altimeter Data Processing on Sea Level Studies  

Directory of Open Access Journals (Sweden)

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

M. Joana Fernandes; Susana Barbosa; Clara Lázaro

2006-01-01

147

Design and Synthesis of Molecular Donors for Solution-Processed High-Efficiency Organic Solar Cells.  

UK PubMed Central (United Kingdom)

Organic semiconductors incorporated into solar cells using a bulk heterojunction (BHJ) construction show promise as a cleaner answer to increasing energy needs throughout the world. Organic solar cells based on the BHJ architecture have steadily increased in their device performance over the past two decades, with power conversion efficiencies reaching 10%. Much of this success has come with conjugated polymer/fullerene combinations, where optimized polymer design strategies, synthetic protocols, device fabrication procedures, and characterization methods have provided significant advancements in the technology. More recently, chemists have been paying particular attention to well-defined molecular donor systems due to their ease of functionalization, amenability to standard organic purification and characterization methods, and reduced batch-to-batch variability compared to polymer counterparts. There are several critical properties for efficient small molecule donors. First, broad optical absorption needs to extend towards the near-IR region to achieve spectral overlap with the solar spectrum. Second, the low lying highest occupied molecular orbital (HOMO) energy levels need to be between -5.2 and -5.5 eV to ensure acceptable device open circuit voltages. Third, the structures need to be relatively planar to ensure close intermolecular contacts and high charge carrier mobilities. And last, the small molecule donors need to be sufficiently soluble in organic solvents (?10 mg/mL) to facilitate solution deposition of thin films of appropriate uniformity and thickness. Ideally, these molecules should be constructed from cost-effective, sustainable building blocks using established, high yielding reactions in as few steps as possible. The structures should also be easy to functionalize to maximize tunability for desired properties. In this Account, we present a chronological description of our thought process and design strategies used in the development of highly efficient molecular donors that achieve power conversion efficiencies greater than 7%. The molecules are based on a modular D(1)-A-D(2)-A-D(1) architecture, where A is an asymmetric electron deficient heterocycle, which allowed us to quickly access a library of compounds and develop structure-property-performance relationships. Modifications to the D1 and D2 units enable spectral coverage throughout the entire visible region and control of HOMO energy levels, while adjustments to the pendant alkyl substituents dictate molecular solubility, thermal transition temperatures, and solid-state organizational tendencies. Additionally, we discuss regiochemical considerations that highlight how individual atom placements can significantly influence molecular and subsequently device characteristics. Our results demonstrate the utility of this architecture for generating promising materials to be integrated into organic photovoltaic devices, call attention to areas for improvement, and provide guiding principles to sustain the steady increases necessary to move this technology forward.

Coughlin JE; Henson ZB; Welch GC; Bazan GC

2013-08-01

148

Levels and Atypical Evolutions of the Romanian Demographic Processes  

Directory of Open Access Journals (Sweden)

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

Mirela Ionela Aceleanu

2007-01-01

149

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.

Bonifaci Nria; Berenguer Antoni; Dez Javier; Reina Oscar; Medina Ignacio; Dopazo Joaqun; Moreno Vctor; Pujana Miguel

2008-01-01

150

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; M. Pelo; K. Leivisk

2013-01-01

151

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; M. Pelo; K. Leivisk

2012-01-01

152

Sequential Remediation Processes for a Low Level Pesticide Wastewater  

Directory of Open Access Journals (Sweden)

Full Text Available The aim of this study was to develop a remediation system for the treatment of a low-level pesticide wastewater that uses available onfarm organic matter as an absorption media, is capable of reducing the concentration of the pesticide to a safe level and is economically viable for implementation by farmers. The absorption capacity of chopped hay and soybean to the fungicide captan was evaluated under batch conditions and the effectiveness of the composting process in depredating captan in contaminated organic materials was evaluated. The results showed that both hay and soybean plant residues were very effective in absorbing 99.2% and 98.5% of captan form the wastewater after 4 hours, respectively. Because of its availability, hay can be used in an onfarm pesticide immobilization system that consists of shallow reinforced concrete pit (filled with hay) with steel bars across the top for machinery to roll onto and be washed. The wastewater can be retained for 24 hours which is a sufficient time for hay to absorb the captan. The contaminated hay can then be composted. The addition of used cooking oil raised the temperature of the composting mixture to 63?C. Small reductions in moisture content (from 60% to 58.9 %) and C:N ratio (from 30:1 to 28:1) were observed while reductions of 18.92%, 15.56% and 4.8% in the volatile solids, total carbon total Kjeldahl nitrogen were achieved after 10 d of composting, respectively. About 92.4% of the captan was degraded in the first 4 days of composting. Most of captan (92.4%) was degraded during the mesophilic stage (first 3 days). The degradation rate constant for the mesophilic stage (0.724 d-1) was 2.74 times the degradation rate constant for the thermophilic stage (0.264 d-1). An onfarm windrow composting process would be very effective in degrading captan contaminated hay. The captan contaminated hay could be mixed with equal amount poultry manure or dairy manure to provide the required bioavailable carbon and nutrients for the composting process. Some used cooking oil could also be added to maintain higher temperature within the compost matrix. The windrows should be mixed on a daily basis to provide sufficient oxygen for the composting microorganisms.

Mariam T. Al hattab; Abdel E. Ghaly

2012-01-01

153

Steered molecular dynamics simulations on the "tail helix latch" hypothesis in the gelsolin activation process.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The molecular basis of the "tail helix latch" hypothesis in the gelsolin activation process has been studied by using the steered molecular dynamics simulations. In the present nanosecond scale simulations, the tail helix of gelsolin was pulled away from the S2 binding surface, and the required forc...

Cheng, Feng; Shen, Jianhua; Luo, Xiaomin; Jiang, Hualiang; Chen, Kaixian

154

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

155

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

Energy Technology Data Exchange (ETDEWEB)

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

Williams, J.M.

1995-12-31

156

Molecular connections between nuclear and ciliary import processes.  

UK PubMed Central (United Kingdom)

As an organelle, the cilium contains a unique complement of protein and lipid. Recent work has begun to shed light on the mechanisms that regulate entry of ciliary proteins into the compartment. Here, we focus on the mechanisms that regulate ciliary entry of cytosolic molecules. Studies have revealed a size exclusion mechanism for ciliary entry that is similar to the barrier to nuclear entry. Active import into the ciliary compartment involves nuclear trafficking components including importins, a Ran-guanosine triphosphate gradient, and nucleoporins. Together, this work indicates that nuclei and cilia share molecular, structural and mechanistic components that regulate import into the compartments.

Kee HL; Verhey KJ

2013-01-01

157

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

International Nuclear Information System (INIS)

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

2007-02-01

158

Unexpected high levels of molecular chlorine observed at Barrow in spring 2009 during OASIS  

Science.gov (United States)

Very high levels of molecular chlorine (Cl2) (up to ~400 pptv) and very little bromine monochloride (BrCl) were observed at Barrow, AK during the ocean-atmosphere- sea ice-snowpack (OASIS) campaign. Diurnal profiles of Cl2 were observed with maximum levels in the early morning and late afternoon and no significant concentrations at night. BrCl was only detected when Cl2 was present. We suggest that BrCl is likely produced from heterogeneous reaction of chlorine compounds (e.g. Cl2, hypochlorous acid (HOCl) or hydrogen chloride (HCl)). The ultimate source of the molecular chlorine was not established but it was found to depend on ozone and actinic flux. The observed HCl levels were generally consistent with HCl levels predicted from the observed Cl2. HOCl concentrations derived from the observed Cl2 were much lower than the observed Cl2 levels. A time dependent model will be used to simulate the average diurnal profiles of Cl2, HOCl, ClO, HCl, and BrCl and investigate the chemical production and loss rates to sustain the diurnal profiles of Cl2 and BrCl. High levels of Cl2 have a significant impact on ozone loss and methane oxidation. Cl atom produced from Cl2 is the dominant oxidant of methane at Barrow in spring. More measurements of Cl2 are needed to investigate whether Cl2 is ubiquitous in polar regions.

Liao, J.; Huey, L. G.; Tanner, D.; Shepson, P. B.; Stephens, C. R.; Flocke, F. M.; Orlando, J. J.; Apel, E. C.; Fried, A.; Weinheimer, A. J.; Knapp, D. J.; Montzka, D.; Hall, S. R.; Ullmann, K.

2011-12-01

159

Separation and molecular-level segregation of complex alkane mixtures in metal-organic frameworks.  

Science.gov (United States)

In this computational work we explore metal-organic frameworks (MOFs) for separating alkanes according to the degree of branching. We show that the structure MOF-1 shows an adsorption hierarchy for a 13-component light naphtha mixture precisely as desired for increasing the research octane number of gasoline. In addition we report an unusual molecular-level segregation of molecules based on their degree of branching. PMID:18651737

Dubbeldam, David; Galvin, Casey J; Walton, Krista S; Ellis, Donald E; Snurr, Randall Q

2008-07-24

160

The SYNROC process for immobilizing high-level nuclear wastes  

International Nuclear Information System (INIS)

[en]The status of the SYNROC process for immobilizing high-level wastes from reprocessed commercial nuclear power reactor fuel is described. The variant of SYNROC designed for this purpose is SYNROC-C; other variants, SYNROC-B,-D,-E and -F, are not discussed in detail. Long-term, quasi-dynamic aqueous leaching tests at 95 to 200 deg. C show that after 10 to 20 days, SYNROC-C is 500 to 10 000 times more resistant to leaching than borosilicate waste glass. The effects of radiation damage on SYNROC phases have been assessed by studying natural zirconolites and perovskites that have experienced large ?-radiation doses from contained radioactive elements over geological time; the doses are often far greater than SYNROC would receive in 1 million years. Isotopic studies show that these minerals, although metamict, have quantitatively retained U, Th and daughter products. In a parallel study, SYNROC-B, SYNROC-C and their constituent phases have been subjected to fast neutron irradiation, simulating 1 million years of SYNROC-C ageing. Volume expansions were observed but all specimens remained intact. The Australian Government is supporting a joint Australian Atomic Energy Commission/Australian National University project which will lead to the construction of a demonstration plant for the production of SYNROC containing simulated non-radioactive waste. The production rate will be about 20 kg of SYNROC per hour and the plant is scheduled to go into operation in 1985. The conceptual flowsheet involves the uniaxial hot pressing of SYNROC containing 2% of admixed fine Ti metal powder in unsupported thin-walled stainless-steel cans with a bellows configuration. The SYNROC process claims to offer several advantages over the current technologies for borosilicate waste glass manufacture. (author)

1984-01-01

 
 
 
 
161

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

DEFF Research Database (Denmark)

The objective of this paper is to introduce the new concept of property integration. It is based on tracking and integrating properties throughout the process. This is made possible by exploiting the unique features at the interface of process and molecular design. Recently developed clustering concepts are employed to identify optimal properties without commitment to specific species. Subsequently, group contribution methods and molecular design techniques are employed to solve the reverse property prediction problem to design molecules possessing the optimal properties.

162

An examination of relationship between subliminal perception, visual information processing, levels of processing, and hemispheric asymmetries.  

Science.gov (United States)

A sublimiinal letter was exposed to the left or right hemisphere for either 15 or 30 msec. Subjective guesses were more accurate for visuo-spatial positional recognition made to presentations in the right hemisphere whereas verbal recognition was more accurate to presentations in the left hemisphere. The 30-msec. exposure increased the accuracy of the guesses. These findings were discussed in terms of differential triggering mechanisms for levels of hemispheric processing. PMID:514764

Charman, D K

1979-10-01

163

An examination of relationship between subliminal perception, visual information processing, levels of processing, and hemispheric asymmetries.  

UK PubMed Central (United Kingdom)

A sublimiinal letter was exposed to the left or right hemisphere for either 15 or 30 msec. Subjective guesses were more accurate for visuo-spatial positional recognition made to presentations in the right hemisphere whereas verbal recognition was more accurate to presentations in the left hemisphere. The 30-msec. exposure increased the accuracy of the guesses. These findings were discussed in terms of differential triggering mechanisms for levels of hemispheric processing.

Charman DK

1979-10-01

164

Rearrangement and predissociation processes in negative molecular ions of nitrobenzenes.  

UK PubMed Central (United Kingdom)

The reactions of resonant electron capture by the molecules of benzene nitroderivatives has been studied in the gas phase. Some fragment negative ions were found to be unstable with respect to electron autodetachment. This circumstance has been used for the determination of their structure. In particular, it has been established that the low measured appearance energy of neutral component of [M-H](-) ion beam is a result of isomerization of nitrobenzenes' molecular ion, leading to the 2-nitrosophenol structure with the subsequent formation of the phenoxide anion in the autodetaching state. The effective yield curves of some types of fragment ions demonstrate fine vibrational structures, testifying the predissociation mechanism of ion formation. For all detected ions, the absolute cross sections of formation have been measured.

Muftakhov MV; Khatymov RV; Shchukin PV; Pogulay AV; Mazunov VA

2010-01-01

165

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

Energy Technology Data Exchange (ETDEWEB)

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

Stimson, Lorna M

2003-07-01

166

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

167

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

Energy Technology Data Exchange (ETDEWEB)

The principal source of negative ion generation in hydrogen discharges is now recognized to be low-energy electron attachment to H/sub 2/(/nu//prime//prime/) molecules excited to the middle portion of the vibrational spectrum. Electron excitation processes are generally taken to be the principal source of H/sub 2/(/nu//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 /nu//prime//prime/, to level /nu//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 H/sub 2//sup +/ and H/sub 3//sup +/ 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 H/sub 2/(/nu//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 H/sub 2//sup /minus// ions formed in the surface selvage. A recent paper has demonstrated the efficacy of Ba surfaces as an active medium for H/sup /minus// formation. Here we shall extend our discussion to H/sub 2//sup +/, H/sub 3//sup +/ collisions on Ba surfaces and inventory the generation of H, H/sub 2/(/nu//prime//prime/), and H/sup /minus// rebounding from these surfaces. 16 refs., 4 figs.

Hiskes, J.R.; Karo, A.M.

1989-07-03

168

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

DEFF Research Database (Denmark)

BACKGROUND: Several studies have shown that type 1 diabetic patients have elevated total levels of the adipocyte-derived adipocytokine adiponectin. However, adiponectin circulates in three different subforms, and the high-molecular-weight (HMW) subform is believed to be the primary biologically active form. The effects of the medium-molecular-weight (MMW) subform and the low-molecular-weight (LMW) subform are still unresolved. PURPOSE: The objective of the study was to investigate the distribution of the three molecular subforms of adiponectin in well-characterized groups of type 1 diabetics with varying degrees of nephropathy as well as in healthy control subjects. STUDY POPULATION: Two hundred seven individuals were included: 58 type 1 diabetics with normoalbuminuria, 46 with microalbuminuria, 46 with macroalbuminuria, and 57 matched controls. METHODS: The HMW, MMW, and LMW subforms were measured using a validated in-house time-resolved immunoflourometric assay after separation by fast protein liquid chromatography. RESULTS: The absolute concentrations of total adiponectin and all subforms were higher in type 1 diabetic patients than healthy controls. However, the relative HMW fraction was up-regulated in type 1 diabetes (P < 0.001), whereas the MMW (P < 0.001) and LMW fractions (P < 0.05) were down-regulated, compared with controls. Accordingly, the increase in concentration of total adiponectin was primarily caused by a major increase of the HMW subform. Levels of total adiponectin and the HMW subform (absolute and relative) were generally unaffected by nephropathy status defined by urinary albumin excretion rate. CONCLUSION: Type 1 diabetes per se is associated with higher adiponectin levels than healthy subjects. This increase is mainly explained by an elevation in the HMW subform. The elevation is unaffected by gender and diabetic kidney disease Udgivelsesdato: 2008/8

Leth, H.; Andersen, K.K.

2008-01-01

169

The Dissolution of Polyols in Salt Solutions and Ionic Liquids at Molecular Level: Ions, Counter Ions, and Hofmeister Effects.  

UK PubMed Central (United Kingdom)

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.

Papanyan Z; Roth C; Wittler K; Reimann S; Ludwig R

2013-07-01

170

Two-electron processes in ionization of molecular hydrogen  

Energy Technology Data Exchange (ETDEWEB)

Cross sections for double ionization and ionization plus excitation of H[sub 2] by high-energy charged particles are calculated as a function of the orientation of the H[sub 2] internuclear axis. The contributions of the double-collision process, and the shake-off or shake-up processes have been considered. The results are compared with the data of Edwards et al. The theoretical and measured cross sections have the same magnitude, and shake-off/up is more important than double collision in the considered energy interval. (orig.)

Nagy, L. (Magyar Tudomanyos Akademia, Debrecen (Hungary). Atommag Kutato Intezete); Vegh, L. (Magyar Tudomanyos Akademia, Debrecen (Hungary). Atommag Kutato Intezete)

1994-03-01

171

Quantitative molecular level understanding of ethoxysilane at poly(dimethylsiloxane)/polymer interfaces.  

Science.gov (United States)

Because of the wide applications of silicone adhesives, it is important to study adhesion mechanisms of silicone elastomers to polymers. Adhesion properties are believed to be directly related to the molecular structures at the adhesive/substrate interfaces. To improve adhesion, adhesion promoters such as silanes are commonly used to modify the interfacial structures. It is difficult to study buried interfacial molecular structures between two materials in situ using conventional analytical techniques. In this study, sum frequency generation (SFG) vibrational spectroscopy was used to investigate molecular structures at buried silicone/poly(ethylene terephthalate) (PET) interfaces. Environmental-friendly epoxysilanes including (3-glycidoxypropyl)triethoxysilane (?-GPES), (3-glycidoxypropyl)methyldiethoxysilane (?-GPDES), and (3-glycidoxypropyl)dimethylethoxysilane (?-GPDMES) and their mixtures with methylvinylsiloxanol (MVS) were used as adhesion promoters to modify silicone adhesion properties to PET. Various PET/silane, PET/uncured silicone, and PET/cured silicone interfaces were examined. The interfacial structures deduced from SFG spectra were correlated to adhesion testing results. It was found that silane headgroup order at the polymer interfaces is an important factor for improving adhesion. The decrease of silane headgroup order due to chemical reaction and disordering of such groups at the polymer interfaces can be associated with improved adhesion. The molecular level understanding on polymer/adhesive interfacial structures helps to design and develop adhesion promoters and polymer adhesives with improved performance. PMID:23241016

Zhang, Chi; Chen, Zhan

2012-12-28

172

Quantitative molecular level understanding of ethoxysilane at poly(dimethylsiloxane)/polymer interfaces.  

UK PubMed Central (United Kingdom)

Because of the wide applications of silicone adhesives, it is important to study adhesion mechanisms of silicone elastomers to polymers. Adhesion properties are believed to be directly related to the molecular structures at the adhesive/substrate interfaces. To improve adhesion, adhesion promoters such as silanes are commonly used to modify the interfacial structures. It is difficult to study buried interfacial molecular structures between two materials in situ using conventional analytical techniques. In this study, sum frequency generation (SFG) vibrational spectroscopy was used to investigate molecular structures at buried silicone/poly(ethylene terephthalate) (PET) interfaces. Environmental-friendly epoxysilanes including (3-glycidoxypropyl)triethoxysilane (?-GPES), (3-glycidoxypropyl)methyldiethoxysilane (?-GPDES), and (3-glycidoxypropyl)dimethylethoxysilane (?-GPDMES) and their mixtures with methylvinylsiloxanol (MVS) were used as adhesion promoters to modify silicone adhesion properties to PET. Various PET/silane, PET/uncured silicone, and PET/cured silicone interfaces were examined. The interfacial structures deduced from SFG spectra were correlated to adhesion testing results. It was found that silane headgroup order at the polymer interfaces is an important factor for improving adhesion. The decrease of silane headgroup order due to chemical reaction and disordering of such groups at the polymer interfaces can be associated with improved adhesion. The molecular level understanding on polymer/adhesive interfacial structures helps to design and develop adhesion promoters and polymer adhesives with improved performance.

Zhang C; Chen Z

2013-01-01

173

A probe to study the toxic interaction of tartrazine with bovine hemoglobin at the molecular level.  

Science.gov (United States)

Tartrazine is an artificial azo dye commonly used in food products, but tartrazine in the environment is potentially harmful. The toxic interaction between tartrazine and bovine hemoglobin (BHb) was investigated using fluorescence, synchronous fluorescence, UV-vis absorption, circular dichroism (CD) and molecular modeling techniques under simulated physiological conditions. The fluorescence data showed that tartrazine can bind with BHb to form a complex. The binding process was a spontaneous molecular interaction, in which van der Waals' forces and hydrogen bonds played major roles. Molecular docking results showed that the hydrogen bonds exist between the oxygen atoms at position 31 of tartrazine and the nitrogen atom NZ7 on Lys99, and also between the oxygen atoms at position 15 of tartrazine and the nitrogen atom NZ7 on Lys104, Lys105. The results of UV-vis and CD spectra revealed that tartrazine led to conformational changes in BHb, including loosening of the skeleton structure and decreasing ? helix in the secondary structure. The synchronous fluorescence experiment revealed that tartrazine binds into the hemoglobin central cavity, and this was verified using a molecular modeling study. Copyright 2013 John Wiley & Sons, Ltd. PMID:23653408

Li, Yating; Wei, Haoran; Liu, Rutao

2013-05-01

174

A probe to study the toxic interaction of tartrazine with bovine hemoglobin at the molecular level.  

UK PubMed Central (United Kingdom)

Tartrazine is an artificial azo dye commonly used in food products, but tartrazine in the environment is potentially harmful. The toxic interaction between tartrazine and bovine hemoglobin (BHb) was investigated using fluorescence, synchronous fluorescence, UV-vis absorption, circular dichroism (CD) and molecular modeling techniques under simulated physiological conditions. The fluorescence data showed that tartrazine can bind with BHb to form a complex. The binding process was a spontaneous molecular interaction, in which van der Waals' forces and hydrogen bonds played major roles. Molecular docking results showed that the hydrogen bonds exist between the oxygen atoms at position 31 of tartrazine and the nitrogen atom NZ7 on Lys99, and also between the oxygen atoms at position 15 of tartrazine and the nitrogen atom NZ7 on Lys104, Lys105. The results of UV-vis and CD spectra revealed that tartrazine led to conformational changes in BHb, including loosening of the skeleton structure and decreasing ? helix in the secondary structure. The synchronous fluorescence experiment revealed that tartrazine binds into the hemoglobin central cavity, and this was verified using a molecular modeling study. Copyright 2013 John Wiley & Sons, Ltd.

Li Y; Wei H; Liu R

2013-05-01

175

The principle of coherence in multi-level brain information processing.  

UK PubMed Central (United Kingdom)

Synchronisation has become one of the major scientific tools to explain biological order at many levels of organisation. In systems neuroscience, synchronised subthreshold and suprathreshold oscillatory neuronal activity within and between distributed neuronal assemblies is acknowledged as a fundamental mode of neuronal information processing. Coherent neuronal oscillations correlate with all basic cognitive functions, mediate local and long-range neuronal communication and affect synaptic plasticity. However, it remains unclear how the very fast and complex changes of functional neuronal connectivity necessary for cognition, as mediated by dynamic patterns of neuronal synchrony, could be explained exclusively based on the well-established synaptic mechanisms. A growing body of research indicates that the intraneuronal matrix, composed of cytoskeletal elements and their binding proteins, structurally and functionally connects the synapses within a neuron, modulates neurotransmission and memory consolidation, and is hypothesised to be involved in signal integration via electric signalling due to its charged surface. Theoretical modelling, as well as emerging experimental evidence indicate that neuronal cytoskeleton supports highly cooperative energy transport and information processing based on molecular coherence. We suggest that long-range coherent dynamics within the intra- and extracellular filamentous matrices could establish dynamic ordered states, capable of rapid modulations of functional neuronal connectivity via their interactions with neuronal membranes and synapses. Coherence may thus represent a common denominator of neurophysiological and biophysical approaches to brain information processing, operating at multiple levels of neuronal organisation, from which cognition may emerge as its cardinal manifestation.

Plankar M; Brean S; Jerman I

2013-01-01

176

Molecular level investigations of the inter- and intramolecular interactions of pH-responsive artificial triblock proteins.  

UK PubMed Central (United Kingdom)

Intelligent materials that can undergo physical gelation in response to environmental stimuli have potential impacts in the bioengineering and biomedical fields where the entrapment of cellular or molecular species is desired. Here, we utilize atomic force microscopy (AFM) to perform molecular level investigations of designer artificial proteins that undergo physical gelation. These are engineered as triblock copolymers with independent interchain binding and solvent retention functions, namely, two terminal leucine zipper-like peptide sequences and a central alanylglycine rich sequence, respectively. AFM force measurements between probes and surfaces functionalized with molecules of this triblock protein revealed adhesive interactions that increased in average force and frequency as the pH was lowered from pH 11.2 to 7.4 to 4.5, reflecting an increase in the numbers of interacting molecular strands. In bulk solution, lowering the pH results in a viscous liquid to gel transition. The modular design of the triblock protein was also exploited for single molecule force spectroscopy investigations, which revealed altered intramolecular interactions in response to changes in pH. An increased understanding of the inter- and intramolecular forces involved in biomolecule driven gelation processes is not only of great fundamental interest in the study of the biomolecular systems involved but may also prove key in enabling the rational design of new generations of intelligent hydrogel systems.

Stevens MM; Allen S; Davies MC; Roberts CJ; Sakata JK; Tendler SJ; Tirrell DA; Williams PM

2005-05-01

177

Molecular level investigations of the inter- and intramolecular interactions of pH-responsive artificial triblock proteins.  

Science.gov (United States)

Intelligent materials that can undergo physical gelation in response to environmental stimuli have potential impacts in the bioengineering and biomedical fields where the entrapment of cellular or molecular species is desired. Here, we utilize atomic force microscopy (AFM) to perform molecular level investigations of designer artificial proteins that undergo physical gelation. These are engineered as triblock copolymers with independent interchain binding and solvent retention functions, namely, two terminal leucine zipper-like peptide sequences and a central alanylglycine rich sequence, respectively. AFM force measurements between probes and surfaces functionalized with molecules of this triblock protein revealed adhesive interactions that increased in average force and frequency as the pH was lowered from pH 11.2 to 7.4 to 4.5, reflecting an increase in the numbers of interacting molecular strands. In bulk solution, lowering the pH results in a viscous liquid to gel transition. The modular design of the triblock protein was also exploited for single molecule force spectroscopy investigations, which revealed altered intramolecular interactions in response to changes in pH. An increased understanding of the inter- and intramolecular forces involved in biomolecule driven gelation processes is not only of great fundamental interest in the study of the biomolecular systems involved but may also prove key in enabling the rational design of new generations of intelligent hydrogel systems. PMID:15877341

Stevens, Molly M; Allen, Stephanie; Davies, Martyn C; Roberts, Clive J; Sakata, Jill K; Tendler, Saul J B; Tirrell, David A; Williams, Philip M

178

PROCESS FOR INCREASING THE LEVEL OF POLYAMINES IN CULTIVATED PLANTS AND PROCESS FOR SELECTING THE BACTERIA USEFUL IN THE PROCESS FOR INCREASING THE LEVEL OF POLYAMINES IN PLANTS  

UK PubMed Central (United Kingdom)

The invention relates to a process for increasing the level of polyamines in cultivated plants concomitantly with the reduction of the phytosanitary risk associated to necrophilic phytopathogenic agents. The process consists in cultivating a protective leguminous plant, during winter, and transforming said green crop into bioactive mulch by herbiciding and treating with bacteria antagonistic to necrophilic phytopathogenic agents, resistant to the total amount of used herbicides and exhibiting a capacity of releasing polyamines and precursors thereof from the vegetable material, seeding and growing the crops in the bioactive mulch.

OANCEA FLORIN; OANA SICUIA; DINU SORINA; ZAMFIROPOL ROXANA; CONSTANTINESCU FLORICA

179

Molecular basis of processing wheat gluten toward biobased materials.  

Science.gov (United States)

The unique properties of the wheat grain reside primarily in the gluten-forming storage proteins of its endosperm. Wheat gluten's structural and functional properties have led to an expanding diversity of applications in food products. However, its viscoelastic properties and low water solubility also are very interesting features for nonfood applications. Moreover, gluten is annually renewable and perfectly biodegradable. In the processing and setting of gluten containing products, temperature plays a very important role. In this review, the structure and reactivity of gluten are discussed and the importance of sulfhydryl (SH) and disulfide (SS) groups is demonstrated. Wheat gluten aggregation upon thermosetting proceeds through direct covalent cross-linking in and between its protein groups, glutenin and gliadin. Predominant reactions include SH oxidation and SH/SS interchange reactions leading to the formation of SS cross-links. Additionally, thermal treatment of gluten can result in the formation of other than SS covalent bonds. We here review two main technological approaches to make gluten-based materials: wet processes resulting in thin films and dry processes, such as extrusion or compression molding, exploiting the thermoplastic properties of proteins under low moisture conditions and potentially resulting in very useful materials. Gluten bioplastics can also be reinforced with natural fibers, resulting in biocomposites. Although a lot of progress has been made the past decade, the current gluten materials are still outperformed by their synthetic polymer counterparts. PMID:20141101

Lagrain, Bert; Goderis, Bart; Brijs, Kristof; Delcour, Jan A

2010-03-01

180

Molecular basis of processing wheat gluten toward biobased materials.  

UK PubMed Central (United Kingdom)

The unique properties of the wheat grain reside primarily in the gluten-forming storage proteins of its endosperm. Wheat gluten's structural and functional properties have led to an expanding diversity of applications in food products. However, its viscoelastic properties and low water solubility also are very interesting features for nonfood applications. Moreover, gluten is annually renewable and perfectly biodegradable. In the processing and setting of gluten containing products, temperature plays a very important role. In this review, the structure and reactivity of gluten are discussed and the importance of sulfhydryl (SH) and disulfide (SS) groups is demonstrated. Wheat gluten aggregation upon thermosetting proceeds through direct covalent cross-linking in and between its protein groups, glutenin and gliadin. Predominant reactions include SH oxidation and SH/SS interchange reactions leading to the formation of SS cross-links. Additionally, thermal treatment of gluten can result in the formation of other than SS covalent bonds. We here review two main technological approaches to make gluten-based materials: wet processes resulting in thin films and dry processes, such as extrusion or compression molding, exploiting the thermoplastic properties of proteins under low moisture conditions and potentially resulting in very useful materials. Gluten bioplastics can also be reinforced with natural fibers, resulting in biocomposites. Although a lot of progress has been made the past decade, the current gluten materials are still outperformed by their synthetic polymer counterparts.

Lagrain B; Goderis B; Brijs K; Delcour JA

2010-03-01

 
 
 
 
181

Molecular changes underlying reduced pineal melatonin levels in Alzheimer disease: alterations in preclinical and clinical stages.  

UK PubMed Central (United Kingdom)

A disturbed sleep-wake rhythm is common in Alzheimer disease (AD) patients and correlated with decreased melatonin levels and a disrupted circadian melatonin rhythm. Melatonin levels in the cerebrospinal fluid are decreased during the progression of AD neuropathology (as determined by the Braak stages), already in cognitively intact subjects with the earliest AD neuropathology (Braak stages I-II) (preclinical AD). To investigate the molecular mechanisms behind the decreased melatonin levels, we measured monoamines and mRNA levels of enzymes of the melatonin synthesis and its noradrenergic regulation in pineal glands from 18 controls, 33 preclinical AD subjects, and 25 definite AD patients. Pineal melatonin levels were highly correlated with cerebrospinal fluid melatonin levels. The circadian melatonin rhythm disappeared because of decreased nocturnal melatonin levels in both the preclinical AD and AD patients. Also the circadian rhythm of beta(1)-adrenergic receptor mRNA disappeared in both patient groups. The precursor of melatonin, serotonin was stepwise depleted during the course of AD, as indicated by the up-regulated monoamine oxidase A mRNA and activity (5-hydroxyindoleacetic acid:serotonin ratio). We conclude that a dysfunction of noradrenergic regulation and the depletion of serotonin by increased monoamine oxidase A result in the loss of melatonin rhythm already in preclinical AD.

Wu YH; Feenstra MG; Zhou JN; Liu RY; Toran JS; Van Kan HJ; Fischer DF; Ravid R; Swaab DF

2003-12-01

182

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

CERN Multimedia

The alignment of the Fermi level of a metal electrode within the gap of the hi ghest occupied (HOMO) and lowest unoccupied orbital (LUMO) of a molecule is a key quantity in molecular electronics, which can vary the electron transparency of a single molecule junction by orders of magnitude. We present a quantitative analysis of the relation between this level alignment (which can be estimated from charging free molecules) and charge transfer for bipyridine and biphenyl dithiolate (BPDT) molecules attached to gold leads based on density functional theory calculations. For both systems the charge distribution is defined by a balance between Pauli repulsion with subsequent electrostatic screening and the filling of the LUMO, where bipyridine loses electrons to the leads and BPDT gains electrons. As a direct consequence the Fermi level of the metal is found close to the LUMO for bipyridine and close to the HOMO for BPDT.

Stadler, R

2006-01-01

183

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.

1987-01-01

184

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

Energy Technology Data Exchange (ETDEWEB)

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

Brewer, K.N.; Herbst, R.S.; Law, J.D.; Todd, T.A.; Olson, A.L.

1996-05-01

185

Molecular structure, processing, and tissue distribution of matrilin-4.  

Science.gov (United States)

Matrilin-4 is the most recently identified member of the matrilin family of von Willebrand factor A-like domain containing extracellular matrix adapter proteins. Full-length matrilin-4 was expressed in 293-EBNA cells, purified using affinity tags, and subjected to biochemical characterization. The largest oligomeric form of recombinantly expressed full-length matrilin-4 is a trimer as shown by electron microscopy, SDS-polyacrylamide gel electrophoresis, and mass spectrometry. Proteolytically processed matrilin-4 species were also detected. The cleavage occurs in the short linker region between the second von Willebrand factor A-like domain and the coiled-coil domain leading to the release of large fragments and the formation of dimers and monomers of intact subunits still containing a trimeric coiled-coil. In immunoblots of calvaria extracts similar degradation products could be detected, indicating that a related proteolytic processing occurs in vivo. Matrilin-4 was first observed at day 7.5 post-coitum in mouse embryos. Affinity-purified antibodies detect a broad expression in dense and loose connective tissue, bone, cartilage, central and peripheral nervous systems and in association with basement membranes. In the matrix formed by cultured primary embryonic fibroblasts, matrilin-4 is found in a filamentous network connecting individual cells. PMID:11279097

Klatt, A R; Nitsche, D P; Kobbe, B; Macht, M; Paulsson, M; Wagener, R

2001-02-14

186

Spatially Resolved Atomic and Molecular Spectroscopy in Microelectronics Processing Plasmas  

Energy Technology Data Exchange (ETDEWEB)

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

Hebner, G.A.

1998-10-14

187

Improvement of the nucleon emission process and the statistical property in molecular dynamics  

CERN Multimedia

We propose to introduce a new stochastic process in molecular dynamics in order to improve the description of the nucleon emission process from a hot nucleus. We give momentum fluctuations originating from the momentum width of the nucleon wave packet to the nucleon stochastically when it is being emitted from the nucleus. We show by calculating the liquid gas phase equilibrium in the case of antisymmetrized molecular dynamics, that with this improvement, we can recover the quantum mechanical statistical property of the nucleus for the particle emission process.

Ono, A; Ono, Akira; Horiuchi, Hisashi

1996-01-01

188

Multiscale characterization of the organization of triglycerides and phospholipids in emmental cheese: from the microscopic to the molecular level.  

Science.gov (United States)

The chemical composition and properties of lipids, both triglycerides and phospholipids, play a major role in the functional and nutritional properties of food products. In this study, the suprastructure of fat, solid fat content, and crystallographic properties of triglycerides were investigated in hard-type cheeses from the microscopic scale to the molecular level using the combination of relevant techniques. Two industrial cheeses with different oiling off properties were compared with experimental cheeses manufactured in the laboratory. Microstructural analysis performed using confocal laser scanning microscopy showed that milk processing led to the disruption of fat globules with the formation of nonglobular fat. For a similar fatty acid composition, oiling off was mainly related to the fat in dry matter content and to the suprastructure of fat in cheese. An exogenous fluorescent phospholipid permitted the localization of milk phospholipids in the cheese matrix, which mainly remain around fat inclusions after disruption of the milk fat globule membrane, and to show heterogeneities. We also showed using differential scanning calorimetry that the suprastructure of fat did not affect the solid fat content in cheese at 4 degrees C: 71.6 +/- 4.9%. The organization of triglyceride molecules in fat crystals, elucidated at a molecular level using X-ray diffraction, corresponded to the coexistence of 2 lamellar structures (2L 40.5 angstroms and 3L 54.6 angstroms) with four polymorphic forms: alpha, two beta' and beta. A schematic representation of the multiscale organization of triglycerides and phospholipids in cheese is proposed. PMID:18338865

Lopez, Christelle; Briard-Bion, Valerie; Beaucher, Eric; Ollivon, Michel

2008-03-14

189

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

190

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.

Fetterman Christina D; Rannala Bruce; Walter Michael A

2008-01-01

191

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

UK PubMed Central (United Kingdom)

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.

Fetterman CD; Rannala B; Walter MA

2008-01-01

192

Determination of molecular-level structural information of uranium in environmentally relevant samples by EXAFS  

International Nuclear Information System (INIS)

Synchrotron-based extended X-ray absorption fine structure (EXAFS) spectroscopy is a powerful technique to study many chemical elements in different states of aggregation. Informations can be obtained on the speciation and the complexation behavior of radionuclides in solutions, the adsorption of radionuclides on mineral or biological surfaces. The obtained structural parameters give molecular-level structural information from ligands surrounding a central radionuclide ion. The results can be used as an input for existing adsorption models, which can describe the migration of radionuclides in the geosphere. The EXAFS experiments we are carried out at SSRL in Stanford (USA) and at HASYLAB in Hamburg (Germany). (orig.)

1998-01-01

193

Inorganic ion exchange process for partitioning high level commercial waste  

International Nuclear Information System (INIS)

[en]Aspects of the Sandia Solidification Process that pertain to the concept of waste partitioning are covered. The general chemistry of the Sandia Solidification Process is reviewed. Experimental observations that relate to the separation of actinides from rare earths are presented

1976-01-01

194

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

CERN Multimedia

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

195

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

Science.gov (United States)

Vascular endothelial growth factor receptor 2 (VEGFR2) is an important angiogenic marker over-expressed in gliomas. With the use of molecular magnetic resonance imaging (mMRI) differing levels of VEGFR2 can be characterized in vivo with in rodent gliomas varying in angiogenesis. VEGFR2 levels were assessed by intravenous administration of an anti-VEGFR2 probe (anti-VEGFR2-albumin-Gd (gadolinium)-DTPA (diethylene triamine penta acetic acid)-biotin) into C6 or RG2 glioma-bearing rats, and visualized with mMRI. A non-specific IgG was coupled to the albumin-Gd-DTPA-biotin construct as a contrast agent molecular weight control. VEGFR2 levels are heterogeneous in different regions of C6 gliomas, whereas VEGFR2 was more homogenous or evenly distributed in RG2 gliomas. RG2 gliomas have less VEGFR2 within tumor periphery and peri-necrotic (p<0.05) regions, but more VEGFR2 within tumor interior regions (p<0.01), compared to C6 gliomas. mMRI results were confirmed with fluorescence staining and mean fluorescence intensity (MFI) quantification of the anti-VEGFR2 probe in excised glioma and brain tissues, as well as detection of VEGFR2 in C6 and RG2 gliomas and corresponding contalateral brain tissues. Ex vivo VEGFR2 levels were found to be significantly higher in C6 gliomas compared to RG2 tumors (p<0.001), which corresponded with in vivo detection using the VEGFR2 probe. Immunohistochemistry staining for HIF-1? (hypoxia inducible factor 1?), which is associated with angiogenesis, indicated higher levels in RG2 (p<0.01) compared to C6 gliomas. The data suggests that C6 gliomas have angiogenesis which is associated more with large blood vessels in tumor periphery and peri-necrotic regions, and less microvascular angiogenesis within the tumor interior, compared to RG2 gliomas.

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

2013-01-01

196

Woodwater 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

197

Mean level signal crossing rate for an arbitrary stochastic process  

DEFF Research Database (Denmark)

The issue of the mean signal level crossing rate for various probability density functions with primary relevance for optics is discussed based on a new analytical method. This method relies on a unique transformation that transforms the probability distribution under investigation into a normal probability distribution, for which the distribution of mean level crossings is known. In general, the analytical results for the mean level crossing rate are supported and confirmed by numerical simulations. In particular, we illustrate the present method by presenting analytic expressions for the mean level crossing rate for various probability distributions, including ones that previously were unavailable, such as the uniform, the so-called gamma-gamma, and the RiceNakagami distribution. However, in a limited number of cases the present results differ somewhat from the result reported in the literature. At present, this discrepancy remains unexplained and is laid open for future discussion.

Yura, Harold T.; Hanson, Steen Grner

2010-01-01

198

Level Crossing Probabilities of the Ornstein Uhlenbeck Process  

Directory of Open Access Journals (Sweden)

Full Text Available The Ornstein Uhlenbeck process is a Gaussian process t X with independentincrements and autocorrelation ( )2st t sE X X e?+ = . First the Laplace transform of theprobability density P(X x X p) t = = 0 is computed. Using this, the Laplace transformof t X first time reaching a given value x is derived. It is proved that these results agreewith the special case derived earlier by Bellman and Harris (Pacific J. Math. 1, 1951).

Jzsef Dnes

2006-01-01

199

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 carboncarbon 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

2007-01-01

200

Diet-disease interactions at the molecular level: an experimental paradigm.  

Science.gov (United States)

High levels of dietary fat enhance the severity of certain cancers, obesity, and cardiovascular diseases in susceptible individuals usually after prolonged exposure. We have been developing methods for identifying and characterizing genes regulated by the level of dietary fat for the purpose of determining their role in diseases promoted by high levels of dietary fat, particularly cancer and atherosclerosis. Our protocol employs semi-purified diets of reproducible composition fed to normal inbred mice to obtain reagents for studying of molecular events that lead to pathology. Our early studies demonstrated that different levels of dietary fat cause the accumulation or change in expression of two genes, designated Lfm-1 and Lfm-2 (low fat mammary) in mouse mammary glands and selected other tissues. The Lfm-2 gene is stearoyl CoA desaturase, a gene known to be regulated by dietary fat and insulin levels. The Lfm-1 gene is highly similar to the e subunits of bovine and rat F1F0-ATPases. A Lfm-1 restriction fragment length polymorphism located on chromosome 8 is associated with atherosclerosis in certain inbred strains of mice warranting additional tests to determine whether it is involved in initiation or promotion of heart disease. The experimental approach has the potential for analyzing genes regulated by approximately 50 essential nutrients or other dietary constituents. A potential outcome of this research is the development of reagents which can be used to predict the risk of diet-related diseases in individuals. PMID:7914920

Kaput, J; Swartz, D; Paisley, E; Mangian, H; Daniel, W L; Visek, W J

1994-08-01

 
 
 
 
201

Diet-disease interactions at the molecular level: an experimental paradigm.  

UK PubMed Central (United Kingdom)

High levels of dietary fat enhance the severity of certain cancers, obesity, and cardiovascular diseases in susceptible individuals usually after prolonged exposure. We have been developing methods for identifying and characterizing genes regulated by the level of dietary fat for the purpose of determining their role in diseases promoted by high levels of dietary fat, particularly cancer and atherosclerosis. Our protocol employs semi-purified diets of reproducible composition fed to normal inbred mice to obtain reagents for studying of molecular events that lead to pathology. Our early studies demonstrated that different levels of dietary fat cause the accumulation or change in expression of two genes, designated Lfm-1 and Lfm-2 (low fat mammary) in mouse mammary glands and selected other tissues. The Lfm-2 gene is stearoyl CoA desaturase, a gene known to be regulated by dietary fat and insulin levels. The Lfm-1 gene is highly similar to the e subunits of bovine and rat F1F0-ATPases. A Lfm-1 restriction fragment length polymorphism located on chromosome 8 is associated with atherosclerosis in certain inbred strains of mice warranting additional tests to determine whether it is involved in initiation or promotion of heart disease. The experimental approach has the potential for analyzing genes regulated by approximately 50 essential nutrients or other dietary constituents. A potential outcome of this research is the development of reagents which can be used to predict the risk of diet-related diseases in individuals.

Kaput J; Swartz D; Paisley E; Mangian H; Daniel WL; Visek WJ

1994-08-01

202

The reorganization energy of electron transfer in nonpolar solvents: Molecular level treatment of the solvent  

International Nuclear Information System (INIS)

The intermolecular electron transfer in a solute pair consisting of pyrene and dimethylaniline is investigated in a nonpolar solvent, n-hexane. The earlier elaborated approach [M. Tachiya, J. Phys Chem. 97, 5911 (1993)] is used; this method provides a physically relevant background for separating inertial and inertialess polarization responses for both nonpolarizable and polarizable molecular level simulations. The molecular-dynamics technique was implemented for obtaining the equilibrium ensemble of solvent configurations. The nonpolar solvent, n-hexane, was treated in terms of OPLS-AA parametrization. Solute Lennard-Jones parameters were taken from the same parametrization. Solute charge distributions of the initial and final states were determined using ab initio level [HF/6-31G(d,p)] quantum-chemical calculations. Configuration analysis was performed explicitly taking into account the anisotropic polarizability of n-hexane. It is shown that the Gaussian law well describes calculated distribution functions of the solvent coordinate, therefore, the rate constant of the ET reaction can be characterized by the reorganization energy. Evaluated values of the reorganization energies are in a range of 0.03-0.11 eV and significant contribution (more then 40% of magnitude) comes from anisotropic polarizability. Investigation of the reorganization energy ? dependence on the solute pair separation distance d revealed unexpected behavior. The dependence has a very sharp peak at the distance d=7 A where solvent molecules are able to penetrate into the intermediate space between the solute pair. The reason for such behavior is clarified. This new effect has a purely molecular origin and cannot be described within conventional continuum solvent models.

2005-12-08

203

The reorganization energy of electron transfer in nonpolar solvents: Molecular level treatment of the solvent  

Science.gov (United States)

The intermolecular electron transfer in a solute pair consisting of pyrene and dimethylaniline is investigated in a nonpolar solvent, n-hexane. The earlier elaborated approach [M. Tachiya, J. Phys Chem. 97, 5911 (1993)] is used; this method provides a physically relevant background for separating inertial and inertialess polarization responses for both nonpolarizable and polarizable molecular level simulations. The molecular-dynamics technique was implemented for obtaining the equilibrium ensemble of solvent configurations. The nonpolar solvent, n-hexane, was treated in terms of OPLS-AA parametrization. Solute Lennard-Jones parameters were taken from the same parametrization. Solute charge distributions of the initial and final states were determined using ab initio level [HF/6-31G(d,p)] quantum-chemical calculations. Configuration analysis was performed explicitly taking into account the anisotropic polarizability of n-hexane. It is shown that the Gaussian law well describes calculated distribution functions of the solvent coordinate, therefore, the rate constant of the ET reaction can be characterized by the reorganization energy. Evaluated values of the reorganization energies are in a range of 0.03-0.11 eV and significant contribution (more then 40% of magnitude) comes from anisotropic polarizability. Investigation of the reorganization energy ? dependence on the solute pair separation distance d revealed unexpected behavior. The dependence has a very sharp peak at the distance d=7 A? where solvent molecules are able to penetrate into the intermediate space between the solute pair. The reason for such behavior is clarified. This new effect has a purely molecular origin and cannot be described within conventional continuum solvent models.

Leontyev, I. V.; Tachiya, M.

2005-12-01

204

Gene expression profiles of the NCI-60 human tumor cell lines define molecular interaction networks governing cell migration processes.  

UK PubMed Central (United Kingdom)

Although there is extensive information on gene expression and molecular interactions in various cell types, integrating those data in a functionally coherent manner remains challenging. This study explores the premise that genes whose expression at the mRNA level is correlated over diverse cell lines are likely to function together in a network of molecular interactions. We previously derived expression-correlated gene clusters from the database of the NCI-60 human tumor cell lines and associated each cluster with function categories of the Gene Ontology (GO) database. From a cluster rich in genes associated with GO categories related to cell migration, we extracted 15 genes that were highly cross-correlated; prominent among them were RRAS, AXL, ADAM9, FN14, and integrin-beta1. We then used those 15 genes as bait to identify other correlated genes in the NCI-60 database. A survey of current literature disclosed, not only that many of the expression-correlated genes engaged in molecular interactions related to migration, invasion, and metastasis, but that highly cross-correlated subsets of those genes engaged in specific cell migration processes. We assembled this information in molecular interaction maps (MIMs) that depict networks governing 3 cell migration processes: degradation of extracellular matrix, production of transient focal complexes at the leading edge of the cell, and retraction of the rear part of the cell. Also depicted are interactions controlling the release and effects of calcium ions, which may regulate migration in a spaciotemporal manner in the cell. The MIMs and associated text comprise a detailed and integrated summary of what is currently known or surmised about the role of the expression cross-correlated genes in molecular networks governing those processes.

Kohn KW; Zeeberg BR; Reinhold WC; Sunshine M; Luna A; Pommier Y

2012-01-01

205

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

International Nuclear Information System (INIS)

[en]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.

2011-05-01

206

Process for charging silver electrodes to monoxide level  

Energy Technology Data Exchange (ETDEWEB)

A method of charging silver electrodes in which an electrode of porous sintered silver is anodized in the conventional manner in alkaline electrolyte to the so-called peroxide level and usually beyond, into the oxygen-evolution level, where the majority of the silver has been electroformed into divalent silver oxide. The charged electrode is then permitted to wet stand in the electrolyte or other alkaline solution to allow the residual unanodized silver in the electrode to convert a portion of the divalent silver oxide to monovalent silver oxide by a reverse disproportionation reaction.

Katan, Th.; Carlen, P.J.

1984-07-24

207

PRODUCT AND PROCESS FOR ELEVATING LIPID BLOOD LEVELS IN LIVESTOCK  

UK PubMed Central (United Kingdom)

The present invention provides feed or food products for consumption by animals or humans which include respective quantities of flax oil and non-flax carbohydrate. The flax oil and carbohydrate are mixed together and simultaneously subjected to an elevated temperature of at least about 120 DEG F. and subsequently cooled the flax oil is used at a level so that the final product contains at least about 5% by weight flax oil. It has been found that the products of the invention, when fed at effective levels, induce increased in vivo synthesis of desirable eicosapentaenoic acid (EPA).

DROUILLARD JAMES S

208

Product and process for elevating lipid blood levels in livestock  

UK PubMed Central (United Kingdom)

The present invention provides feed or food products for consumption by animals or humans which include respective quantities of flax oil and non-flax carbohydrate. The flax oil and carbohydrate are mixed together and simultaneously subjected to an elevated temperature of at least about 120 DEG F. and subsequently cooled; the flax oil is used at a level so that the final product contains at least about 5% by weight flax oil. It has been found that the products of the invention, when fed at effective levels, induce increased in vivo synthesis of desirable eicosapentaenoic acid (EPA).

DROUILLARD JAMES S

209

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

1982-01-01

210

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

211

Lithography budget analysis at the process module level  

Science.gov (United States)

A simple experimentally characterized lumped-parameter budget model is developed with the goal of quantifying the most significant components of critical dimension (CD) variation through an integrated process module. Tracked components include mask fabrication budgets, mask error factor, scanner field variation, optical proximity correction error, CD errors over chip topography, wafer-to-wafer and lot-to-lot variation. The components of variation are quantified for lithography and etch where appropriate and are fed into a simple interaction model to construct an overall patterning module CD budget. Normalized experimental results for this budget analysis are presented for 65 nm technology node contact patterning processes.

Brodsky, Colin J.; Chu, William

2006-04-01

212

How Effective Are Simulated Molecular-Level Experiments for Teaching Diffusion and Osmosis?  

Science.gov (United States)

Diffusion and osmosis are central concepts in biology, both at the cellular and organ levels. They are presented several times throughout most introductory biology textbooks (e.g., Freeman, 2002), yet both processes are often difficult for students to understand (Odom, 1995; Zuckerman, 1994; Sanger "et al.", 2001; and results herein). Students

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

2005-01-01

213

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

Diffusion and osmosis are central concepts in biology, both at the cellular and organ levels. They are presented several times throughout most introductory biology textbooks (e.g., Freeman, 2002), yet both processes are often difficult for students to understand (Odom, 1995; Zuckerman, 1994; Sanger ...

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

214

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 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)

2001-01-01

215

Processing of inflected nouns and levels of cognitive sensitivity  

Directory of Open Access Journals (Sweden)

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

Kosti? Aleksandar ?.; Mirkovi? Jelena

2002-01-01

216

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

217

Multi-study integration of brain cancer transcriptomes reveals organ-level molecular signatures.  

Science.gov (United States)

We utilized abundant transcriptomic data for the primary classes of brain cancers to study the feasibility of separating all of these diseases simultaneously based on molecular data alone. These signatures were based on a new method reported herein--Identification of Structured Signatures and Classifiers (ISSAC)--that resulted in a brain cancer marker panel of 44 unique genes. Many of these genes have established relevance to the brain cancers examined herein, with others having known roles in cancer biology. Analyses on large-scale data from multiple sources must deal with significant challenges associated with heterogeneity between different published studies, for it was observed that the variation among individual studies often had a larger effect on the transcriptome than did phenotype differences, as is typical. For this reason, we restricted ourselves to studying only cases where we had at least two independent studies performed for each phenotype, and also reprocessed all the raw data from the studies using a unified pre-processing pipeline. We found that learning signatures across multiple datasets greatly enhanced reproducibility and accuracy in predictive performance on truly independent validation sets, even when keeping the size of the training set the same. This was most likely due to the meta-signature encompassing more of the heterogeneity across different sources and conditions, while amplifying signal from the repeated global characteristics of the phenotype. When molecular signatures of brain cancers were constructed from all currently available microarray data, 90% phenotype prediction accuracy, or the accuracy of identifying a particular brain cancer from the background of all phenotypes, was found. Looking forward, we discuss our approach in the context of the eventual development of organ-specific molecular signatures from peripheral fluids such as the blood. PMID:23935471

Sung, Jaeyun; Kim, Pan-Jun; Ma, Shuyi; Funk, Cory C; Magis, Andrew T; Wang, Yuliang; Hood, Leroy; Geman, Donald; Price, Nathan D

2013-07-25

218

Multi-study integration of brain cancer transcriptomes reveals organ-level molecular signatures.  

UK PubMed Central (United Kingdom)

We utilized abundant transcriptomic data for the primary classes of brain cancers to study the feasibility of separating all of these diseases simultaneously based on molecular data alone. These signatures were based on a new method reported herein--Identification of Structured Signatures and Classifiers (ISSAC)--that resulted in a brain cancer marker panel of 44 unique genes. Many of these genes have established relevance to the brain cancers examined herein, with others having known roles in cancer biology. Analyses on large-scale data from multiple sources must deal with significant challenges associated with heterogeneity between different published studies, for it was observed that the variation among individual studies often had a larger effect on the transcriptome than did phenotype differences, as is typical. For this reason, we restricted ourselves to studying only cases where we had at least two independent studies performed for each phenotype, and also reprocessed all the raw data from the studies using a unified pre-processing pipeline. We found that learning signatures across multiple datasets greatly enhanced reproducibility and accuracy in predictive performance on truly independent validation sets, even when keeping the size of the training set the same. This was most likely due to the meta-signature encompassing more of the heterogeneity across different sources and conditions, while amplifying signal from the repeated global characteristics of the phenotype. When molecular signatures of brain cancers were constructed from all currently available microarray data, 90% phenotype prediction accuracy, or the accuracy of identifying a particular brain cancer from the background of all phenotypes, was found. Looking forward, we discuss our approach in the context of the eventual development of organ-specific molecular signatures from peripheral fluids such as the blood.

Sung J; Kim PJ; Ma S; Funk CC; Magis AT; Wang Y; Hood L; Geman D; Price ND

2013-07-01

219

Molecular markers in key steroidogenic pathways, circulating steroid levels, and prostate cancer progression.  

UK PubMed Central (United Kingdom)

PURPOSE: Prostate cancer is a heterogeneous genetic disease, and molecular methods for predicting prognosis in patients with aggressive form of the disease are urgently needed to better personalize treatment approaches. The objective was to identify host genetic variations in candidate steroidogenic genes affecting hormone levels and prostate cancer progression. EXPERIMENTAL DESIGN: The study examined two independent cohorts composed of 526 Caucasian men with organ-confined prostate cancer and 601 Taiwanese men on androgen-deprivation therapy. Caucasians were genotyped for 109 haplotype-tagging single-nucleotide polymorphisms (SNP) in CYP17A1, ESR1, CYP19A1, and HSD3B1, and their prognostic significance on disease progression was assessed using Kaplan-Meier survival curves and Cox regression models. Positive findings, including previously identified SRD5A1, SRD5A2, HSD17B2, HSD17B3, and HSD17B12 polymorphisms, were then explored in Taiwanese men (n = 32 SNPs). The influence of positive markers on the circulating hormonal levels was then appraised in Caucasians using specific and sensitive mass spectrometry-based methods. RESULTS: After adjusting for known risk factors, variants of CYP17A1 (rs6162), HSD17B2 (rs4243229 and rs7201637), and ESR1 (rs1062577) were associated with progressive disease in both cohorts. Indeed, the presence of these variations was significantly associated with progression in Caucasians (HR, 2.29-4.10; P = 0.0014-2 10(-7)) and survival in Taiwanese patients [HR = 3.74; 95% confidence interval (CI): 1.71-8.19, P = 0.009]. Remarkably, the CYP17A1 rs6162 polymorphism was linked to plasma dehydroepiandrosterone-sulfate (DHEA-S) levels (P = 0.03), HSD17B2 rs7201637 with levels of dihydrotestosterone (P = 0.03), and ESR1 rs1062577 with levels of estrone-S and androsterone-glucuronide (P ? 0.05). CONCLUSION: This study identifies, in different ethnic groups and at different disease stages, CYP17A1, HSD17B2, and ESR1 as attractive prognostic molecular markers of prostate cancer progression.

Lvesque ; Huang SP; Audet-Walsh ; Lacombe L; Bao BY; Fradet Y; Laverdire I; Rouleau M; Huang CY; Yu CC; Caron P; Guillemette C

2013-02-01

220

The role of core levels in scintillation processes  

Energy Technology Data Exchange (ETDEWEB)

The Auger decay of a core hole results in appearance of several strongly correlated excitations. This excited region strongly polarizes the lattice and thus the defect creation is possible. In all cases the core hole causes the strong local perturbation of electronic and lattice subsystems. The creation of such excited region with mutual relaxation of correlated electrons and holes can result in the increase of the efficiency of energy transfer to activators, acceleration of the luminescence kinetics, and the appearance of radiation-induced luminescence centers. These effects have been studied using VUV and soft X-ray synchrotron radiation, when the selective excitation of different core levels is possible.

Belsky, A.N. [Moscow State Univ. (Russian Federation)]|[Univ. Lyon 1, Villeurbanne (France). Lab. de Physico-Chimie des Materiaux Luminescents; Kamenskikh, I.A.; Vasil`ev, A.N. [Moscow State Univ. (Russian Federation); Gektin, A.V. [Inst. for Single Crystals, Kharkov (Ukraine); Pedrini, C. [Univ. Lyon 1, Villeurbanne (France). Lab. de Physico-Chimie des Materiaux Luminescents; Martin, P. [Centre Univ. Paris-Sud, Orsay (France)

1994-12-31

 
 
 
 
221

The role of core levels in scintillation processes  

International Nuclear Information System (INIS)

[en]The Auger decay of a core hole results in appearance of several strongly correlated excitations. This excited region strongly polarizes the lattice and thus the defect creation is possible. In all cases the core hole causes the strong local perturbation of electronic and lattice subsystems. The creation of such excited region with mutual relaxation of correlated electrons and holes can result in the increase of the efficiency of energy transfer to activators, acceleration of the luminescence kinetics, and the appearance of radiation-induced luminescence centers. These effects have been studied using VUV and soft X-ray synchrotron radiation, when the selective excitation of different core levels is possible

1994-01-01

222

Vitrification processing method and device for high level liquid waste  

Energy Technology Data Exchange (ETDEWEB)

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

Nishi, Shigehiko; Teranishi, Norifumi

1997-03-18

223

Corrosion and failure processes in high-level waste tanks  

Energy Technology Data Exchange (ETDEWEB)

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.

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

1992-11-01

224

A molecular level prototype for mechanoelectrical transducer in mammalian hair cells.  

UK PubMed Central (United Kingdom)

The mechanoelectrical transducer (MET) is a crucial component of mammalian auditory system. The gating mechanism of the MET channel remains a puzzling issue, though there are many speculations, due to the lack of essential molecular building blocks. To understand the working principle of mammalian MET, we propose a molecular level prototype which constitutes a charged blocker, a realistic ion channel and its surrounding membrane. To validate the proposed prototype, we make use of a well-established ion channel theory, the Poisson-Nernst-Planck equations, for three-dimensional (3D) numerical simulations. A wide variety of model parameters, including bulk ion concentration, applied external voltage, blocker charge and blocker displacement, are explored to understand the basic function of the proposed MET prototype. We show that our prototype prediction of channel open probability in response to blocker relative displacement is in remarkable accordance with experimental observation of rat cochlea outer hair cells. Our results appear to suggest that tip links which connect hair bundles gate MET channels.

Park J; Wei GW

2013-10-01

225

Impacts of pr-10a Overexpression at the Molecular and the Phenotypic Level  

Directory of Open Access Journals (Sweden)

Full Text Available Biotechnological approaches using genetic modifications such as homologous gene overexpression can be used to decode gene functions under well-defined circumstances. However, only the recording of the resulting phenotypes allows inferences about the impact of the modification on the organisms evolutionary, ecological or economic performance. We here compare a potato wild-type cell line with two genetically engineered cell cultures homologously overexpressing Pathogenesis Related Protein 10a (pr-10a). A detailed analysis of the relative gene-expression patterns of pr-10a and its regulators sebf and pti4 over time provides insights into the molecular response of heterotrophic cells to distinct osmotic and salt-stress conditions. Furthermore, this system serves as an exemplar for the tracing of respiration kinetics as a faster and more sensitive alternative to the laborious and time-consuming recording of growth curves. The utility and characteristics of the resulting data type and the requirements for its appropriate analysis are figured out. It is demonstrated how this novel type of phenotypic information together with the gene-expression-data provides valuable insights into the effect of genetic modifications on the behaviour of cells on both the molecular and the macroscopic level.

Lea A. I. Vaas; Maja Marheine; Johannes Sikorski; Markus Gker; Heinz-Martin Schumacher

2013-01-01

226

Molecular Level Understanding of Adhesion Mechanisms at the Epoxy/Polymer Interfaces.  

UK PubMed Central (United Kingdom)

It is important to understand the buried interfacial structures containing epoxy underfills as such structures determine the interfacial adhesion properties. Weak adhesion or delamination at such interfaces leads to failure of microelectronic devices. Sum frequency generation (SFG) vibrational spectroscopy was used to examine buried interfaces at polymer/model epoxy and polymer/commercial epoxy resins (used as underfills in flip chip devices) at the molecular level. We investigated a model epoxy: bisphenol A digylcidyl ether (BADGE) at the interfaces of poly (ethylene terephthalate) (PET) before and after curing. Furthermore, small amounts of different silanes including (3-glycidoxypropyl) trimethoxysilane (?-GPS), (3-Aminopropyl)trimethoxysilane (ATMS), Octadecyltrimethoxysilane (OTMS(18C)), and Octyltrimethoxysilane (OTMS(8C)) were mixed with BADGE. Silane influences on the polymer/epoxy interfacial structures were studied. SFG was also used to study molecular interfacial structures between polymers and two commercial epoxy resins. The interfacial structures probed by SFG were correlated to the adhesion strengths measured for corresponding interfaces. The results indicated that a small amount of silane molecules added to epoxy could substantially change the polymer/epoxy interfacial structure, greatly affecting the adhesion strength at the interface. It was found that ordered methyl groups at the interface lead to weak adhesion, and disordered interfaces lead to strong adhesion.

Zhang C; Hankett J; Chen Z

2012-07-01

227

A molecular level prototype for mechanoelectrical transducer in mammalian hair cells.  

Science.gov (United States)

The mechanoelectrical transducer (MET) is a crucial component of mammalian auditory system. The gating mechanism of the MET channel remains a puzzling issue, though there are many speculations, due to the lack of essential molecular building blocks. To understand the working principle of mammalian MET, we propose a molecular level prototype which constitutes a charged blocker, a realistic ion channel and its surrounding membrane. To validate the proposed prototype, we make use of a well-established ion channel theory, the Poisson-Nernst-Planck equations, for three-dimensional (3D) numerical simulations. A wide variety of model parameters, including bulk ion concentration, applied external voltage, blocker charge and blocker displacement, are explored to understand the basic function of the proposed MET prototype. We show that our prototype prediction of channel open probability in response to blocker relative displacement is in remarkable accordance with experimental observation of rat cochlea outer hair cells. Our results appear to suggest that tip links which connect hair bundles gate MET channels. PMID:23625048

Park, Jinkyoung; Wei, Guo-Wei

2013-04-28

228

Investigating Students' Ability to Transfer Ideas Learned from Molecular Animations of the Dissolution Process  

Science.gov (United States)

Animations of the particulate level of matter are widely available for use in chemistry classes and are often the primary means of representing molecular behavior. These animations may also be viewed by individual students using textbook Web sites, although without reinforcement or feedback. It is not known to what extent the material in these

Kelly, Resa M.; Jones, Loretta L.

2008-01-01

229

Kinetics of electron-molecular processes on the semiconductor film surface  

International Nuclear Information System (INIS)

One possible type of kinetics of electron-molecular processes on the semiconductor-film surface is analysed. The expressions for chemisorption time constant tsub(i0) and transition time tsub(t) from chemisorption of one type of the particles to chemisorption of the other one give a very good description of the experimental results

1985-01-01

230

Geographic variation in adaptation at the molecular level: a case study of plant immunity genes.  

Science.gov (United States)

Natural selection imposed by interacting species frequently varies among geographic locations and can lead to local adaptation, where alternative phenotypes are found in different populations. Little is known, however, about whether geographically variable selection acting on traits that mediate species interactions is consistent or strong enough to influence patterns of nucleotide variation at individual loci. To investigate this question, we examined patterns of nucleotide diversity and population structure at 16 plant innate immunity genes, with putative functions in defending plants against pathogens or herbivores, from six populations of teosinte (Zea mays ssp. parviglumis). Specifically, we tested whether patterns of population structure and within-population diversity at immunity genes differed from patterns found at nonimmunity (reference) loci and from neutral expectations derived from coalescent simulations of structured populations. For the majority of genes, we detected no strong evidence of geographically variable selection. However, in the wound-induced serine protease inhibitor (wip1), which inhibits the hydrolysis of dietary proteins in insect herbivores, one population showed unusually high levels of genetic differentiation, very low levels of nucleotide polymorphism, and was fixed for a novel replacement substitution in the active site of the protein. Taken together, these data suggest that wip1 experienced a recent selective sweep in one geographic region; this pattern may reflect local adaptation or an ongoing species-wide sweep. Overall, our results indicate that a signature of local adaptation at the molecular level may be uncommon-particularly for traits that are under complex genetic control. PMID:18786191

Moeller, David A; Tiffin, Peter

2008-09-11

231

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.

2012-01-01

232

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)

2004-01-01

233

Molecular Characterization of Banana (AA) Diploids with Contrasting Levels of Black and Yellow Sigatoka Resistance  

Directory of Open Access Journals (Sweden)

Full Text Available Most banana cultivars are susceptible to many diseases, whereas Sigatoka leads to greatest yield losses. One of the strategies to overcome this disease is thorough banana genetic breeding which consists in the obtainment of improved (AA) diploids which are then crossed with triploids obtaining (AAAB) tetraploid disease resistant bananas also presenting other important agronomic characteristics. The prior knowledge of the genetic diversity of (AA) diploids, is therefore considered indispensable in order to direct the crosses being made. The objective of the present work was to analyze the genetic diversity of 20 (AA) banana diploids with contrasting levels of reaction to yellow and black Sigatoka caused by Mycosphaerella musicola and M. fijensis, respectively, using molecular markers. From the dendrogram data it is shown that a great number of experimental hybrids can be obtained from the combination of genetically different diploids, therefore making the banana genetic breeding program more efficient regarding its objectives.

Claudia F. Ferreira; Sebastiao O. Silva; Nivia P.D. Sobrinho; Sandra Cristina; Santana Damascena; Fabiane S.D.A.A.O. Alves; Osvaldo P.D. Paz

2004-01-01

234

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

2013-03-05

235

High level radioactive waste vitrification process equipment component testing  

International Nuclear Information System (INIS)

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.

1985-01-01

236

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

237

High levels of melatonin generated during the brewing process.  

UK PubMed Central (United Kingdom)

Beer is a beverage consumed worldwide. It is produced from cereals (barley or wheat) and contains a wide array of bioactive phytochemicals and nutraceutical compounds. Specifically, high melatonin concentrations have been found in beer. Beers with high alcohol content are those that present the greatest concentrations of melatonin and vice versa. In this study, gel filtration chromatography and ELISA were combined for melatonin determination. We brewed beer to determine, for the first time, the beer production steps in which melatonin appears. We conclude that the barley, which is malted and ground in the early process, and the yeast, during the second fermentation, are the largest contributors to the enrichment of the beer with melatonin.

Garcia-Moreno H; Calvo JR; Maldonado MD

2013-08-01

238

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; Wijeratne Asela J; Wijeratne Saranga; Kornacker Karl; Sudhamalla Babu; Rivera-Vega Loren J; Hoelmer Andrew; Meulia Tea; Jones Susan C; Mittapalli Omprakash

2012-01-01

239

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

UK PubMed Central (United Kingdom)

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 P; Wijeratne AJ; Wijeratne S; Kornacker K; Sudhamalla B; Rivera-Vega LJ; Hoelmer A; Meulia T; Jones SC; Mittapalli O

2012-01-01

240

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

2010-01-01

 
 
 
 
241

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

Parallelism in the download process of large files is an efficient mechanism for distributed systems. In such systems, some peers (clients) exploit the power of parallelism to download blocks of data stored in a distributed way over some other peers (servers). Determining response times in parallel ...

Dandoush, Abdulhalim; Jean-Marie, Alain

242

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

Parallelism in the download process of large files is an efficient mechanism for distributed systems. In such systems, some peers (clients) exploit the power of parallelism to download blocks of data stored in a distributed way over some other peers (servers). Determining response times in parallel ...

Dandoush, Abdulhalim; Jean-Marie, Alain

243

A microwave digestion-based determination of low molecular weight organic acids in Bayer process liquor.  

UK PubMed Central (United Kingdom)

A new technique for the determination of low molecular weight organic acids in Bayer process liquors is reported. The acids are partitioned from acidified liquor into butanol, followed by butylation using microwave heating. This method is both rapid (sample preparation time < 15 min) and capable of detecting acids larger than previously reported in the low molecular weight fraction (up to RMM 176). A standard solution containing 15 acids was used to calibrate the technique and 13 of these acids were detected and quantified in a Bayer liquor sample.

Baker AR; Greenaway AM; Ingram CW

1995-10-01

244

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.

2009-09-16

245

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

246

Removal of higher molecular weight organic compounds by the granular activated carbon adsorption unit process  

Energy Technology Data Exchange (ETDEWEB)

The granular activated carbon adsorption unit process in drinking water treatment typically removes purgeable organic compounds for time periods on the order of a few weeks. Experimental evidence indicates that less volatile compounds of generally higher molecular weight than the purgeable fraction, but still detectable by gas chromatography, are efficiently removed for longer periods. Field data substantiate this. Explanatory mechanisms may include stronger adsorption affinities or biodegradation. Non-gas chromatographable, higher molecular weight materials such as humic acids, as measured by Total Organic Carbon (TOC) or trihalomethane formation potential, revert to lower removal efficiencies. Biodegradation may be responsible for a continued long term removal of a fraction of these materials.

Stevens, A.A.; Seeger, D.R.; DeMarco, J.; Moore, L.

1987-09-01

247

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 25C 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; Jae S. Park; Hye J. Ahn; Hye J. Yum; Vasudevan Ayyappan; Lakshmi S. Vijayachandran; Ji S. Kim; Sei C. Kim; Chang W. Choi

2006-01-01

248

Tapping natural variation at functional level reveals allele specific molecular characteristics of potato invertase Pain-1.  

UK PubMed Central (United Kingdom)

Biochemical, molecular and genetic studies emphasize the role of the potato vacuolar invertase Pain-1 in the accumulation of reducing sugars in potato tubers upon cold storage, and thereby its influence on the quality of potato chips and French fries. Previous studies showed that natural Pain-1 cDNA alleles were associated with better chip quality and higher tuber starch content. In this study, we focused on the functional characterization of these alleles. A genotype-dependent transient increase of total Pain-1 transcript levels in cold-stored tubers of six different genotypes as well as allele-specific expression patterns were detected. 3D modelling revealed putative structural differences between allelic Pain-1 proteins at the molecule's surface and at the substrate binding site. Furthermore, the yeast SUC2 mutant was complemented with Pain-1 cDNA alleles and enzymatic parameters of the heterologous expressed proteins were measured at 30 and 4?C. Significant differences between the alleles were detected. The observed functional differences between Pain-1 alleles did not permit final conclusions on the mechanism of their association with tuber quality traits. Our results show that natural allelic variation at the functional level is present in potato, and that the heterozygous genetic background influences the manifestation of this variation.

Draffehn AM; Durek P; Nunes-Nesi A; Stich B; Fernie AR; Gebhardt C

2012-12-01

249

Sea Level Change, A Fundamental Process When Interpreting Coastal Geology and Geography.  

Science.gov (United States)

Discusses the meaning of sea level change and identifies the major factors responsible for this occurrence. Elaborates on the theory and processes involved in indirect measurement of changes in sea volume. Also explains how crustal movement affects sea level. (ML)

Zeigler, John M.

1985-01-01

250

Gender differences in serum high-molecular-weight adiponectin levels in metabolic syndrome.  

UK PubMed Central (United Kingdom)

OBJECTIVE: The objective of this study was to estimate gender-specific associations between metabolic syndrome (MS) and high-molecular-weight (HMW) adiponectin in an Estonian adult population. METHODS: Plasma HMW adiponectin was measured in 458 subjects (191 men) who participated in a population-based cross-sectional multicenter study (n=495) on the prevalence of metabolic disorders in Estonia. MS was defined according to National Cholesterol Education Program Adult Treatment Panel III criteria. RESULTS: Median HMW adiponectin levels (?g/ml) were significantly lower among all subjects with MS compared with subjects without MS: 2.1 vs 2.8 in men (P=0.002) and 3.1 vs 5.1 in women (P<0.001). In a fully adjusted, logistic regression model containing HMW adiponectin, homeostasis model assessment of insulin resistance (HOMA-IR), BMI, and age, HMW adiponectin was significantly associated with MS only in women. Comparison of HMW adiponectin and HOMA-IR as markers for MS indicated that HOMA-IR predicted MS better than did HMW adiponectin in both genders. However, after adjusting for age and BMI, HOMA-IR was a significantly better predictor only in men. HMW adiponectin and HOMA-IR predicted the presence of MS at the same level in women. Areas under the receiver operating characteristic curves for HMW adiponectin and HOMA-IR were 0.833 vs 0.88 in men (P=0.02) and 0.897 vs 0.907 in women (P=0.5). CONCLUSIONS: These data suggest that the association between low HMW adiponectin levels and presence of MS might be stronger in women compared with men.

Eglit T; Lember M; Ringmets I; Rajasalu T

2013-03-01

251

Model Based Control For Interacting And Non-Interacting Level Process Using Labview  

Directory of Open Access Journals (Sweden)

Full Text Available Recent advancements in process industries have enabled the development of combination of interacting and non-interacting of process tank level control system. An experimental setup of three tank level process in interacting and non- interacting mode was studied, to obtain the process models. Different control schemes such as Internal model controller (IMC), IMC-PID and Proportional Integral and Derivative (PID) were implemented. The goal of the model-based controller is to compensate for shifts in the process and maintain the liquid level on target. The performance of different control schemes were investigated through computer simulation.

M.LAVANYA, P.ARAVIND, M.VALLUVAN, DR.B.ELIZABETH CAROLINE

2013-01-01

252

An overview of atomic and molecular processes in critical velocity ionization  

Energy Technology Data Exchange (ETDEWEB)

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

Lai, S.T.; Murad, E.; McNeil, W.J.

1989-04-01

253

An overview of atomic and molecular processes in critical velocity ionization  

International Nuclear Information System (INIS)

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

1989-01-01

254

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.

2011-01-01

255

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

Directory of Open Access Journals (Sweden)

Full Text Available Agrobacterium tumefaciens o agente causal da galha-da-coroa, doena que afeta a maioria das plantas dicotiledneas e caracteriza-se pelo crescimento de tumores na juno entre o caule e a raiz (coroa). A formao desses tumores o resultado de um processo natural de transferncia de genes de Agrobacterium spp. para o genoma da planta infetada. Esses genes esto contidos em um plasmdio de alto peso molecular (120 a 250 kb), denominado Ti ("tumor inducing"), presente em todas as linhagens patognicas de Agrobacterium spp. Duas regies do plasmdio Ti esto diretamente envolvidas na induo do tumor: a regio-T, que corresponde ao segmento de DNA transferido para a clula vegetal, e a regio de virulncia (regio vir), que contm genes envolvidos na sntese de protenas responsveis pelo processo de transferncia da regio-T. Esta regio, uma vez transferida e integrada no genoma da clula vegetal, passa a ser denominada de T-DNA ("transferred DNA"). Os genes presentes no T-DNA codificam enzimas envolvidas na via de biossntese de reguladores de crescimento, auxinas e citocininas. A sntese desses reguladores pelas clulas transformadas causa um desbalano hormonal, levando formao do tumor no local da infeco. Outro grupo de genes presentes no T-DNA codifica enzimas responsveis pela sntese de opinas, que so catabolisadas especificamente pela bactria colonizadora, como fonte de nutrientes. O conhecimento preliminar das bases moleculares envolvidas no processo de infeco de uma planta hospedeira por Agrobacterium spp., permitiu a utilizao desta bactria como vetor natural de transformao gentica 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; Laudete M. Sartoretto; Ana C. M. Brasileiro

2003-01-01

256

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

Scientific Electronic Library Online (English)

Full Text Available Abstract in portuguese Agrobacterium tumefaciens o agente causal da galha-da-coroa, doena que afeta a maioria das plantas dicotiledneas e caracteriza-se pelo crescimento de tumores na juno entre o caule e a raiz (coroa). A formao desses tumores o resultado de um processo natural de transferncia de genes de Agrobacterium spp. para o genoma da planta infetada. Esses genes esto contidos em um plasmdio de alto peso molecular (120 a 250 kb), denominado Ti ("tumor inducing"), (more) presente em todas as linhagens patognicas de Agrobacterium spp. Duas regies do plasmdio Ti esto diretamente envolvidas na induo do tumor: a regio-T, que corresponde ao segmento de DNA transferido para a clula vegetal, e a regio de virulncia (regio vir), que contm genes envolvidos na sntese de protenas responsveis pelo processo de transferncia da regio-T. Esta regio, uma vez transferida e integrada no genoma da clula vegetal, passa a ser denominada de T-DNA ("transferred DNA"). Os genes presentes no T-DNA codificam enzimas envolvidas na via de biossntese de reguladores de crescimento, auxinas e citocininas. A sntese desses reguladores pelas clulas transformadas causa um desbalano hormonal, levando formao do tumor no local da infeco. Outro grupo de genes presentes no T-DNA codifica enzimas responsveis pela sntese de opinas, que so catabolisadas especificamente pela bactria colonizadora, como fonte de nutrientes. O conhecimento preliminar das bases moleculares envolvidas no processo de infeco de uma planta hospedeira por Agrobacterium spp., permitiu a utilizao desta bactria como vetor natural de transformao gentica 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. 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. st (more) rains. 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.

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

2003-10-01

257

Increased levels of DUSP6 phosphatase stimulate tumourigenesis in a molecularly distinct melanoma subtype.  

UK PubMed Central (United Kingdom)

The mitogen-activated protein kinase (MAPK) pathway is important in melanoma. In this pathway, DUSP6 phosphatase negatively controls the activation of extracellular signal-regulated (ERK) kinase. Through comparison of melanoma signalling pathways between immortal mouse melanocytes and their tumourigenic derivatives, retrieved from mouse xenografts, we identified a molecularly distinct subtype of melanoma, characterized by reduced ERK activity and increased DUSP6 expression. Overexpression of DUSP6 enhanced anchorage-independent growth and invasive ability of immortal mouse melanocytes, suggesting that increased DUSP6 expression contributes to melanoma formation in the mouse xenografts. In contrast, reduced tumourigenicity was observed after DUSP6 overexpression in human melanoma cells. A minority of thick human primary melanomas had high DUSP6 expression and the same poor melanoma-specific survival as the majority of thick primaries with low DUSP6 levels. We have demonstrated that DUSP6 is important in melanoma and that it plays a different role in our distinct subtype of mouse melanoma compared with that in classic human melanoma.

Li W; Song L; Ritchie AM; Melton DW

2012-03-01

258

An alphabetic code based atomic level molecular similarity search in databases  

Directory of Open Access Journals (Sweden)

Full Text Available Atomic level molecular similarity and diversity studies have gained considerable importance through their wide application in Bioinformatics and Chemo-informatics for drug design. The availability of large volumes of data on chemical compounds requires new methodologies for efficient and effective searching of its archives in less time with optimal computational power. We describe an alphabetic algorithm for similarity searching based on atom-atom bonding preference for ligands. We represented 170 cyclin-dependent kinase 2 inhibitors using strings of pre-defined alphabets for searching using known protein sequence alignment tools. Thus, a common pattern was extracted using this set of compounds for database searching to retrieve similar active compounds. Area under the receiver operating characteristic (ROC) curve was used for the discrimination of similar and dissimilar compounds in the databases. An average retrieval rate of about 60% is obtained in cross-validation using the home-grown dataset and the directory of useful decoys (DUD, formally known as the ZINC database) data. This will help in the effective retrieval of similar compounds using database search.

Saranya Nallusamy; Samuel Selvaraj

2012-01-01

259

Linking Molecular and Population Processes in Mathematical Models of Quorum Sensing.  

UK PubMed Central (United Kingdom)

Many bacteria alter their behaviors as a function of population density, via a process known as quorum sensing (QS). QS is achieved by the synthesis and detection of diffusible signal molecules, often involving complex signal transduction pathways and regulatory networks. Mathematical models have been developed to investigate a number of aspects of QS, resulting in a wide range of model structures; many have focused on either the molecular or the population scale. In this paper, Ishow that many published models fail to satisfy physical constraints (such as conservation of matter) or rely on apriori assumptions that may not be valid. Ipresent new, simple models of canonical Gram-negative and Gram-positive QS systems, in both well-mixed and biofilm populations, focusing on the interaction between molecular and population processes. Ishow that this interaction may be crucial for several important features of QS, including bistability and the localization of QS in space. The results highlight the need to link molecular and population processes carefully in QS models, provide a general framework for understanding the behavior of complex system-specific models, and suggest new directions for both theoretical and experimental work.

Brown D

2013-07-01

260

Is the link between anatomical structure and function equally strong at all cognitive levels of processing?  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Whereas low-level sensory processes can be linked to macroanatomy with great confidence, the degree to which high-level cognitive processes map onto anatomy is less clear. If function respects anatomy, more accurate intersubject anatomical registration should result in better functional alignment. H...

Tahmasebi, AM; Davis, MH; Wild, CJ; Rodd, JM; Hakyemez, H; Abolmaesumi, P; Johnsrude, IS

 
 
 
 
261

Role of molecular dynamics on descriptions of shock-front processes  

Energy Technology Data Exchange (ETDEWEB)

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

Karo, A.M.

1981-07-22

262

Multi-level post-processing for Korean character recognition using morphological analysis and linguistic evaluation  

CERN Multimedia

Most of the post-processing methods for character recognition rely on contextual information of character and word-fragment levels. However, due to linguistic characteristics of Korean, such low-level information alone is not sufficient for high-quality character-recognition applications, and we need much higher-level contextual information to improve the recognition results. This paper presents a domain independent post-processing technique that utilizes multi-level morphological, syntactic, and semantic information as well as character-level information. The proposed post-processing system performs three-level processing: candidate character-set selection, candidate eojeol (Korean word) generation through morphological analysis, and final single eojeol-sequence selection by linguistic evaluation. All the required linguistic information and probabilities are automatically acquired from a statistical corpus analysis. Experimental results demonstrate the effectiveness of our method, yielding error correction r...

Lee, G; Yoo, J H; Lee, Geunbae; Lee, Jong-Hyeok; Yoo, JinHee

1996-01-01

263

Process for the cracking of feedstocks containing high levels of nitrogen  

Energy Technology Data Exchange (ETDEWEB)

This patent describes a process for the catalytic cracking of a hydrocarbon feedstock containing greater than about 0.25 weight percent total nitrogen, calculated as the element. It comprises contacting the feedstock with a cracking catalyst under cracking conditions in the substantial absence of added molecular hydrogen in a cracking zone to convert components of the feedstock into lower molecular weight constitutes. The cracking catalyst comprises greater than about 25 weight percent of a Y zeolite dispersed in a matrix comprising a clay and a synthetic silica-alumina component.

Scherzer, J.

1989-11-14

264

Studies on Deformation Mechanism and Punch Taper Effects on Nanoimprint Processes by Molecular Dynamics  

Science.gov (United States)

A molecular dynamics analysis model is proposed to study the effects of parameters on nanoimprint process, for example: taper angle, imprint depth and spring back. The nanoimprint process comprises one punch and one specimen at an isothermal state of 400K, while the deformed material is a copper FCC single crystal and the punch material is a nickel FCC single crystal. There were a total of 10,080 atoms in copper measuring 12.02 nm 5.72 nm in length and height, respectively. There were a total of 4,200 atoms in nickel where the typical length and depth in punch tooth are 6.24 nm 3.52 nm, respectively. Computer simulation codes based on Hamiltonian dynamics, periodical boundary conditions and Morse potential function were used to simulate the nanoimprint processes. By varying the punch taper angle and the imprinting depth, useful information for nanoimprint process has been obtained.

Hsu, Quang-Cherng; Wu, Chen-Da; Fang, Te-Hua

2004-06-01

265

Studies on deformation mechanism and punch taper effects on nanoimprint processes by molecular dynamics  

International Nuclear Information System (INIS)

A molecular dynamics analysis model is proposed to study the effects of parameters on nanoimprint process, for example: taper angle, imprint depth and spring back. The nanoimprint process comprises one punch and one specimen at an isothermal state of 400K, while the deformed material is a copper FCC single crystal and the punch material is a nickel FCC single crystal. There were a total of 10,080 atoms in copper measuring 12.02 nm x 5.72 nm in length and height, respectively. There were a total of 4,200 atoms in nickel where the typical length and depth in punch tooth are 6.24 nm x 3.52 nm, respectively. Computer simulation codes based on Hamiltonian dynamics, periodical boundary conditions and Morse potential function were used to simulate the nanoimprint processes. By varying the punch taper angle and the imprinting depth, useful information for nanoimprint process has been obtained

2004-06-10

266

Deformation Mechanism and Punch Taper Effects on Nanoimprint Process by Molecular Dynamics  

Science.gov (United States)

A molecular dynamics analysis model is proposed to study the effects of parameters on the nanoimprint process, for example, taper angle, imprint depth and spring back. The nanoimprint process comprises one punch and one specimen at an isothermal state of 400 K, while the deformed material is a copper fcc single crystal and the punch material is a nickel fcc single crystal. There were a total of 10,080 atoms in copper measuring 12.02 nm and 5.72 nm in length and height, respectively. There were a total of 4,200 atoms in nickel with a typical length and depth in a punch tooth of 6.24 nm and 3.52 nm, respectively. Computer simulation codes based on Hamiltonian dynamics, periodical boundary conditions and the Morse potential function were used to simulate the nanoimprint process. By varying the punch taper angle and the imprint depth, useful information about the nanoimprint process was obtained.

Hsu, Quang-Cherng; Wu, Chen-Da; Fang, Te-Hua

2004-11-01

267

Molecular processes of inhibition and stimulation of ATP synthase caused by the phytotoxin tentoxin.  

Science.gov (United States)

F1-ATPase is the smallest mechanical motor known. Tentoxin, a cyclic peptide produced by phytopathogenic fungi, inactivates the F1 motor in sensitive plants at nanomolar to micromolar concentrations, whereas higher concentrations surpass the natural activity of the enzyme. Single molecule studies now have clarified the molecular steps involved in both processes. Inactivation delays the dwell time of a single step in the complete 360 degrees turn and results in an asymmetric rotation of the central rotor subunit. In contrast, rotation in the stimulated F1 particle is smooth and accompanied by strongly reduced ADP inhibition. Our study provides for the first time the direct observation of a noncompetitively inhibited state of the enzyme and directly visualizes the regulation of the molecular motor by an external natural compound. In addition, the ADP release step during catalysis was revealed by analysis of the single molecule rotation behavior. Hence, tentoxin is a sophisticated molecular tool to mark and control certain catalytic steps within the reaction pathway of the molecular F1 motor. PMID:18579520

Meiss, Erik; Konno, Hiroki; Groth, Georg; Hisabori, Toru

2008-06-25

268

Molecular processes of inhibition and stimulation of ATP synthase caused by the phytotoxin tentoxin.  

UK PubMed Central (United Kingdom)

F1-ATPase is the smallest mechanical motor known. Tentoxin, a cyclic peptide produced by phytopathogenic fungi, inactivates the F1 motor in sensitive plants at nanomolar to micromolar concentrations, whereas higher concentrations surpass the natural activity of the enzyme. Single molecule studies now have clarified the molecular steps involved in both processes. Inactivation delays the dwell time of a single step in the complete 360 degrees turn and results in an asymmetric rotation of the central rotor subunit. In contrast, rotation in the stimulated F1 particle is smooth and accompanied by strongly reduced ADP inhibition. Our study provides for the first time the direct observation of a noncompetitively inhibited state of the enzyme and directly visualizes the regulation of the molecular motor by an external natural compound. In addition, the ADP release step during catalysis was revealed by analysis of the single molecule rotation behavior. Hence, tentoxin is a sophisticated molecular tool to mark and control certain catalytic steps within the reaction pathway of the molecular F1 motor.

Meiss E; Konno H; Groth G; Hisabori T

2008-09-01

269

Molecular Processes of Inhibition and Stimulation of ATP Synthase Caused by the Phytotoxin Tentoxin*S?  

Science.gov (United States)

F1-ATPase is the smallest mechanical motor known. Tentoxin, a cyclic peptide produced by phytopathogenic fungi, inactivates the F1 motor in sensitive plants at nanomolar to micromolar concentrations, whereas higher concentrations surpass the natural activity of the enzyme. Single molecule studies now have clarified the molecular steps involved in both processes. Inactivation delays the dwell time of a single step in the complete 360 turn and results in an asymmetric rotation of the central rotor subunit. In contrast, rotation in the stimulated F1 particle is smooth and accompanied by strongly reduced ADP inhibition. Our study provides for the first time the direct observation of a noncompetitively inhibited state of the enzyme and directly visualizes the regulation of the molecular motor by an external natural compound. In addition, the ADP release step during catalysis was revealed by analysis of the single molecule rotation behavior. Hence, tentoxin is a sophisticated molecular tool to mark and control certain catalytic steps within the reaction pathway of the molecular F1 motor.

Meiss, Erik; Konno, Hiroki; Groth, Georg; Hisabori, Toru

2008-01-01

270

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

271

Development of a molecular method for the typing of Brettanomyces bruxellensis (Dekkera bruxellensis) at the strain level.  

UK PubMed Central (United Kingdom)

AIMS: In recent years, Brettanomyces/Dekkera bruxellensis has caused increasingly severe quality problems in the wine industry. A typing method at the strain level is needed for a better knowledge of the dispersion and the dynamics of these yeasts from grape to wine. METHODS AND RESULTS: Three molecular tools, namely random-amplified polymorphic DNA, PCR fingerprinting with microsatellite oligonucleotide primers and SAU-PCR, were explored for their relevance to typing strains of Brettanomyces bruxellensis. The results indicated that discrimination of each individual strain was not possible with a single PCR typing technique. We described a typing method for B. bruxellensis based on restriction enzyme analysis and pulse field gel electrophoresis (REA-PFGE). Results showed that electrophoretic profiles were reproducible and specific for each strain under study. CONCLUSIONS: Consequently, REA-PFGE should be considered for the discrimination of B. bruxellensis strains. This technique allowed a fine discrimination of B. bruxellensis, as strains were identified by a particular profile. SIGNIFICANCE AND IMPACT OF THE STUDY: This study constitutes a prerequisite for accurate and appropriate investigations on the diversity of strains throughout the winemaking and ageing process. Such studies will probably give clearer and more up-to-date information on the origin of the presence of Brettanomyces in wine after vinification when they are latent spoilage agents.

Miot-Sertier C; Lonvaud-Funel A

2007-02-01

272

A naphthalimide based chemosensor for Zn2+, pyrophosphate and H2O2: sequential logic operations at the molecular level.  

UK PubMed Central (United Kingdom)

A naphthalimide based fluorescent probe has been synthesized which shows ratiometric fluorescence response towards Zn(2+) ions and the in situ prepared -Zn(2+) complex was used for the detection of pyrophosphate and hydrogen peroxide which mimics the functions of sequential logic circuits at the molecular level.

Kumar M; Kumar N; Bhalla V

2013-01-01

273

The effect of the molecular adsorbent recirculating system on moxifloxacin and meropenem plasma levels.  

UK PubMed Central (United Kingdom)

BACKGROUND: Adequate plasma antibiotic concentrations are necessary for effective elimination of invading microorganism; however, extracorporeal organ support systems are well known to alter plasma concentrations of antibiotics, requiring dose adjustments to achieve effective minimal inhibitory concentrations in the patient's blood. METHODS: A mock molecular adsorbent recirculating system (MARS) circuit was set using 5000 ml of bovine heparinized whole blood to simulate an 8-h MARS treatment session. After the loading dose of 400 mg of moxifloxacin or 2 g of meropenem had been added, blood was drawn from the different parts of the MARS circuit at various time points and analyzed by high-performance liquid chromatography. The experiments were performed in triplicate. Additionally, meropenem concentrations were determined in the plasma of one patient treated with MARS suffering from acute liver failure due to an idiosyncratic reaction to immunosuppressive medication. RESULTS: In our single-compartment model, a significant decrease in the quasi-systemic concentration of moxifloxacin and meropenem could be detected as early as 15 min after the commencing of the MARS circuit. Moreover, within 60 min the moxifloxacin and meropenem concentrations were less than 50% of the initial value. The activated charcoal removed the majority of moxifloxacin and meropenem in the albumin circuit. In our patient, the meropenem concentrations in the return line after MARS were constantly lower than in the access line, indicating a likely removal of meropenem through MARS. CONCLUSION: Our data provide evidence that moxifloxacin and meropenem are effectively removed from the patient's blood by MARS, leading to low plasma levels. Dose adjustments of both antibiotic compounds may be required.

Roth GA; Sipos W; Hferl M; Bhmdorfer M; Schmidt EM; Hetz H; Schebesta K; Klaus D; Motal M; Jger W; Krenn CG

2013-04-01

274

Solute diffusion in lipid bilayer membranes: an atomic level study by molecular dynamics simulation.  

Science.gov (United States)

To elucidate the mechanism of solute diffusion through lipid bilayer membranes, nearly 4 ns of molecular dynamics simulations of solutes in phospholipid bilayers was conducted. The study, the first atomic level study of solute diffusion in a lipid bilayer, involved four simulations of an all-atom representation of a fully solvated dimyristoylphosphatidylcholine (DMPC) bilayer in the L alpha phase with benzene molecules as solutes, totaling over 7100 atoms. These simulations agree with experimental evidence that the presence of small solutes does not affect bilayer thickness but does result in slight perturbations in the ordering of the hydrocarbon chains. At room temperature, the benzene molecules have essentially isotropic motion and rotate freely. The rate of translational diffusion varies with position within the bilayer and is faster in the center than near the zwitterionic headgroups and is in excellent agreement with experimental values for the diffusion of small solutes in a bilayer. These simulations have elucidated the mechanism of diffusion in a bilayer to be similar to the "hopping" mechanism found for the diffusion of gases through soft polymers. Jumps of up to 8 A can occur in as little as 5 ps whereas average motions for that time period are only approximately 1.5 A. In many cases, the jumps are moderated by torsional changes in the hydrocarbon chains which serve as "gates" between voids through which the benzene molecules move. Comparison of these simulations with another 1000-ps simulation of benzene in a pure alkane provides evidence that lipid bilayers should not be treated as a homogeneous bulk hydrocarbon phase. PMID:8251480

Bassolino-Klimas, D; Alper, H E; Stouch, T R

1993-11-30

275

Solute diffusion in lipid bilayer membranes: an atomic level study by molecular dynamics simulation.  

UK PubMed Central (United Kingdom)

To elucidate the mechanism of solute diffusion through lipid bilayer membranes, nearly 4 ns of molecular dynamics simulations of solutes in phospholipid bilayers was conducted. The study, the first atomic level study of solute diffusion in a lipid bilayer, involved four simulations of an all-atom representation of a fully solvated dimyristoylphosphatidylcholine (DMPC) bilayer in the L alpha phase with benzene molecules as solutes, totaling over 7100 atoms. These simulations agree with experimental evidence that the presence of small solutes does not affect bilayer thickness but does result in slight perturbations in the ordering of the hydrocarbon chains. At room temperature, the benzene molecules have essentially isotropic motion and rotate freely. The rate of translational diffusion varies with position within the bilayer and is faster in the center than near the zwitterionic headgroups and is in excellent agreement with experimental values for the diffusion of small solutes in a bilayer. These simulations have elucidated the mechanism of diffusion in a bilayer to be similar to the "hopping" mechanism found for the diffusion of gases through soft polymers. Jumps of up to 8 A can occur in as little as 5 ps whereas average motions for that time period are only approximately 1.5 A. In many cases, the jumps are moderated by torsional changes in the hydrocarbon chains which serve as "gates" between voids through which the benzene molecules move. Comparison of these simulations with another 1000-ps simulation of benzene in a pure alkane provides evidence that lipid bilayers should not be treated as a homogeneous bulk hydrocarbon phase.

Bassolino-Klimas D; Alper HE; Stouch TR

1993-11-01

276

An allometric interpretation of the spatio-temporal organization of molecular and cellular processes.  

Science.gov (United States)

Different levels of organization distinguished by characteristics spatial dimensions, Ec, and relaxation times, Tr, of biological processes ranging from electron transport in energy transduction to growth of microbial and plant cells, are shown to be related through a relation that may be interpreted as allometric and characterized by two different slopes. Processes, at levels of organization occurring in spatial dimensions of micrometers and relaxing in the order of minutes, delimit a 'transition point' between the two curves, that we interpret as a limit for the emergence of macroscopic coherence. The characteristic spatial dimension, Ec, and the relaxation time, Tr, contain dynamical information about the processes occurring at a given level of organization. When a steady state of a biological process at a certain level of organization becomes unstable, the system undergoes a transition to another level of organization. To exemplify the appearance of macroscopic order at levels of organization further from the 'transition point' we present in this report various experimental systems involving many levels of organization allometrically related that exhibit different kinds of self-organized behavior, i.e. bi-stability, oscillations, changes in (a)symmetry. PMID:8459799

Aon, M A; Cortassa, S

1993-03-10

277

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

Science.gov (United States)

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 DNAcation complexes.

Chai, Ai-Hua; Ran, Shi-Yong; Zhang, Dong; Jiang, Yang-Wei; Yang, Guang-Can; Zhang, Lin-Xi

2013-09-01

278

Spectroscopic Studies of Atomic and Molecular Processes in the Edge Region of Magnetically Confined Fusion Plasmas  

Science.gov (United States)

Edge plasma studies are of vital importance for understanding plasma-wall interactions in magnetically confined fusion devices. These interactions determine the transport of neutrals into the plasma, and the properties of the plasma discharge. This presentation deals with optical spectroscopic studies of the plasma boundary, and their rle in elucidating the prevailing physical conditions. Recorded spectra are of four types: emission spectra of ions and atoms, produced by electron impact excitation and by charge-exchange recombination, atomic spectra arising from electron impact-induced molecular dissociation and ionisation, visible spectra of molecular hydrogen and its isotopic combinations, and laser-induced fluorescence (LIF) spectra. The atomic spectra are strongly influenced by the confining magnetic field (Zeeman and Paschen-Back effects), which produces characteristic features useful for species identification, temperature determination by Doppler broadening, and studies of chemical and physical sputtering. Detailed analysis of the Zeeman components in both optical and LIF spectra shows that atomic hydrogen is produced in various velocity classes, some related to the relevant molecular Franck-Condon energies. The latter reflect the dominant electron collision processes responsible for production of atoms from molecules. This assignment has been verified by gas-puffing experiments through special test limiters. The higher-energy flanks of hydrogen line profiles probably also show the influence of charge-exchange reactions with molecular ions accelerated in the plasma sheath (`scrape-off layer') separating limiter surfaces from the edge plasma, in analogy to acceleration in the cathode-fall region of gas discharges. While electron collisions play a vital rle in generating the spectra, ion collisions with excited atomic radiators act through re-distribution of population among the atomic fine-structure sublevels, and momentum transfer to the atomic nuclei via ion-induced dipole collisions with the bound electrons. The ions are thus important in randomising and equilibrating the velocity distribution of atomic products of molecular dissociation.

Hey, J. D.; Brezinsek, S.; Mertens, Ph.; Unterberg, B.

2006-12-01

279

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. Zhao; G.R. Huang; M.N. Zhang; W.W. Chen; J.X. Jiang

2011-01-01

280

Model of the photoexcitation processes of a two-level molecule coherently coupled to an optical antenna.  

Science.gov (United States)

We theoretically investigate photoexcitation processes of a two-level molecular system coherently coupled with an antenna system having a significant dissipation. The auxiliary antenna enables the whole system to exhibit anomalous optical effects by controlling the coupling with the molecule. For example, in the weak excitation regime, the quantum interference yields a distinctive energy transparency through the antenna, which drastically reduces the energy dissipation. On the other hand, in the strong excitation regime, a population inversion of the two-level molecule appears due to the nonlinear effect. Both phenomena can be explained by regarding the antenna and molecule as one quantum-mechanically coupled system. Such an approach drives further research to exploit the full potential of the coupled systems. PMID:23599121

Nakatani, Masatoshi; Nobuhiro, Atsushi; Yokoshi, Nobuhiko; Ishihara, Hajime

2013-04-19

 
 
 
 
281

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2011-07-01

282

An overview of atomic and molecular processes in critical velocity ionization  

International Nuclear Information System (INIS)

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

1988-01-01

283

Molecular Chemical Engines: Pseudo-Static Processes and the Mechanism of Energy Transduction  

CERN Document Server

We propose a simple theoretical model for a molecular chemical engine that catalyzes a chemical reaction and converts the free energy released by the reaction into mechanical work. Binding and unbinding processes of reactant and product molecules to and from the engine are explicitly taken into account. The work delivered by the engine is calculated analytically for infinitely slow (``pseudo-static'') processes, which can be reversible (quasi-static) or irreversible, controlled by an external agent. It is shown that the work larger than the maximum value limited by the second law of thermodynamics can be obtained in a single cycle of operation by chance, although the statistical average of the work never exceeds this limit and the maximum work is delivered if the process is reversible. The mechanism of the energy transductionis also discussed.

Sasaki, K

2005-01-01

284

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

CERN Multimedia

Molecular simulations provide an increasingly useful insight into the static and dynamic characteristics of materials. In this thesis molecular simulations of macro-molecular liquid crystalline materials are reported. The first liquid crystalline material that has been investigated is a side chain liquid crystal polymer (SCLCP). In this study semi-atomistic molecular dynamics simulations have been conducted at a range of temperatures and an aligning potential has been applied to mimic the effect of a magnetic field. In cooling the SCLCP from an isotropic melt, microphase separation was observed yielding a domain structure. The application of a magnetic field to this structure aligns the domains producing a stable smectic mesophase. This is the first study in which mesophases have been observed using an off-lattice model of a SCLCP. The second material that has been investigated is a dendrimer with terminal mesogenic functionalization. Here, a multi-scale approach has been taken with Monte Carlo studies of a s...

Stimson, L M

2003-01-01

285

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.

1988-01-01

286

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

287

Reorganization energy of electron transfer processes in ionic fluids: a molecular Debye-Huckel approach.  

UK PubMed Central (United Kingdom)

The reorganization energy of electron transfer processes in ionic fluids is studied under the linear response approximation using a molecule Debye-Hckel theory. Reorganization energies of some model reactants of electron transfer reactions in molten salts are obtained from molecular simulations and a molecule Debye-Hckel approach. Good agreements between simulation results and the results from our theoretical calculations using the same model Hamiltonian are found. Applications of our theory to electron transfer reactions in room temperature ionic liquids further demonstrate that our theoretical approach presents a reliable and accurate methodology for the estimation of reorganization energies of electron transfer reactions in ionic fluids.

Xiao T; Song X

2013-03-01

288

GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles.  

UK PubMed Central (United Kingdom)

Systems that extract structured information from natural language passages have been highly successful in specialized domains. The time is opportune for developing analogous applications for molecular biology and genomics. We present a system, GENIES, that extracts and structures information about cellular pathways from the biological literature in accordance with a knowledge model that we developed earlier. We implemented GENIES by modifying an existing medical natural language processing system, MedLEE, and performed a preliminary evaluation study. Our results demonstrate the value of the underlying techniques for the purpose of acquiring valuable knowledge from biological journals.

Friedman C; Kra P; Yu H; Krauthammer M; Rzhetsky A

2001-01-01

289

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2008-12-17

290

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

International Nuclear Information System (INIS)

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

2008-12-17

291

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

International Nuclear Information System (INIS)

[en]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

2008-06-19

292

Low-level wastewater treatment facility process control operational test report  

International Nuclear Information System (INIS)

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

1996-01-01

293

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.

Kerrien Samuel; Orchard Sandra; Montecchi-Palazzi Luisa; Aranda Bruno; Quinn Antony F; Vinod Nisha; Bader Gary D; Xenarios Ioannis; Wojcik Jrme; Sherman David; Tyers Mike; Salama John J; Moore Susan; Ceol Arnaud; Chatr-aryamontri Andrew; Oesterheld Matthias; Stmpflen Volker; Salwinski Lukasz; Nerothin Jason; Cerami Ethan; Cusick Michael E; Vidal Marc; Gilson Michael; Armstrong John; Woollard Peter; Hogue Christopher; Eisenberg David; Cesareni Gianni; Apweiler Rolf; Hermjakob Henning

2007-01-01

294

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

Directory of Open Access Journals (Sweden)

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

Pluskal Tom; Castillo Sandra; Villar-Briones Alejandro; Orei? Matej

2010-01-01

295

MOLECULAR SIEVES AS CATALYSTS FOR METHANOL DEHYDRATION IN THE LPDMEtm PROCESS  

Energy Technology Data Exchange (ETDEWEB)

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

Andrew W. Wang

2002-04-01

296

Theory of Point Processes and Some Basic Notions in Energy Level Statistics  

CERN Multimedia

Although it is not explicitly stated in physics literature, energy level statistics is based upon the hypothesis that the spectrum of a quantum Hamiltonian, after suitably normalized (unfolded), and observed in thermodynamic or semiclassical limit, looks like a typical realization of a stationary point process. In this survey article, we present a purely phenomenological view of energy level statistics based on the theory of point processes.

Minami, N

2006-01-01

297

Nucleosome-remodelling machines and other molecular motors observed at the single-molecule level.  

UK PubMed Central (United Kingdom)

Through its capability to transiently pack and unpack our genome, chromatin is a key player in the regulation of gene expression. Single-molecule approaches have recently complemented conventional biochemical and biophysical techniques to decipher the complex mechanisms ruling chromatin dynamics. Micromanipulations with tweezers (magnetic or optical) and imaging with molecular microscopy (electron or atomic force) have indeed provided opportunities to handle and visualize single molecules, and to measure the forces and torques produced by molecular motors, along with their effects on DNA or nucleosomal templates. By giving access to dynamic events that tend to be blurred in traditional biochemical bulk experiments, these techniques provide critical information regarding the mechanisms underlying the regulation of gene activation and deactivation by nucleosome and chromatin structural changes. This minireview describes some single-molecule approaches to the study of ATP-consuming molecular motors acting on DNA, with applications to the case of nucleosome-remodelling machines.

Lavelle C; Praly E; Bensimon D; Le Cam E; Croquette V

2011-10-01

298

Studies on actinide separation process from high-level liquid waste. Document on collaborative study  

International Nuclear Information System (INIS)

The present report describes the results of a joint study between Japan Nuclear Cycle Development Institute (JNC) and Japan Atomic Energy Research Institute (JAERI) on actinide separation process from high-level liquid waste, which was performed for three and half years from September, 1998 to March, 2002. The purpose of the joint study is to point out common subjects in process development by an overall evaluation of each actinide separation process: TRUEX/SETFICS Process studied in JNC and DIDPA Extraction Process studied in JAERI. This would contribute to more effective process development. The result of the evaluation showed that both processes have common subjects to be studied in sub-processes such as treatment step for spent solvent or DTPA waste solution and solvent washing step for recycling, although the main process for actinide separation is different from each other. In the way to the demonstration of both processes in an engineering scale, it is necessary to develop the sub-processes and to test the whole process including the sub-processes. Two essential requirements in the process development are the cost reduction and the minimization of secondary wastes. Future continuing research and development should be performed for more rational and effective actinide separation process so as to fulfill these requirements as much as possible. (author)

2002-01-01

299

SCRUB-PA: A Multi-Level Multi-Dimensional Anonymization Tool for Process Accounting  

CERN Document Server

In the UNIX/Linux environment the kernel can log every command process created by every user using process accounting. This data has many potential uses, including the investigation of security incidents. However, process accounting data is also sensitive since it contains private user information. Consequently, security system administrators have been hindered from sharing these logs. Given that many interesting security applications could use process accounting data, it would be useful to have a tool that could protect private user information in the logs. For this reason we introduce SCRUB-PA, a tool that uses multi-level multi-dimensional anonymization on process accounting log files in order to provide different levels of privacy protection. It is our goal that SCRUB-PA will promote the sharing of process accounting logs while preserving privacy.

Luo, K; Li, Y; Slagell, A J; Yurcik, W; Ermopoulos, Charis; Li, Yifan; Luo, Katherine; Slagell, Adam; Yurcik, William

2006-01-01

300

Signal processing for molecular and cellular biological physics: an emerging field.  

UK PubMed Central (United Kingdom)

Recent advances in our ability to watch the molecular and cellular processes of life in action--such as atomic force microscopy, optical tweezers and Forster fluorescence resonance energy transfer--raise challenges for digital signal processing (DSP) of the resulting experimental data. This article explores the unique properties of such biophysical time series that set them apart from other signals, such as the prevalence of abrupt jumps and steps, multi-modal distributions and autocorrelated noise. It exposes the problems with classical linear DSP algorithms applied to this kind of data, and describes new nonlinear and non-Gaussian algorithms that are able to extract information that is of direct relevance to biological physicists. It is argued that these new methods applied in this context typify the nascent field of biophysical DSP. Practical experimental examples are supplied.

Little MA; Jones NS

2013-02-01

 
 
 
 
301

Observation of the amorphous zinc oxide recrystalline process by molecular dynamics simulation.  

UK PubMed Central (United Kingdom)

The detailed structural variations of amorphous zinc oxide (ZnO) as well as wurtzite (B4) and zinc blende (B3) crystal structures during the temperature elevation process were observed by molecular dynamics simulation. The amorphous ZnO structure was first predicted through the simulated-annealing basin-hopping algorithm with the criterion to search for the least stable structure. The density and X-ray diffraction profiles of amorphous ZnO of the structure were in agreement with previous reports. The local structural transformation among different local structures and the recrystalline process of amorphous ZnO at higher temperatures are observed and can explain the structural transformation and recrystalline mechanism in a corresponding experiment [Bruncko et al., Thin Solid Films 520, 866-870 (2011)].

Lin KH; Sun SJ; Ju SP; Tsai JY; Chen HT; Hsieh JY

2013-02-01

302

Simulation for Nanoimprint Lithography Process Using Temperature Controlled Nonequilibrium Molecular Dynamics  

International Nuclear Information System (INIS)

[en]Temperature is an essential process variable in NanoImprint Lithography(NIL) where the temperature varies between room temperature and above the glass transition temperature. To simulate NIL process, we employ both the Nose-Poincare method for temperature controlled Molecular Dynamics(MD) and force field for polymer material i.e. PolyMethyl MethAcrylate(PMMA), which is most widely selected as NIL resist. Nose-Poincare method, which convinces the conservation of Hamiltonian structure and time-reversal symmetry, overcomes the drawbacks inherent in the conventional methods such as Nose thermostat and Nose-Hoover thermostat. Thus, this method exhibits enhanced numerical stability even when the temperature fluctuation is large. To describe PMMA, we adopt the force field which account for bond stretch, bending, torsion, inversion, partial charge, and van der Waals energy

2007-06-01

303

Simulation for Nanoimprint Lithography Process Using Temperature Controlled Nonequilibrium Molecular Dynamics  

Energy Technology Data Exchange (ETDEWEB)

Temperature is an essential process variable in NanoImprint Lithography(NIL) where the temperature varies between room temperature and above the glass transition temperature. To simulate NIL process, we employ both the Nose-Poincare method for temperature controlled Molecular Dynamics(MD) and force field for polymer material i.e. PolyMethyl MethAcrylate(PMMA), which is most widely selected as NIL resist. Nose-Poincare method, which convinces the conservation of Hamiltonian structure and time-reversal symmetry, overcomes the drawbacks inherent in the conventional methods such as Nose thermostat and Nose-Hoover thermostat. Thus, this method exhibits enhanced numerical stability even when the temperature fluctuation is large. To describe PMMA, we adopt the force field which account for bond stretch, bending, torsion, inversion, partial charge, and van der Waals energy.

Kwon, Sung Jin; Lee, Young Min; Im, Se Young [Korea Advanced Institute of Science and Technology, Daejeon (Korea, Republic of)

2007-07-01

304

Acceleration of early-photon fluorescence molecular tomography with graphics processing units.  

UK PubMed Central (United Kingdom)

Fluorescence molecular tomography (FMT) with early-photons can improve the spatial resolution and fidelity of the reconstructed results. However, its computing scale is always large which limits its applications. In this paper, we introduced an acceleration strategy for the early-photon FMT with graphics processing units (GPUs). According to the procedure, the whole solution of FMT was divided into several modules and the time consumption for each module is studied. In this strategy, two most time consuming modules (Gd and W modules) were accelerated with GPU, respectively, while the other modules remained coded in the Matlab. Several simulation studies with a heterogeneous digital mouse atlas were performed to confirm the performance of the acceleration strategy. The results confirmed the feasibility of the strategy and showed that the processing speed was improved significantly.

Wang X; Zhang B; Cao X; Liu F; Luo J; Bai J

2013-01-01

305

Chemistry of interstellar ices: molecular simulations of photochemical and thermal processes  

Science.gov (United States)

Processes at interstellar ice surfaces form a challenging field of study, well suited for molecular simulation techniques. To date the number of computational studies remains rather limited. Computer simulations are a valuable complement to experiments on astrochemically relevant systems. An overview will be given of suitable computational tools to study thermal and UV induced processes. Some examples will be taken from recent simulations on the photodesorption of porous and compact water ice, the hydrogenation of CO ice, and diffusion of atoms and molecules at cold surfaces. The influence of quantum tunneling on chemical reactions and diffusion will be highlighted. In addition, differences in the diffusion properties of hydrogen at amorphous and crystalline ice surfaces will be discussed. Comparison will be made with available experimental data.

Andersson, Stefan

2012-07-01

306

Molecular dynamics simulations of crystal growth from melted silicon: Defect formation processes  

Energy Technology Data Exchange (ETDEWEB)

Molecular dynamics calculations have been performed to simulate crystal growth from melted silicon (Si) and defect formation processes based on the ordinary Langevin equation employing the Tersoff interatomic potential. The findings of this investigation are as follows: (1) The [110] bonds at the solid-liquid interface induce the eclipsed configurations or hexagonal Si structures which stabilize microfacets composed of the {l{underscore}brace}111{r{underscore}brace} planes. (2) Defect formation during crystal growth processes is due to misorientations at the {l{underscore}brace}111{r{underscore}brace} interfaces which result in an elementary grown-in defect structure including five- and seven-member rings. (3) The elementary grown-in defect migrates in c-Si by bond-switching motions during further crystal pulling or annealing.

Ishimaru, Manabu; Motooka, Teruaki

1999-07-01

307

PROCESS FOR PRODUCING HIGH-MOLECULAR-WEIGHT COMPOUNDS OF PHENOLIC COMPOUNDS, ETC. AND USE THEREOF  

UK PubMed Central (United Kingdom)

A process for producing high-molecular-weight compounds of phenolic or aromatic amine compounds by the action of a catalyst comprising an enzyme having a polyphenol oxidizing activity in the alkali region; applications of the compounds obtained by the above process to thickener, stabilizer, coagulant, emulsifier, dispersant, water retainer, antioxidant, adhesive, concrete admixture, dye, coating material, petroleum recovering agent, soil conditioner, a blow-applied seed bearing surface soil stabilizer, deodorant, smell eliminator, pesticide spreader, feed binder, bactericide, antimicrobial drug, viral infection inhibitor, bioadhesion preventive, biotic repellent, insecticide, cataplasma, ink base or wood treatment; and a method of waste water disposal, a method of deoxygenation and a method of treating wood, concrete or soil in which use is made of the above reaction.

ECHIGO Takashi; OHNO Ritsuko

308

Molecular genetics of the incision step in the DNA excision repair process  

Energy Technology Data Exchange (ETDEWEB)

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.

Rubin, J.S.

1988-09-01

309

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

1983-01-01

310

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

Energy Technology Data Exchange (ETDEWEB)

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{mu}l Ep-tube amplified reaction, which indicates a promising clinic molecular diagnostics in the droplet amplification.

Huang Guoliang; Yang Xiaoyong [Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing, 100084 (China); Ma Li; Yang Xu, E-mail: tshgl@tsinghua.edu.cn [National Engineering Research Center for Beijing Biochip Technology, Beijing, 102206 (China)

2011-01-01

311

Recognition processes at a functionalized lipid surface observed with molecular resolution  

DEFF Research Database (Denmark)

The specific binding of proteins to functionalized lipid monolayers on aqueous subphases was characterized by neutron reflectivity and fluorescence microscopy measurements. Due to the high affinity and high specificity of their noncovalent interaction, streptavidin (SA) and biotin (vitamin H) were chosen as a model system to investigate the structural characteristics of a recognition process on a molecular length scale. Changes in the neutron reflection from the surfaces of NaCl aqueous (H2O or D2O) protein solutions (10(-8) M SA) were used to monitor the interaction of the protein with a monolayer of a biotinylated lipid in situ. Refinement of the reflectivity data and independent fluorescence microscopic observation of the interface using FITC-labeled SA showed that the protein forms macroscopically homogeneous (and presumably crystalline) domains covering a large portion of the surface. Moreover, the neutron reflection experiments clearly showed the formation of a monomolecular protein layer with an effective thickness, d(p) = 43.7 +/- 2 angstrom. The area per protein molecule occupied in the film was A0 = 2860 +/- 200 angstrom 2 and n(w) = 260 +/- 100 water molecules were associated with each protein molecule. Quantitative binding was found to occur at biotin surface concentrations as low as 1 molecule/1,250 angstrom 2 (compared with approximately 1 molecule/40 angstrom 2 for dense packing). This study demonstrates the application of a promising new tool for the systematic investigation of molecular recognition processes in protein/lipid model systems.

Vaknin, D.; Als-Nielsen, J.

1991-01-01

312

Preparation of a novel molecularly imprinted polymer by the sol-gel process for sensing creatinine.  

UK PubMed Central (United Kingdom)

A novel molecularly imprinted polymer (MIP) was prepared and used as an artificial receptor for creatinine (Cre). A sol-gel process was used to prepare the MIP. Tetraethoxysilane (TEOS) was employed as the crosslinker for the formation of a silica matrix for the MIP. Aluminum ion (Al(3+)) was chosen as the dopant to generate Lewis acid sites in the silica matrix for interactions with Cre. Through the sol-gel process, a polymeric matrix with memory sites for Cre was obtained, and this is mentioned here as the molecularly imprinted polymer for creatinine (MIP(Cre)). The imprinting efficiency of MIP(Cre) was evaluated by contrasting the adsorbed amount of Cre by MIP(Cre) with that by the corresponding non-imprinted polymer (NIP). Creatine (Cn), N-hydroxysuccinimide (NHS), and L-tyrosine (L-tyr) were selected as interferences to study the selectivity of the MIP(Cre). The interference studies were also conducted using binary mixtures, such as Cre/Cn, Cre/NHS, and Cre/L-tyr. All these studies reveal that the MIP(Cre) possess a remarkable affinity for Cre. The crucial role of Al(3+) in this system is discussed in detail. Furthermore, the effects of concentrations of Al(3+) and TEOS on the adsorbed amount of Cre by MIP(Cre) were also investigated.

Li TJ; Chen PY; Nien PC; Lin CY; Vittal R; Ling TR; Ho KC

2012-01-01

313

Preparation of a novel molecularly imprinted polymer by the sol-gel process for sensing creatinine.  

Science.gov (United States)

A novel molecularly imprinted polymer (MIP) was prepared and used as an artificial receptor for creatinine (Cre). A sol-gel process was used to prepare the MIP. Tetraethoxysilane (TEOS) was employed as the crosslinker for the formation of a silica matrix for the MIP. Aluminum ion (Al(3+)) was chosen as the dopant to generate Lewis acid sites in the silica matrix for interactions with Cre. Through the sol-gel process, a polymeric matrix with memory sites for Cre was obtained, and this is mentioned here as the molecularly imprinted polymer for creatinine (MIP(Cre)). The imprinting efficiency of MIP(Cre) was evaluated by contrasting the adsorbed amount of Cre by MIP(Cre) with that by the corresponding non-imprinted polymer (NIP). Creatine (Cn), N-hydroxysuccinimide (NHS), and L-tyrosine (L-tyr) were selected as interferences to study the selectivity of the MIP(Cre). The interference studies were also conducted using binary mixtures, such as Cre/Cn, Cre/NHS, and Cre/L-tyr. All these studies reveal that the MIP(Cre) possess a remarkable affinity for Cre. The crucial role of Al(3+) in this system is discussed in detail. Furthermore, the effects of concentrations of Al(3+) and TEOS on the adsorbed amount of Cre by MIP(Cre) were also investigated. PMID:22152800

Li, Ta-Jen; Chen, Po-Yen; Nien, Po-Chin; Lin, Chia-Yu; Vittal, R; Ling, Tzong-Rong; Ho, Kuo-Chuan

2011-11-03

314

Indistinguishability and interference in the coherent control of atomic and molecular processes  

International Nuclear Information System (INIS)

The subtle and fundamental issue of indistinguishability and interference between independent pathways to the same target state is examined in the context of coherent control of atomic and molecular processes, with emphasis placed on possible 'which-way' information due to quantum entanglement established in the quantum dynamics. Because quantum interference between independent pathways to the same target state occurs only when the independent pathways are indistinguishable, it is first shown that creating useful coherence between nondegenerate states of a molecule for subsequent quantum interference manipulation cannot be achieved by collisions between atoms or molecules that are prepared in momentum and energy eigenstates. Coherence can, however, be transferred from light fields to atoms or molecules. Using a particular coherent control scenario, it is shown that this coherence transfer and the subsequent coherent phase control can be readily realized by the most classical states of light, i.e., coherent states of light. It is further demonstrated that quantum states of light may suppress the extent of phase-sensitive coherent control by leaking out some which-way information while 'incoherent interference control' scenarios proposed in the literature have automatically ensured the indistinguishability of multiple excitation pathways. The possibility of quantum coherence in photodissociation product states is also understood in terms of the disentanglement between photodissociation fragments. Results offer deeper insights into quantum coherence generation in atomic and molecular processes.

2010-02-07

315

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

316

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).

317

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

Energy Technology Data Exchange (ETDEWEB)

A Monte Carlo impurity transport code based on object-oriented method has been developed. Edge plasma in fusion devices has a lot of impurity atoms and molecules such as hydrocarbon species, C{sub x}H{sub y} due to low electron temperature in the edge. Various atomic/molecular processes have been considered in the edge plasma region and we need to determine which process is essential in edge plasma conditions. To take such complicated processes into account in a systematic way, Monte Carlo impurity simulation, which has a strong flexibility in dealing with various atomic and molecular processes, would be useful. By employing the object-oriented method in the simulation code, we can handle arbitrary atomic and molecular processes. (orig.)

Asano, K.; Ohno, N.; Takamura, S. [Nagoya Univ. (Japan). Dept. of Energy Engineering and Science

2002-07-01

318

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

International Nuclear Information System (INIS)

[en]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

1989-01-01

319

Right hemisphere advantage in processing Cantonese level and contour tones Evidence from dichotic listening.  

UK PubMed Central (United Kingdom)

The brain lateralization pattern of Cantonese tonal processing was examined with the dichotic listening (DL) paradigm. Three factors were manipulated systematically in the study. First, the processing of level tones was compared with that of contour tones. Second, the influence of a linguistic context in tonal processing was studied by contrasting the patterns of brain lateralization for real syllables, pseudo-syllables, and hums. Finally, the discrimination and the identification tasks were used to test how processing depth might modulate the results obtained. A right hemisphere advantage (RHA) was obtained regardless of tone type, stimulus type, and task. In addition, the performance on level tones was in general better than that on contour tones. These findings suggest that Cantonese speakers are highly sensitive to the acoustic features of lexical tones, which supports the acoustic view about tonal processing.

Jia S; Tsang YK; Huang J; Chen HC

2013-10-01

320

Impaired global, and compensatory local, biological motion processing in people with high levels of autistic traits.  

UK PubMed Central (United Kingdom)

People with Autism Spectrum Disorder (ASD) are hypothesized to have poor high-level processing but superior low-level processing, causing impaired social recognition, and a focus on non-social stimulus contingencies. Biological motion perception provides an ideal domain to investigate exactly how ASD modulates the interaction between low and high-level processing, because it involves multiple processing stages, and carries many important social cues. We investigated individual differences among typically developing observers in biological motion processing, and whether such individual differences associate with the number of autistic traits. In Experiment 1, we found that individuals with fewer autistic traits were automatically and involuntarily attracted to global biological motion information, whereas individuals with more autistic traits did not show this pre-attentional distraction. We employed an action adaptation paradigm in the second study to show that individuals with more autistic traits were able to compensate for deficits in global processing with an increased involvement in local processing. Our findings can be interpreted within a predictive coding framework, which characterizes the functional relationship between local and global processing stages, and explains how these stages contribute to the perceptual difficulties associated with ASD.

van Boxtel JJ; Lu H

2013-01-01

 
 
 
 
321

Impaired global, and compensatory local, biological motion processing in people with high levels of autistic traits.  

Science.gov (United States)

People with Autism Spectrum Disorder (ASD) are hypothesized to have poor high-level processing but superior low-level processing, causing impaired social recognition, and a focus on non-social stimulus contingencies. Biological motion perception provides an ideal domain to investigate exactly how ASD modulates the interaction between low and high-level processing, because it involves multiple processing stages, and carries many important social cues. We investigated individual differences among typically developing observers in biological motion processing, and whether such individual differences associate with the number of autistic traits. In Experiment 1, we found that individuals with fewer autistic traits were automatically and involuntarily attracted to global biological motion information, whereas individuals with more autistic traits did not show this pre-attentional distraction. We employed an action adaptation paradigm in the second study to show that individuals with more autistic traits were able to compensate for deficits in global processing with an increased involvement in local processing. Our findings can be interpreted within a predictive coding framework, which characterizes the functional relationship between local and global processing stages, and explains how these stages contribute to the perceptual difficulties associated with ASD. PMID:23630514

van Boxtel, Jeroen J A; Lu, Hongjing

2013-04-23

322

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2001-04-01

323

Proton transfer step in the carbon dioxide capture by monoethanol amine: a theoretical study at the molecular level.  

UK PubMed Central (United Kingdom)

An aqueous solution of monoethanol amine (MEA) has been utilized in an industrial process of CO(2) absorption. The chemical reaction between CO(2) and MEA, which is employed in the process, consists of two steps. After the formation of the MEA-CO(2) complex ("capture"), a proton transfers from the complex to give a final product. In the present study, the overall mechanism of the reaction is discussed, especially focusing on the proton transfer step. Using RISM-SCF-SEDD, a hybrid method of electronic structure theory and statistical mechanics for molecular liquid, we clarified that the role of MEA as a base is crucial in the proton transfer step.

Iida K; Sato H

2012-02-01

324

The early molecular processes underlying the neurological manifestations of an animal model of Wilson's disease.  

UK PubMed Central (United Kingdom)

The Long-Evans Cinnamon (LEC) rat shows age-dependent hepatic manifestations that are similar to those of Wilson's disease (WD). The pathogenic process in the brain has, however, not been evaluated in detail due to the rarity of the neurological symptoms. However, copper accumulation is noted in LEC rat brain tissue from 24 weeks of age, which results in oxidative injuries. The current study investigated the gene expression profiles of LEC rat brains at 24 weeks of age in order to identify the important early molecular changes that underlie the development of neurological symptoms in WD. Biological ontology-based analysis revealed diverse altered expressions of the genes related to copper accumulation. Of particular interest, we found altered expression of genes connected to mitochondrial respiration (Sdhaf2 and Ndufb7), calcineurin-mediated cellular processes (Ppp3ca, Ppp3cb, and Camk2a), amyloid precursor protein (Anks1b and A2m) and alpha-synuclein (Snca). In addition to copper-related changes, compensatory upregulations of Cp and Hamp reflect iron-mediated neurotoxicity. Of note, reciprocal expression of Asmt and Bhmt is an important clue that altered S-adenosylhomocysteine metabolism underlies brain injury in WD, which is directly correlated to the decreased expression of S-adenosylhomocysteine hydrolase in hepatic tissue in LEC rats. In conclusion, our study indicates that diverse molecular changes, both variable and complex, underlie the development of neurological manifestations in WD. Copper-related injuries were found to be the principal pathogenic process, but Fe- or adenosylhomocysteine-related injuries were also implicated. Investigations using other animal models or accessible human samples will be required to confirm our observations.

Lee BH; Kim JH; Kim JM; Heo SH; Kang M; Kim GH; Choi JH; Yoo HW

2013-05-01

325

Low environmentally relevant levels of bioactive xenobiotics and associated degradation products cause cryptic perturbations of metabolism and molecular stress responses in Arabidopsis thaliana.  

UK PubMed Central (United Kingdom)

Anthropic changes and chemical pollution confront wild plant communities with xenobiotic combinations of bioactive molecules, degradation products, and adjuvants that constitute chemical challenges potentially affecting plant growth and fitness. Such complex challenges involving residual contamination and mixtures of pollutants are difficult to assess. The model plant Arabidopsis thaliana was confronted by combinations consisting of the herbicide glyphosate, the fungicide tebuconazole, the glyphosate degradation product aminomethylphosphonic acid (AMPA), and the atrazine degradation product hydroxyatrazine, which had been detected and quantified in soils of field margins in an agriculturally intensive region. Integrative analysis of physiological, metabolic, and gene expression responses was carried out in dose-response experiments and in comparative experiments of varying pesticide combinations. Field margin contamination levels had significant effects on plant growth and metabolism despite low levels of individual components and the presence of pesticide degradation products. Biochemical and molecular analysis demonstrated that these less toxic degradation products, AMPA and hydroxyatrazine, by themselves elicited significant plant responses, thus indicating underlying mechanisms of perception and transduction into metabolic and gene expression changes. These mechanisms may explain observed interactions, whether positive or negative, between the effects of pesticide products (AMPA and hydroxyatrazine) and the effects of bioactive xenobiotics (glyphosate and tebuconazole). Finally, the metabolic and molecular perturbations induced by low levels of xenobiotics and associated degradation products were shown to affect processes (carbon balance, hormone balance, antioxidant defence, and detoxification) that are likely to determine environmental stress sensitivity.

Serra AA; Nuttens A; Larvor V; Renault D; Coue I; Sulmon C; Gouesbet G

2013-07-01

326

Processability analysis of candidate waste forms. [For SRP high-level wastes  

Energy Technology Data Exchange (ETDEWEB)

A quantitative merit evaluation, or processability analysis, was performed to assess the relative difficulty of remote processing of Savannah River Plant high-level wastes for seven alternative waste form candidates. The reference borosilicate glass process was rated as the simplest, followed by FUETAP concrete, glass marbles in a lead matrix, high-silica glass, crystalline ceramics (SYNROC-D and tailored ceramics), and coated ceramic particles. Cost estimates for the borosilicate glass, high-silica glass, and ceramic waste form processing facilities are also reported.

Gould, Jr, T H; Dunson, Jr, J B; Eisenberg, A M; Haight, Jr, H G; Mello, V E; Schuyler, III, R L

1982-01-01

327

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

International Nuclear Information System (INIS)

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

1977-01-01

328

In Search of Microscopic Evidence for Molecular Level Negative Thermal Expansion in Fullerenes  

CERN Multimedia

We report the high-resolution far infrared vibrational properties of C60 and endohedral Kr@C60 fullerene as a function of temperature. Anomalous softening of the F1u(1) mode (526 cm-1) is observed throughout the temperature range of investigation (300 - 10 K) suggesting that the fullerene cage may expand at low temperature in these molecular solids. To test this idea, we combine these results with temperature and pressure dependent Raman, infrared, and Kr extended x-ray absorption fine structure data from the literature to provide a comprehensive view of local cage size effects. The results are consistent with a recent molecular dynamics study [Kwon et al., Phys. Rev. Lett. 92, 15901 (2004)] that predicts negative thermal expansion in carbon fullerenes.

Brown, S; Musfeldt, J L; Dragoe, N; Cimpoesu, F; Ito, S; Takagi, H; Cross, R J

2006-01-01

329

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

UK PubMed Central (United Kingdom)

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

Hu X; Yu Z; Liu R

2013-05-01

330

Science Process Skills Levels of Primary School Seventh Grade Students in Science and Technology Lesson  

Directory of Open Access Journals (Sweden)

Full Text Available The aim of this study was to determine the science process skill achievement level of primary school seventh grade students in a Science and Technology lesson and relations among academic background of the parents, monthly income of the parents, having a computer, having own room and students science process skill levels. To this end, Science Process Skills Test (SPST) was prepared and used as a data collection means by the researchers. The Cronbach Alpha reliability coefficient of the test was found 0,88. The sample of the study consists of 828 seventh grade students from 21 primary schools which are choosen by chance from Kocaeli Province Center (within Turkey). Scanning model has been used in the study. The data were analyzed by using frequency, percentage, arithmetic average, standard deviation values, and t-test and ANOVA analyze techniques. According to the research findings, it was found that students science process skill levels were in middle level. As a result, primary school seventh grade students science process skill levels did display differences according to parents academic background, their monthly income, having a computer, having own room, but the students SPS do not change in terms of gender.

Nurhan ZTRK; zden TEZEL; M. Bahaddin ACAT

2010-01-01

331

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

332

Gene expression patterns unveil a new level of molecular heterogeneity in colorectal cancer.  

UK PubMed Central (United Kingdom)

The recognition that colorectal cancer (CRC) is a heterogeneous disease in terms of clinical behaviour and response to therapy translates into an urgent need for robust molecular disease subclassifiers that can explain this heterogeneity beyond current parameters (MSI, KRAS, BRAF). Attempts to fill this gap are emerging. The Cancer Genome Atlas (TGCA) reported two main CRC groups, based on the incidence and spectrum of mutated genes, and another paper reported an EMT expression signature defined subgroup. We performed a prior free analysis of CRC heterogeneity on 1113 CRC gene expression profiles and confronted our findings to established molecular determinants and clinical, histopathological and survival data. Unsupervised clustering based on gene modules allowed us to distinguish at least five different gene expression CRC subtypes, which we call surface crypt-like, lower crypt-like, CIMP-H-like, mesenchymal and mixed. A gene set enrichment analysis combined with literature search of gene module members identified distinct biological motifs in different subtypes. The subtypes, which were not derived based on outcome, nonetheless showed differences in prognosis. Known gene copy number variations and mutations in key cancer-associated genes differed between subtypes, but the subtypes provided molecular information beyond that contained in these variables. Morphological features significantly differed between subtypes. The objective existence of the subtypes and their clinical and molecular characteristics were validated in an independent set of 720 CRC expression profiles. Our subtypes provide a novel perspective on the heterogeneity of CRC. The proposed subtypes should be further explored retrospectively on existing clinical trial datasets and, when sufficiently robust, be prospectively assessed for clinical relevance in terms of prognosis and treatment response predictive capacity. Original microarray data were uploaded to the ArrayExpress database (http://www.ebi.ac.uk/arrayexpress/) under Accession Nos E-MTAB-990 and E-MTAB-1026. 2013 Swiss Institute of Bioinformatics. Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.

Budinska E; Popovici V; Tejpar S; D'Ario G; Lapique N; Sikora KO; Di Narzo AF; Yan P; Hodgson JG; Weinrich S; Bosman F; Roth A; Delorenzi M

2013-09-01

333

GLYCOSIDASES IN HUMAN BLOOD PLASMA AND URINE. MOLECULAR FORMS AND ACTIVITY LEVELS  

Directory of Open Access Journals (Sweden)

Full Text Available The isoe lect r i c f ocusing p a t terns and pH activity cur ves of f i ve glycosidas e e nzymes i n blood plasma and ur i ne were s t ud i e d . This s tudy demons trated the presence o f a sing le molecular f onn in a -glucosidase and of two mole cul a r fonns of the enzymes H-a ce t yl-B-D-gluco sarni nidase, Na c e t y l -p-D-g a l a c t o s amin i ua s e and S-glucuronidase i n both plasma and urine . B-Galactosidase existed as a s i ng le major molecular f orm i n p l asma and a t l e a st t wo molecular forms in urine. Spe cific activity of each~ le n zyme was determined in p lasma and urine The validity o f taking the ratio between two e n zvrne activities as an index for scr een .l.ng of fr ene t ic di s e a s e is discussed.

Reza Seyed Yazdani

1982-01-01

334

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

UK PubMed Central (United Kingdom)

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.

Liang J; Yin J; Chen T; Chen H; Ding X; Shen M

2012-04-01

335

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

Science.gov (United States)

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

Gou, Jihua

336

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

Directory of Open Access Journals (Sweden)

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

Youssef Jihan; Elbi Cem; Warren Barbour; Yourtee David; Nagarur Raghavendra; Molteni Agostino; Cunningham Michael L; Badr Mostafa

2003-01-01

337

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

UK PubMed Central (United Kingdom)

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

Pizzarello S; Davidowski SK; Holland GP; Williams LB

2013-09-01

338

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

Science.gov (United States)

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

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

2013-09-09

339

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

UK PubMed Central (United Kingdom)

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 (P<0.05 for each parameter). Cilnidipine treatment improved glucose and insulin sensitivity in DIO mice. In addition, cilnidipine treatment dramatically increased the level of adiponectin in white adipose tissue (P<0.05) and the circulating levels of total and high-molecular weight (HMW) adiponectin in DIO mice (P<0.01 for each parameter). Furthermore, the secretion of HMW adiponectin and the ratio of HMW adiponectin/total adiponectin were both increased after cilnidipine 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.

Ueno D; Masaki T; Gotoh K; Chiba S; Kakuma T; Yoshimatsu H

2013-03-01

340

Many-body processes in atomic and molecular physics. Progress report  

Energy Technology Data Exchange (ETDEWEB)

A proposal is presented for theoretical efforts towards the following projects: (1) carry out rotational predissociation lifetime calculations of several van der Waals molecules for which accurate potential energy surfaces were obtained recently by van der Waals molecular spectroscopic methods; (2) development and extension of the complex coordinate - coupled channel formalism to vibrational predissociation studies; (3) Floquet theory study of the quantum dynamics of multiphoton excitation of vibrational-rotational states of small molecules by laser light; (4) development and extension of the method of complex quasi-vibrational energy formalism to the study of intense field multiphoton dissociation of diatomic molecules and to photodissociation process in the presence of shape resonances; (5) investigation of the external field effects in multiphoton excitation and dissociation of small molecules. Depending on time and resources, several other projects may also be pursued. A detailed discussion covering these proposed projects is presented.

Chu, S.I.

1981-01-01

 
 
 
 
341

Molecular Dynamics Simulation of Sputtering Process of Hydrogen and Graphene Sheets  

CERN Multimedia

To clarify the yielding mechanism of small hydrocarbon molecules in chemical sputtering between hydrogen and graphene sheets, we made classical molecular dynamics simulation with modified Brenner's REBO potential which we proposed to deal with chemical reaction. As the simulation model, we prepared more realistic physical system, which is composed of 160 incident hydrogen atoms and ten graphene multilayers, than our previous model. From the present work, we found the following fact: breaking the covalent bonds between carbon atoms by hydrogen does not play an important role during destruction process of graphene structure, but momentum transfer from incident hydrogen to graphene causes to destroy graphene structure. Moreover, it is found that almost all fragments of graphene sheets form chain-shaped molecules, and that yielded hydrocarbon molecules are composed of carbon chain and single hydrogen-atom.

Nakamura, H; Nakamura, Hiroaki; Ito, Atsushi

2006-01-01

342

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

Energy Technology Data Exchange (ETDEWEB)

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.

Chen Zhihui [Key Laboratory of Information Photonics and Optical Communications (Beijing University of Posts and Telecommunications), Ministry of Education, P.O. Box 49 (BUPT), Beijing 100876 (China); Yu Zhongyuan, E-mail: yuzhongyuan30@gmail.co [Key Laboratory of Information Photonics and Optical Communications (Beijing University of Posts and Telecommunications), Ministry of Education, P.O. Box 49 (BUPT), Beijing 100876 (China); Lu Pengfei; Liu Yumin [Key Laboratory of Information Photonics and Optical Communications (Beijing University of Posts and Telecommunications), Ministry of Education, P.O. Box 49 (BUPT), Beijing 100876 (China)

2009-11-15

343

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.

1008-01-00

344

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

345

A molecular dynamics study for ultrafast process of radiation damage in materials  

International Nuclear Information System (INIS)

Molecular dynamics calculations are performed to simulate displacement damage processes in irradiated metals. The interaction of atoms is described using the embedded atom method (EAM) potential that is modified at close atomic separation to merge smoothly with the universal ZBL-potential for description of high energy atoms. The displacement events of high energy atoms simulated here are initiated both from a single recoil atom with the kinetic energy of 20 keV in vanadium and from dimer recoil atoms of 2 keV in copper. The initial evolution of the displacement events is represented by replacement collision sequences (RCSs) and subsequent molten-structure at the center of the events. The monomer recoil event in vanadium shows a higher probability of defect production and lower probability of defect clustering, compared to the MD cascades in other metals. The dimer-recoil events in copper show a higher probability of defect clustering compared to a monomer-recoil event. (orig.)

1997-01-01

346

Identification of molecular processes needed for vascular formation through transcriptome analysis of different vascular systems.  

UK PubMed Central (United Kingdom)

BACKGROUND: Vascular system formation has been studied through molecular and genetic approaches in Arabidopsis, a herbaceous dicot that is used as a model system. Different vascular systems have developed in other plants such as crops and trees. Uncovering shared mechanisms underlying vascular development by transcriptome analysis of different vascular systems may help to transfer knowledge acquired from Arabidopsis to other economically important species. RESULTS: Conserved vascular genes and biological processes fundamental to vascular development were explored across various plants. Through comparative transcriptome analysis, 226 genes from Arabidopsis, 217 genes from poplar and 281 genes from rice were identified as constituting 107 conserved vascular gene groups. These gene groups are expressed mainly in vascular tissues and form a complex coexpression network with multiple functional connections. To date, only half of the groups have been experimentally investigated. The conserved vascular gene groups were classified into 9 essential processes for vascular development. 18 groups (17%) lack of annotations were classified as having unknown functions. CONCLUSION: The study provides a map of fundamental biological processes conserved across different vascular systems. It identifies gaps in the experimental investigation of pathways active in vascular formation, which if explored, could lead to a more complete understanding of vascular development.

Xu P; Kong Y; Li X; Li L

2013-01-01

347

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.

2009-05-01

348

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 tooths 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.

Wu Cheng-Da; Lin Jen-Fin; Fang Te-Hua

2009-01-01

349

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2004-01-15

350

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

International Nuclear Information System (INIS)

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

2004-01-01

351

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

Energy Technology Data Exchange (ETDEWEB)

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.)

Andernacht, Martin [TUEV NORD SysTec GmbH und Co. KG, Hamburg (Germany); Glaser, Hendrik [Ministerium fuer Soziales, Gesundheit, Familie, Jugend un Senioren des Landes Schleswig-Holstein, Kiel (Germany). Dept. of Reactor Safety and Radiation Protection; Sonnenkalb, Martin [Gesellschaft fuer Anlagen- und Reaktorsicherheit mbH (GRS), Koeln (Germany). Dept. of Barrier Effectiveness

2009-01-15

352

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 ten years by the utility. In the past, a PSR only included a plant-specific probabilistic safety analysis (PSA) Level 1 study. 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. 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. This paper will focus on conclusions and findings from an 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) 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. The paper is followed by the slides of the presentation. (authors)

2013-01-01

353

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.)

2009-01-01

354

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 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.

2011-01-01

355

Platinum(II)-bis(aryleneethynylene) complexes for solution-processible molecular bulk heterojunction solar cells.  

UK PubMed Central (United Kingdom)

Four new solution-processible small-molecular platinum(II)-bis(aryleneethynylene) complexes consisting of benzothiadiazole as the electron acceptor and triphenylamine and/or thiophene as the electron donor were conveniently synthesized and characterized by physicochemical and computational methods, and utilized as the electron-donor materials in the fabrication of solution-processed bulk heterojunction (BHJ) solar cells. The effect of different electron-donor groups in these small molecules on the optoelectronic and photovoltaic properties was also examined. The optical and time-dependent density functional theory studies showed that the incorporation of stronger electron-donor groups significantly enhanced the solar-absorption abilities of the complexes. These molecular complexes can serve as good electron donors for fabricating BHJ devices by blending them with the [6,6]-phenyl-C(71)-butyric acid methyl ester (PC(70)BM) as the electron acceptor. The best power conversion efficiency of 2.37% was achieved with the open-circuit voltage of 0.83 V, short-circuit current density of 7.10 mA cm(-2) and fill factor of 0.40 under illumination of an AM 1.5 solar-cell simulator. The spin-coated thin films showed p-channel field-effect charge transport with hole mobilities of up to 2.410(-4) cm(2) V(-1) s(-1) for these molecules. The present work illuminates the potential of well-defined organometallic complexes in developing light-harvesting small molecules for efficient power generation in organic photovoltaics implementation.

Dai FR; Zhan HM; Liu Q; Fu YY; Li JH; Wang QW; Xie Z; Wang L; Yan F; Wong WY

2012-01-01

356

Diagrammatic analysis of multiphoton processes in a ladder-type three-level atomic system  

Energy Technology Data Exchange (ETDEWEB)

We present a diagrammatic method for complete characterization of multiphoton processes in three-level atomic systems. By considering the interaction routes of the coupling and probe photons for a ladder-type, three-level, noncycling (or cycling) atomic system, we are able to completely discriminate between the pure one-photon and the pure two-photon resonance effects, and the effect of their combination in electromagnetically induced transparency (EIT) using our diagrammatic method. We show that the proposed diagrammatic method is very useful for the analysis of multiphoton processes in ladder-type EIT.

Noh, Heung-Ryoul [Department of Physics, Chonnam National University, Gwangju 500-757 (Korea, Republic of); Moon, Han Seb [Department of Physics, Pusan National University, Busan 609-735 (Korea, Republic of)

2011-11-15

357

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

Directory of Open Access Journals (Sweden)

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

Ploner Alexander; Miller Lance D; Hall Per; Bergh Jonas; Pawitan Yudi

2005-01-01

358

Advanced treatment processes for low and intermediate level radwastes in India  

Energy Technology Data Exchange (ETDEWEB)

Development of improved treatment processes for low and intermediate level radwastes is being pursued in India in view of the increasing environmental and regulatory concerns. Copper hexacyanoferrate loaded, macroporous anion exchange resin was developed as an effective sorbent for the removal of radiocesium from low level aqueous effluents and spent fuel storage pool water. The reverse osmosis process using cellulose acetate membranes was tested in pilot scale as an alternative treatment process for low level aqueous wastes. A treatment scheme for alkaline intermediate level aqueous wastes based on the selective uptake of radiocesium by a resorcinol-formaldehyde polycondensate resin was developed in the laboratory and found satisfactory in trials with the alkaline waste of a reprocessing plant. Synthetic zeolites are being tested for fixation of activity released in solution in wet oxidative destruction of spent ion exchange resin, arising from reactors and other nuclear facilities. All these processes are being critically evaluated for possible application in the treatment of low and intermediate level radwastes in India.

Samanta, S.K.; Singh, I.J.; Ramaswamy, M.; Theyyunni, T.K. [Bhabha Atomic Research Centre, Bombay (India)

1993-12-31

359

Variations of serum potassium level and risk of hyperkalemia in inpatients receiving low-molecular-weight heparin.  

UK PubMed Central (United Kingdom)

OBJECTIVES: To observe the variations of serum potassium level in patients receiving low-molecular weight heparin, assess the consequent risk of hyperkalemia and evaluate the clinical contributory factors. METHODS: A prospective study was performed on consecutive inpatients treated with low-molecular-weight heparin as indicated by the attending physicians. The changes of serum potassium level observed within 5-8 days were tested by univariate and multivariate analysis according to demographic and clinical variables and concomitant pharmacological therapy. RESULTS: Four hundred and sixteen patients (mean age 73 years; 64% female) were enrolled in the study over 15 months. After receiving nadroparin or enoxaparin (mean daily dosage: 76.3 anti-factor Xa unit/kg) for a median 6-day period, their mean (+/-SD) serum potassium level increased from 4.2+/-0.5 mmol/l to 4.5+/-0.5 mmol/l ( P<0.0001). This change was significantly correlated with baseline potassium, interval between potassium samplings, history of hypertension or renal insufficiency, and marginally with aldosterone antagonist treatment. Hyperkalemia, defined as potassium exceeding 5.5 mmol/l, developed in ten patients (2.4%) and the highest value observed was 7.6 mmol/l; by multivariate logistic-regression analysis, history of diabetes was the only significant independent predictor (odds ratio 6.5; 95% C.I.=1.7-24.8). CONCLUSION: Short-term treatment with low-molecular-weight heparin induces a significant increase in serum potassium level but the related incidence of relevant hyperkalemia is low. However, given the high absolute number of patients currently exposed to the risk in many clinical settings and the limitation of risk prediction, clinicians should prevent this life-threatening complication by a high index of suspicion and, accordingly, a quite routine monitoring of serum potassium.

Gheno G; Cinetto L; Savarino C; Vellar S; Carraro M; Randon M

2003-09-01

360

Energy levels and redox properties of aqueous Mn(2+/3+) from photoemission spectroscopy and density functional molecular dynamics simulation.  

UK PubMed Central (United Kingdom)

Energy-resolved photoemission spectroscopy and density functional molecular dynamics simulations are combined to construct an energy level diagram for the Mn(2+/3+) redox reaction in aqueous solution. Two peaks centered at 8.88 and 10.26 eV electron binding energies can be assigned to the Mn2+ hexa-aquo complex with a peak area ratio of 2:2.83. Using the notation of crystal field theory, the peak at lower energies can be interpreted as arising from ionization from the e(g) levels (highest occupied molecular orbital, HOMO), and the peak at higher energies are from ionization of the t(2g) levels. The difference corresponds to the average crystal field splitting, 1.38 eV. From the position of the HOMO level and the absolute redox potential, an experimental value for the reorganization free energy of the aqueous Mn3+ hexa-aquo complex is estimated to be 2.98 eV. Density functional molecular dynamics simulations can reproduce the experimental vertical ionization energy, redox free energy, and reorganization free energies fairly well, provided that the absolute potential shift in periodic boundary conditions, finite size effects, and inaccuracies of the exchange correlation functional are taken into account. Most strikingly, in the simulations, we observe spontaneous and reversible deprotonation of the aqueous Mn3+ hexa-aquo complex to form MnOH(H2O)5(2+) + H+, in line with the low experimental pKa value of this ion. The interconversion between protonation states leads to interesting redox phenomena for aqueous Mn3+, culminating in a bimodal thermal distribution of the electron affinity.

Moens J; Seidel R; Geerlings P; Faubel M; Winter B; Blumberger J

2010-07-01

 
 
 
 
361

Energy levels and redox properties of aqueous Mn(2+/3+) from photoemission spectroscopy and density functional molecular dynamics simulation.  

Science.gov (United States)

Energy-resolved photoemission spectroscopy and density functional molecular dynamics simulations are combined to construct an energy level diagram for the Mn(2+/3+) redox reaction in aqueous solution. Two peaks centered at 8.88 and 10.26 eV electron binding energies can be assigned to the Mn2+ hexa-aquo complex with a peak area ratio of 2:2.83. Using the notation of crystal field theory, the peak at lower energies can be interpreted as arising from ionization from the e(g) levels (highest occupied molecular orbital, HOMO), and the peak at higher energies are from ionization of the t(2g) levels. The difference corresponds to the average crystal field splitting, 1.38 eV. From the position of the HOMO level and the absolute redox potential, an experimental value for the reorganization free energy of the aqueous Mn3+ hexa-aquo complex is estimated to be 2.98 eV. Density functional molecular dynamics simulations can reproduce the experimental vertical ionization energy, redox free energy, and reorganization free energies fairly well, provided that the absolute potential shift in periodic boundary conditions, finite size effects, and inaccuracies of the exchange correlation functional are taken into account. Most strikingly, in the simulations, we observe spontaneous and reversible deprotonation of the aqueous Mn3+ hexa-aquo complex to form MnOH(H2O)5(2+) + H+, in line with the low experimental pKa value of this ion. The interconversion between protonation states leads to interesting redox phenomena for aqueous Mn3+, culminating in a bimodal thermal distribution of the electron affinity. PMID:20666394

Moens, Jan; Seidel, Robert; Geerlings, Paul; Faubel, Manfred; Winter, Bernd; Blumberger, Jochen

2010-07-22

362

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

UK PubMed Central (United Kingdom)

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 C; Xue Y; Liu R; Wang M

2011-09-01

363

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. PMID:21646043

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

2011-05-14

364

Comb-linked, cavity ring-down spectroscopy for measurements of molecular transition frequencies at the kHz-level.  

UK PubMed Central (United Kingdom)

We present a low uncertainty measurement technique for determining molecular transition frequencies. This approach is complementary to sub-Doppler saturation spectroscopies and is expected to enable new frequency measurements for a wide variety of molecular species with uncertainties at the kHz-level. The technique involves measurements of Doppler broadened lines using cavity ring-down spectroscopy whereby the probe laser is actively locked to the ring-down cavity and the spectrum frequencies are linked directly to an optical frequency comb that is referenced to an atomic frequency standard. As a demonstration we have measured the transition frequency of the (30012) ? (00001) P14e line of CO2 near 1.57 ?m with a combined standard uncertainty of ~9 kHz. This technique exhibits exceptional promise for measurements of transition frequencies and pressure shifting parameters of many weak absorbers, and indicates the potential for substantially improved measurements when compared to those obtained with conventional spectroscopic methods.

Truong GW; Long DA; Cygan A; Lisak D; van Zee RD; Hodges JT

2013-03-01

365

Development of novel drug delivery prototypes devices for targeted delivery drug therapy at the molecular level in aqueous media.  

UK PubMed Central (United Kingdom)

A novel approach in target specific molecular prototype drug delivery system concerns the attempt to employ radical affording substances (RAS) or radical quenching substances (RQS) as prodrugs able to produce irreversible damage on the desired target and therefore to stimulate cellular apoptosis. However, radical species generated can react quickly within the chemical environment prior to reaching its proper site of action. In this short communication, we report our investigations towards developing two alternative novel, simple, flexible and effective drug delivery systems that provide optimal dosage of drugs precisely where and when needed and therefore achieve and sustain a complex delivery profile. We have demonstrated the application of two effective molecular prototype delivery systems able to harness free radical reactivity within the laboratory where biological processes can be studied and controlled, leading to the prevention of disease and the development of new treatments for disease states mediated by free radicals.

George R; Oberhozer TG; Perchyonok VT

2011-09-01

366

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

Energy Technology Data Exchange (ETDEWEB)

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

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

1983-01-01

367

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

International Nuclear Information System (INIS)

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

1983-03-03

368

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

UK PubMed Central (United Kingdom)

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.

Martel-Pelletier J; Pelletier JP

2010-04-01

369

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

370

Deep level defects in Ga- and N-polarity GaN grown by molecular beam epitaxy on si(111)  

Science.gov (United States)

Deep level transient spectroscopy has been used to characterize the deep level traps in Ga- and N-polarity GaN films grown by plasma assisted molecular beam epitaxy on Si(111) substrate. The two deep level traps at Ec?Et0.21eV (E1) and Ec?Et0.48eV (E2) have been detected in Ga-polarity GaN. The E1 level commonly observed deep trap related to the nitrogen vacancy in GaN. It is found that, the E2 level exhibits logarithmic capture kinetic behavior and substantially increases its capture cross section from 10?15 to 10?12cm2 by employing different pulse width ranging from 5ms to 35ms. Such behavior of E2 trap with filling pulse length attributes that, the trap is originated from threading dislocations. In case of N-polarity GaN, we observed two deep level traps with activation energies of Ec?Et0.53eV (E3) and Ec?Et0.89eV (E4). The estimated capture cross-sections (?S) for these defects were found to be 2.5110?15cm2 and 5.2110?16cm2 respectively. The E3 and E4 are nitrogen antisite point defect and extended defect related to dislocation deep levels, results from growth on N-polarity crystal structure.

Peta, Koteswara Rao; Lee, Sang-Tae; Moon-Deock, Kim; Oh, Jae-Eung; Kim, Song-Gang; Kim, Tae-Geun

2013-09-01

371

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

2012-10-11

372

Molecular-Level Investigations of Nucleation Mechanisms and Kinetics of Formation of Environmental Nanoparticles  

Energy Technology Data Exchange (ETDEWEB)

Environmental nanoparticles are often poorly-crystalline or metastable structures, whose kinetics of formation and growth are poorly understood. Further, the sorption or growth of nanoparticles on mineral surfaces may control the mineral surface's reactivity and modify its ability to influence contaminant transport. Due to the characteristic length scale, a holistic understanding of the nucleation mechanisms and kinetics of nanoparticle formation on mineral surfaces is difficult to achieve with traditional methodology. In this work, our intent is to determine the molecular nature of nucleation on surfaces, the kinetics of surface nucleation and growth, and the effect of crystal surface topology using new synchrotron-based techniques. We have approached these objectives by: (1) combining state-of-the-art crystal-truncation rod diffraction (CTR) and grazing incidence x-ray absorption fine structure spectroscopy (GIXAS) techniques to investigate the three-dimensional molecular-scale geometry of silicate monomer sorption on the r-plane of hematite; and (2) developing a new grazing-incidence small angle x-ray scattering (GISAXS) setup at SSRL (0.08 nm{sup -1} < q < 8 nm{sup -1}) to explore the initial development of environmental nanoparticles on various mineral surfaces. This study also includes complementary techniques such as atomic force microscopy (AFM), bulk SAXS, dynamic light scattering (DLS), XRD, and TEM.

Young-Shin Jun; Glenn A. Waychunas

2007-04-19

373

Integration and coarse coding: right hemisphere processing of message-level contextual information.  

Science.gov (United States)

A number of different models have been proposed in order to explain the underlying processing mechanisms of each hemisphere for contextual information in sentences. While the coarse-coding hypothesis (Beeman, 1998) remains prominent in the literature, it is inconsistent in its current form with strong evidence suggesting that the RH has a capacity for comprehension that extends beyond word-level processing. Experiment 1 set out to investigate the proposed special role of the RH for integrating broad concepts by centrally presenting one, two, or three sentences followed by an associated word or nonword target to either the left or right visual field. Each sentence, in itself, provided only minimal cues to the nature of the target, but in combination with others created a much more powerful context. A total of 32 right-handed undergraduate psychology students participated in a computer-based lexical decision task where reaction time and error rates were recorded. In contrast to expectations based on the coarse-coding hypothesis, targets presented to the RVF/LH were as strongly facilitated as targets presented to the LVF/RH at all levels of contextual support. Due to some ambiguity in the results as to the level of processing of each hemisphere, an additional experiment was conducted which aimed to resolve this difficulty through a modification to the scrambled sentence condition. Experiment 2 provided a clear demonstration that the equality of facilitation observed in both experiments occurred as a result of message-level processing. This finding indicates that the coarse/fine-coding distinction between left and right hemisphere processing cannot be applied to message-level processing. PMID:19657950

Gouldthorp, Bethanie; Coney, Jeffrey

2009-08-05

374

Integration and coarse coding: right hemisphere processing of message-level contextual information.  

UK PubMed Central (United Kingdom)

A number of different models have been proposed in order to explain the underlying processing mechanisms of each hemisphere for contextual information in sentences. While the coarse-coding hypothesis (Beeman, 1998) remains prominent in the literature, it is inconsistent in its current form with strong evidence suggesting that the RH has a capacity for comprehension that extends beyond word-level processing. Experiment 1 set out to investigate the proposed special role of the RH for integrating broad concepts by centrally presenting one, two, or three sentences followed by an associated word or nonword target to either the left or right visual field. Each sentence, in itself, provided only minimal cues to the nature of the target, but in combination with others created a much more powerful context. A total of 32 right-handed undergraduate psychology students participated in a computer-based lexical decision task where reaction time and error rates were recorded. In contrast to expectations based on the coarse-coding hypothesis, targets presented to the RVF/LH were as strongly facilitated as targets presented to the LVF/RH at all levels of contextual support. Due to some ambiguity in the results as to the level of processing of each hemisphere, an additional experiment was conducted which aimed to resolve this difficulty through a modification to the scrambled sentence condition. Experiment 2 provided a clear demonstration that the equality of facilitation observed in both experiments occurred as a result of message-level processing. This finding indicates that the coarse/fine-coding distinction between left and right hemisphere processing cannot be applied to message-level processing.

Gouldthorp B; Coney J

2011-01-01

375

High level nuclear waste treatment in the Defense Waste Processing Facility: Overview and integrated flowsheet model  

Energy Technology Data Exchange (ETDEWEB)

Design and construction of the world's largest vitrification facility for high level nuclear waste has been nearly completed at the US Department of Energy's Savannah River Site. Equipment testing and calibration are currently being performed in preparation for the nonradioactive Chemical Runs in the late 1991. In 1993, the Defense Waste Processing Facility (DWPF) will begin producing 100 kg/hr of radioactive waste glass at 28 wt% waste oxide loading. This paper describes all phases of waste processing operations in DWPF and waste tank farms using the integrated flowsheet modeling approach. Particular emphases are given to recent developments in the DWPF processes and design.

Choi, A.S.; Fowler, J.R.; Edwards, R.E. Jr.; Randall, C.T.

1991-01-01

376

High level nuclear waste treatment in the Defense Waste Processing Facility: Overview and integrated flowsheet model  

Energy Technology Data Exchange (ETDEWEB)

Design and construction of the world`s largest vitrification facility for high level nuclear waste has been nearly completed at the US Department of Energy`s Savannah River Site. Equipment testing and calibration are currently being performed in preparation for the nonradioactive Chemical Runs in the late 1991. In 1993, the Defense Waste Processing Facility (DWPF) will begin producing 100 kg/hr of radioactive waste glass at 28 wt% waste oxide loading. This paper describes all phases of waste processing operations in DWPF and waste tank farms using the integrated flowsheet modeling approach. Particular emphases are given to recent developments in the DWPF processes and design.

Choi, A.S.; Fowler, J.R.; Edwards, R.E. Jr.; Randall, C.T.

1991-12-31

377

Changes in sodium levels in processed and restaurant foods, 2005 to 2011.  

UK PubMed Central (United Kingdom)

IMPORTANCE: Excess consumption of sodium is an important cause of hypertension, a major risk factor for heart disease and stroke. The higher the level of consumption, the greater is a person's likelihood of developing hypertension. Numerous organizations have recommended reductions in sodium intake in the United States. Roughly 80% of the sodium consumed by Americans has been added by food manufacturers and restaurants. OBJECTIVE: To compare the mean (SD) levels of sodium for identical products ascertained in 2005, 2008, and 2011. DESIGN AND SETTING: Comparison study in an academic research setting. PARTICIPANTS AND EXPOSURES: Center for Science in the Public Interest staff have monitored sodium levels in selected processed foods and fast-food restaurant foods for many years. MAIN OUTCOMES AND MEASURES: The sodium content in identical foods, as measured in 2005, 2008, and 2011. RESULTS: Between 2005 and 2011, the sodium content in 402 processed foods declined by approximately 3.5%, while the sodium content in 78 fast-food restaurant products increased by 2.6%. Although some products showed decreases of at least 30%, a greater number of products showed increases of at least 30%. The predominant finding is the absence of any appreciable or statistically significant changes in sodium content during 6 years. CONCLUSIONS AND RELEVANCE: Based on our sample, reductions in sodium levels in processed and restaurant foods are inconsistent and slow. These findings are in accord with other data indicating the slow pace of voluntary reductions in sodium levels in processed and restaurant foods. Stronger action (eg, phased-in limits on sodium levels set by the federal government) is needed to lower sodium levels and reduce the prevalence of hypertension and cardiovascular diseases.

Jacobson MF; Havas S; McCarter R

2013-07-01

378

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

International Nuclear Information System (INIS)

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

1993-01-01

379

Sources and processes affecting levels and composition of atmospheric particulate matter in the Western Mediterranean  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This study is focused on the identification of the sources and processes affecting levels and composition of PM10 and PM2.5 from air quality monitoring networks in Eastern Spain. This is a multidisciplinary study. Time series of TSP and PM10 recorded from 1996 to 2000 are interpreted to assess the r...

Rodrguez Gonzlez, Sergio

380

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

International Nuclear Information System (INIS)

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

1994-01-01

 
 
 
 
381

Effect of household and industrial processing on levels of pesticide residues and degradation products in melons  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract Two varieties of melons (Cucumis melo) were treated by two fungicides (carbendazim and maneb) and four insecticides (acetamiprid, cyromazin, imazalil and thiamethoxam) to quantify the effect of household processing on the pesticide residues. To ensure sufficiently high levels of re...

382

Molecular Biology at the Quantum Level: Can Modern Density Functional Theory Forge the Path?  

CERN Document Server

Recent years have seen vast improvements in the ability of rigorous quantum-mechanical methods to treat systems of interest to molecular biology. In this review article, we survey common computational methods used to study such large, weakly bound systems, starting from classical simulations and reaching to quantum chemistry and density functional theory. We sketch their underlying frameworks and investigate their strengths and weaknesses when applied to potentially large biomolecules. In particular, density functional theory---a framework that can treat thousands of atoms on firm theoretical ground---can now accurately describe systems dominated by weak van der Waals interactions. This newfound ability has rekindled interest in using this tried-and-true approach to investigate biological systems of real importance. In this review, we focus on some new methods within density functional theory that allow for accurate inclusion of the weak interactions that dominate binding in biological macromolecules. Recent ...

Kolb, Brian; 10.1142/S1793984412300063

2012-01-01

383

Sigma level performance of the innovated process in the imaging department at a Mexican health institute.  

UK PubMed Central (United Kingdom)

The National Institute of Respiratory Diseases is a third level public hospital in Mexico City, which in 2007 acquired an RIS-PACS to be implemented at its Imaging Department (ID), with the objective to enhance its service. This department attends an average of 3,500 patients per month developing different image modalities. The objective of this work was to determine the overall sigma level performance of four processes of the ID: reception, X-ray, computed tomography, and radiologist diagnosis, considering process analysis and innovation through Six Sigma methodology, measuring the innovation effectiveness by means of indicators and learning curves. Initially, a first measurement (M 1) of the original processes was determined; once 13 innovations were implemented in a pilot program, two more measurements were done, 15 days after (M 2) and 30 days after (M 3), in order to know the impact of the innovations in the ID processes. The initial sigma level of the ID before innovations was ? 1?=?2.0, which means that there were 36 patients per day with a process defect during their stay at the ID. In the two following measurements, ? 2?=?2.2 which means that there were 28 patients per day with a process defect, and ? 3?=?2.3 with 24 patients per day with a process defect. These results demonstrate that the percentage of performance enhancement between the original process and 15 days later was 23 % and 30 days later an enhancement of 15 %. In total, an overall enhancement of 38 % was obtained at the ID of the institute.

Garca-Porres J; Ortiz-Posadas MR

2013-04-01

384

Complete NLO QCD Corrections for Tree Level Delta F = 2 FCNC Processe  

CERN Multimedia

Anticipating the important role of tree level FCNC processes in the indirect search for new physics at distance scales as short as 10^-19-10^-21 m, we present complete NLO QCD corrections to tree level Delta F=2 processes mediated by heavy colourless gauge bosons and scalars. Such contributions can be present at the fundamental level when GIM mechanism is absent as in numerous Z' models, gauged flavour models with new heavy neutral gauge bosons and Left-Right symmetric models with heavy neutral scalars. They can also be generated at one loop in models having GIM at the fundamental level and MFV of which Two-Higgs Doublet models with and without SUSY are the best known examples. In models containing vectorial heavy fermions that mix with the standard chiral quarks and models in which Z and SM neutral Higgs H mix with new heavy gauge bosons and scalars also tree-level Z and SM neutral Higgs contributions to Delta F=2 processes are possible. In all these extensions new local operators are generated having Wilson...

Buras, Andrzej J

2012-01-01

385

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. equitans. These results suggest that, under laboratory conditions, N. equitans diverts some of its host's metabolism and cell cycle control to compensate for its own metabolic shortcomings, thus appearing to be entirely dependent on small, transferable metabolites and energetic precursors from I. hospitalis.

Giannone, Richard J [ORNL; Huber, Dr. Harald [Universitat Regensburg, Regensburg, Germany; Karpinets, Tatiana V [ORNL; Heimerl, Dr. Thomas [Universitat Regensburg, Regensburg, Germany; Kueper, Dr. Ulf [Universitat Regensburg, Regensburg, Germany; Rachel, Dr. Reinhard [Universitat Regensburg, Regensburg, Germany; Keller, Martin [ORNL; Hettich, Robert {Bob} L [ORNL; Podar, Mircea [ORNL

2011-01-01

386

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

UK PubMed Central (United Kingdom)

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 pre-mature 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,